cssi/SciSciGPT-SciSciNet huggingface dataset:
Retrieval and on-the-fly alignment of sequence fragments from the HIV database.

Motivation: The amount of HIV-1 sequence data generated (presently around 42 000 sequences, of which more than 22 000 are from the V3 region of the viral envelope) presents a challenge for anyone working on the analysis of these data. A major problem is obtaining the region of interest from the stored sequences, which often contain but are not limited to that region. In addition, multiple alignment programs generally cannot deal with the large numbers of sequences that are available for many HIV-1 regions. We set out to provide our users with a tool that will retrieve and create an initial alignment of the HIV sequences that are available for a given genomic region. Results: The MPAlign (M ultiple Pairwise Alignment) web interface is a collection of Perl scripts that retrieves sequences from the Los Alamos HIV sequence database based on a number of search parameters. All sequences were pairwise-aligned to a model sequence using the Hidden Markov Model-based program HMMER. The HMMER model is general enough to accommodate virtually all HIV1 sequences stored in the database. To create a multiple sequence alignment, gaps were inserted into the sequences during retrieval, so that they are aligned to one another. Retrieving and aligning the almost 560 gp120 sequences (∼1500 nt) stored in the database is at least 1500 times faster than a similar Clustal alignment. Availability: At http://www.hiv.lanl.gov/ Contact: Brian Gaschen at bkg@lanl.gov
Focusing attention on objects of interest using multiple matched filters

In order to be of use to scientists, large image databases need to be analyzed to create a catalog of the objects of interest. One approach is to apply a multiple tiered search algorithm that uses reduction techniques of increasing computational complexity to select the desired objects from the database. The first tier of this type of algorithm, often called a focus of attention (FOA) algorithm, selects candidate regions from the image data and passes them to the next tier of the algorithm. In this paper we present a new approach to FOA that employs multiple matched filters (MMF), one for each object prototype, to detect the regions of interest. The MMFs are formed using k-means clustering on a set of image patches identified by domain experts as positive examples of objects of interest. An innovation of the approach is to radically reduce the dimensionality of the feature space, used by the k-means algorithm, by taking block averages (spoiling) the sample image patches. The process of spoiling is analyzed and its applicability to other domains is discussed. The combination of the output of the MMFs is achieved through the projection of the detections back into an empty image and then thresholding. This research was motivated by the need to detect small volcanos in the Magellan probe data from Venus. An empirical evaluation of the approach illustrates that a combination of the MMF plus the average filter results in a higher likelihood of 100% detection of the objects of interest at a lower false positive rate than a single matched filter alone.
Identification of Ssm1b, a novel modifier of DNA methylation, and its expression during mouse embryogenesis

The strain-specific modifier Ssm1 is responsible for the strain-dependent methylation of particular E. coli gpt-containing transgenic sequences. Here, we identify Ssm1 as the KRAB-zinc finger (ZF) gene 2610305D13Rik located on distal chromosome 4. Ssm1b is a member of a gene family with an unusual array of three ZFs. Ssm1 family members in C57BL/6 (B6) and DBA/2 (D2) mice have various amino acid changes in their ZF domain and in the linker between the KRAB and ZF domains. Ssm1b is expressed up to E8.5; its target transgene gains partial methylation by this stage as well. At E9.5, Ssm1b mRNA is no longer expressed but by then its target has become completely methylated. By contrast, in D2 embryos the transgene is essentially unmethylated. Methylation during B6 embryonic development depends on Dnmt3b but not Mecp2. In differentiating B6 embryonic stem cells methylation spreads from gpt to a co-integrated neo gene that has a similarly high CpG content as gpt, but neo alone is not methylated. In adult B6 mice, Ssm1b is expressed in ovaries, but in other organs only other members of the Ssm1 family are expressed. Interestingly, the transgene becomes methylated when crossed into some, but not other, wild mice that were kept outbred in the laboratory. Thus, polymorphisms for the methylation patterns seen among laboratory inbred strains are also found in a free-living population. This may imply that mice that do not have the Ssm1b gene may use another member of the Ssm1 family to control the potentially harmful expression of certain endogenous or exogenous genes.
A Generalized Self-Tuning Decoupling Controller with Pole-Placement for a Class of Multivariable Systems

In this paper, a new multivariable generalized self-tuning decoupling controller is proposed combining classical pole placement strategy with the optimal strategy of self-tuning control. This controller can not only control the stochastic systems with arbitrary, unknown and/or varying time delay structure, but also can directly decouple closed loop systems both at steady state and dynamically. Since it is not necessary to solve polynomial matrix equations the algorithm is simple. It is proved that the controller adopting slight modified least squares algorithm is stable and convergent even for unstable open loop and/or nonminimum phase systems under some conditions. The simulation results demonstrate the effectiveness of the algorithm.
An Ounce of Prevention....

Five behavior management techniques, including classroom environment, behavior management, scheduling, lesson planning, and interpersonal relationships
A method for measuring hydraulic conductivity and embolism in xylem

Abstract Hydraulic conductivity of the xylem is computed as the quotient of mass flow rate and pressure gradient. Measurements on excised plant stems can be difficult to interpret because of time-dependent reductions in flow rate, and because of variable degrees of embolism. Using Acer saccharum Marsh. stems, we found that certain perfusing solutions including dilute fixatives (e.g. 0.05% formaldehyde) and acids with pH below 3 (e.g. 10 mol m−3 oxalic) prevent long-term decline in conductivity. Xylem embolism can be quantified by expressing the initial conductivity as a percentage of the maximum obtained after flow-impeding air emboli have been removed by repeated high-pressure (175 kPa) flushes. Correlation between microbial contamination and declining conductivity suggests that long-term (> 4h) declines are caused by microbial growth within the vessels. Unpredictable trends in short-term (< 4h) measurements may be caused by movements of air emboli in vessels and/or participate matter.
Validity of Estimated Dietary Eicosapentaenoic Acid and Docosahexaenoic Acid Intakes Determined by Interviewer-Administered Food Frequency Questionnaire Among Older Adults With Mild-to-Moderate Cognitive Impairment or Dementia

Epidemiologic research is increasingly being focused on elderly persons, many of whom exhibit mild-to-moderate cognitive impairment. This presents a challenge for collection and interpretation of self-reported dietary data. There are few reports on the impact of cognitive function and dementia on the validity of self-reported dietary intakes. Using plasma phospholipid fatty acid profiles as a biomarker of intake, the authors assessed the validity of an interviewer-administered food frequency questionnaire (FFQ) to estimate intakes of 2 marine-based omega-3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), among 273 community-dwelling adults aged > or =60 years participating in the Nutrition, Aging, and Memory in Elders Study (Boston, Massachusetts, 2002-2008). Age- and energy-adjusted Pearson correlation coefficients for correlations between dietary intakes and plasma phospholipids were consistent across categories of high and low cognitive function (r = 0.48), based on Mini-Mental State Examination score, and were similar across clinically diagnosed categories of normal functioning (r = 0.49), mild cognitive impairment (r = 0.45), and dementia (r = 0.52). The FFQ ranked 78% of subjects to within 1 quartile of their plasma phospholipid EPA + DHA quartile. This frequency was consistently high across all cognitive categories. With interviewer administration, this FFQ seems to be a valid method of assessing dietary EPA + DHA intake in older adults with mild-to-moderate cognitive impairment.
Nitrate removal in stream ecosystems measured by 15N addition experiments: Denitrification

We measured denitrification rates using a field 15N–NO { tracer-addition approach in a large, cross-site study of nitrate uptake in reference, agricultural, and suburban–urban streams. We measured denitrification rates in 49 of 72 streams studied. Uptake length due to denitrification (SWden) ranged from 89 m to 184 km (median of 9050 m) and there were no significant differences among regions or land-use categories, likely because of the wide range of conditions within each region and land use. N2 production rates far exceeded N2O production rates in all streams. The fraction of total NO { removal from water due to denitrification ranged from 0.5% to 100% among streams (median of 16%), and was related to NH z concentration and ecosystem respiration rate (ER). Multivariate approaches showed that the most important factors controlling SWden were specific discharge (discharge / width) and NO { concentration (positive effects), and ER and transient storage zones (negative effects). The relationship between areal denitrification rate (Uden) and NO { concentration indicated a partial saturation effect. A power function with an exponent of 0.5 described this relationship better than a Michaelis– Menten equation. Although Uden increased with increasing NO { concentration, the efficiency of NO { removal from water via denitrification declined, resulting in a smaller proportion of streamwater NO { load removed over a given length of stream. Regional differences in stream denitrification rates were small relative to the proximate factors of NO { concentration and ecosystem respiration rate, and land use was an important but indirect control on denitrification in streams, primarily via its effect on NO { concentration.
Laminar free convection in a vertical slot

This is largely an experimental study of the interaction of buoyancy and shear forces in the free convective flow of a liquid in a rectangular cavity across which there is a uniform temperature difference, ΔT, produced by maintaining the two vertical walls at two different temperatures. The height of the cavity, H, is made larger than the width of the cavity, L, and the cavity is sufficiently long in the third dimension for the mean flow to be nearly everywhere two-dimensional. The flow is specified by three dimensionless parameters: σ, the Prandtl number; h = H|L, the aspect ratio; A = γgΔTL3|κν, the Rayleigh number. The experiments are generally restricted to h = 1–60, σ ÷ 103 and A < 108.For A < 103 the temperature field closely satisfies Laplace's equation but a weak stable unicellular circulation is generated. The flow is vertical throughout the slot except for regions within a distance of order L from the ends.For 103 < A < 105, large temperature gradients grow near the walls, and in an interior region a uniform vertical temperature gradient is established. The flow is similar to that near an isolated, heated, vertical plate except that the vertical growth of the wall layers is inhibited in the central part of the slot by the presence of the other layer which prevents entrainment of fluid.Near A = 105 the interior region of the flow generates a steady secondary flow. A regular cellular pattern becomes superimposed on the basic flow to produce a ‘cats-eye’ pattern of streamlines. Near A = 106 when the secondary cell amplitude is large, a further steady cellular motion is generated in the weak shear regions between each cell.
Con: aprotinin should not be used in patients undergoing hypothermic circulatory arrest.

ANTIFIBRINOLYTIC AGENTS reduce blood loss and transfusion during cardiac surgery using cardiopulmonary bypass.1,2 This effect has been shown for synthetic agents ( -aminocaproic acid and tranexamic acid) and the naturally occurring aprotinin. Hemostatic superiority of one antifibrinolytic agent over another has not been shown, however.1,2 Because procedures involving deep hypothermic circulatory arrest (DHCA) in adults have often been termed “bloodbaths” by clinicians, support for the prophylactic use of aprotinin in such cases has emerged.3,4 The bulk of the rather limited existing literature on this subject addresses adults undergoing DHCA for thoracic aortic procedures, so this discussion is limited to that clinical context. The discussion addresses two questions: 1. Is aprotinin safe for DHCA? 2. Is aprotinin desirable for DHCA?
Pulmonary Artery Catheterization and Clinical Outcomes: National Heart, Lung, and Blood Institute and Food and Drug Administration Workshop Report

ObjectiveThe efficacy and safety of the pulmonary artery catheter are under scrutiny because of its association with increased morbidity and mortality in observational studies. In response, the National Heart, Lung, and Blood Institute (NHLBI) and the US Food and Drug Administration (FDA) conducted the Pulmonary Artery Catheterization and Clinical Outcomes workshop in Alexandria, Va, on August 25 and 26, 1997, to develop recommendations regarding actions to improve pulmonary artery catheter utility and safety.ParticipantsThe NHLBI and FDA planning task force selected a workshop chairperson, subcommittee chairs, and participants. Approximately 85 participants were selected for their collective expertise in critical care, pulmonary medicine, cardiovascular medicine and surgery, pediatrics, nursing, biostatistics, and medical economics. The meeting was open to industry representatives and other government and lay observers. This workshop was funded by the NHLBI and the FDA's Division of Devices.EvidencePublished reports relating to the efficacy and safety of the pulmonary artery catheter, especially consensus documents developed by professional societies.Consensus ProcessThe planning task force disseminated materials, held teleconferences, and developed draft position papers prior to the workshop. These were modified during the workshop and thereafter in the course of several teleconferences, and presented to the entire group for final modifications and approval.ConclusionsA need exists for collaborative education of physicians and nurses in performing, obtaining, and interpreting information from the use of pulmonary artery catheters. This effort should be led by professional societies, in collaboration with federal agencies, with the purpose of developing and disseminating standardized educational programs. Areas given high priority for clinical trials were pulmonary artery catheter use in persistent/refractory congestive heart failure, acute respiratory distress syndrome, severe sepsis and septic shock, and low-risk coronary artery bypass graft surgery.
Dissection and Immunohistochemistry of Larval, Pupal and Adult Drosophila Retinas

The compound eye of Drosophila melanogaster consists of about 750 ommatidia (unit eyes). Each ommatidium is composed of about 20 cells, including lens-secreting cone cells, pigment cells, a bristle cell and eight photoreceptors (PRs) R1-R8. The PRs have specialized microvillar structures, the rhabdomeres, which contain light-sensitive pigments, the Rhodopsins (Rhs). The rhabdomeres of six PRs (R1-R6) form a trapezoid and contain Rh1. The rhabdomeres of R7 and R8 are positioned in tandem in the center of the trapezoid and share the same path of light. R7 and R8 PRs stochastically express different combinations of Rhs in two main subtypes: In the 'p' subtype, Rh3 in pR7s is coupled with Rh5 in pR8s, whereas in the 'y' subtype, Rh4 in yR7s is associated with Rh6 in yR8s. Early specification of PRs and development of ommatidia begins in the larval eye-antennal imaginal disc, a monolayer of epithelial cells. A wave of differentiation sweeps across the disc and initiates the assembly of undifferentiated cells into ommatidia. The 'founder cell' R8 is specified first and recruits R1-6 and then R7. Subsequently, during pupal development, PR differentiation leads to extensive morphological changes, including rhabdomere formation, synaptogenesis and eventually rh expression. In this protocol, we describe methods for retinal dissections and immunohistochemistry at three defined periods of retina development, which can be applied to address a variety of questions concerning retinal formation and developmental pathways. Here, we use these methods to visualize the stepwise PR differentiation at the single-cell level in whole mount larval, midpupal and adult retinas (Figure 1).
Selected kinematic characteristics of intercollegiate women triple jumpers.

Eight women triple jump finalists at the 1986 Big Ten Track and Field Championships and 10 women triple jump finalists at the 1986 National Track and Field Competition were filmed during competition. Among selected kinematic characteristics, the following high correlations (r > 0.70) were found: the distance of the hop phase correlated highly with the total jump dis tance ; the horizontal position of the center of gravity of the body in relation to the support foot at takeoff correlated highly with the distance of the hop and the jump phases; the horizontal velocity into the step phase correlated highly with the total distance of the jump; the vertical velocity into the hop and step phases cor related highly with the respective phase distance; and there was an inverse correlation between the maximum height of the center of gravity during the flight phase of the step and the total distance. A significant difference was found between men and women triple jumpers in relation to the contribution of the step p...
ABA, ethylene and the control of shoot and root growth under water stress

The question of whether abscisic acid (ABA) acts as an inhibitor or promoter of shoot growth in plants growing in drying soil is examined, drawing on current understanding of the role of ABA in root growth maintenance. Particular consideration is given to studies of endogenous ABA deficiency, which have shown that an important role of ABA is to limit ethylene production, and that this interaction is involved in the effects of ABA status on shoot and root growth.
Effect of Male Hormone upon Uterine Motility and the Uterus.

SummaryThe male hormone, testosterone propionate, inhibited the oestrous rhythm of the rabbit uterus. This was manifested by a disturbed rhythm, a lowered height of contraction or complete quiescence. Such inhibitions appeared in animals whose uteri showed but little or no progestational response. During the period of quiescence, pituitrin failed to elicit a strong contraction. Testosterone prevented castration atrophy in the rabbit's uterus with or without minimal progestational changes.
Physical Activity, Type 2 Diabetes, and Ethnicity Recent Findings and Implications

Diabetes is a major public health problem that affects certain ethnicities disproportionately. Physical activity (PA) (exercise) is a key component necessary for the prevention and treatment of type 2 diabetes. Adults with and without diabetes may face challenges that interfere with following exercise recommendations. This article reviews the relationships among PA, race/ethnicity, behaviors, and health outcomes of adults with prediabetes and type 2 diabetes. The authors review recent cross-sectional and intervention studies and assess their relevance to clinical practice. This is a focused review of the literature from January 2010 to September 2012 on the relationship among PA, type 2 diabetes, and race/ ethnicity with respect to the following components: (1) PA and the likelihood of persons with prediabetes developing diabetes; (2) PA and improvements in health outcomes of persons with prediabetes; (3) PA and improvements in health outcomes of persons with type 2 diabetes; and (4) enablers of and barri...
Predicting failure of glyburide therapy in gestational diabetes.

We sought to develop a prediction model to identify women with gestational diabetes (GDM) who require insulin to achieve glycemic control. Retrospective cohort of all singletons with GDM treated with glyburide from 2007 to 2013. Glyburide failure was defined as reaching glyburide 20 mg day−1 and receiving insulin. Glyburide success was defined as any glyburide dose without insulin and >70% of visits with glycemic control. Multivariable logistic regression analysis was performed to create a prediction model. Of the 360 women, 63 (17.5%) qualified as glyburide failure and 157 (43.6%) as glyburide success. The final prediction model for glyburide failure included prior GDM, GDM diagnosis ⩽26 weeks, 1-h glucose challenge test ⩾228 mg dl−1, 3-h glucose tolerance test 1-h value ⩾221 mg dl−1, ⩾7 postprandial blood sugars >120 mg dl−1 in the week glyburide started and ⩾1 blood sugar >200 mg dl−1. The model accurately classified 81% of subjects. Women with GDM who will require insulin can be identified at the initiation of pharmacological therapy.
Foundation of e-commercial affairs development—internal construction of enterprise

Beginning from the internal necessary condition of the enterprises' development of the e-commercial affairs the construction which the enterprise should make is expounded.
The AIM-HIGH (Atherothrombosis Intervention in Metabolic Syndrome With Low HDL/High Triglycerides: Impact on Global Health Outcomes) Trial: To Believe or Not to Believe?

The beneficial effect of lowering low-density lipoprotein cholesterol (LDL-C) in clinical trials ([1][1]) has transformed our ability to reduce cardiovascular risk. However, increasing recognition that many patients experience a clinical event, despite the use of LDL-C lowering therapies, has
Writing a Literature Review

Most undergraduate research papers, and many graduate and professional research papers as well, are based on literature reviews. The aims of a literature review are different from those of an empirical research paper, and hence the skills required differ somewhat as well. The goals of literature reviews are the following (American Psychological Association, 2009): To define and clarify problems To inform the reader about a subject by summarizing and evaluating studies To identify inconsistencies, gaps, contradictions, and relationships in the literature To suggest future steps and approaches to solve the issues identified There are five kinds of literature reviews that can be distinguished on the basis of the aim of the review. Reviews can strive to (a) generate new knowledge, (b) test theories, (c) integrate theories, (d) develop a new theory, or (e) integrate existing knowledge. If you plan to submit your literature review to a journal and have to decide where to submit it, you may want to read some literature reviews that have been published in the journals you are considering to find out whether your paper is a good fit to the journal. Generally, the probability of an article being accepted is highest when you develop new knowledge, a new theory, or integrate several theories (instead of just reviewing and summarizing the literature on a particular topic) (Eisenberg, 2000).
Abstract 121: Role of Leukocyte Gpr120 in Atherosclerosis Development in Polyunsaturated Fatty Acid Diet Induced Atheroprotection in LDLrKO Mice

Introduction Diets enriched in polyunsaturated n-3 and n-6 fatty acids (PUFAs) are atheroprotective. FO, which is enriched in n-3 PUFAs, reduces plasma lipids and has anti-inflammatory effects. Recent studies have shown that GPR120 is the physiological n-3 PUFA receptor and its ligation by n-3 PUFAs blunts pro-inflammatory signaling pathways. However, the role of GRP120 in atherogenesis is unknown. Hypothesis We hypothesized that leukocyte GPR120 contributes to the atheroprotective effects of n-3, but not n-6, PUFUs by ligation of GRP120, resulting in decreased leukocyte inflammation. Methods Female LDLr-/- mice were transplanted with bone marrow from male wild type or GPR120 knockout mice. After recovery from transplantation, recipient LDLr-/- mice were fed atherogenic diets containing 0.2% cholesterol and enriched in saturated/monounsaturated fat (palm oil, PO), n-6 PUFA (borage, BO), a botanical n-3 PUFA (echium oil, EO) or FO for 16 weeks. Periodic blood samples were taken for lipid and lipoprotein measurements and aortas were harvested after 16 weeks of diet feeding to quantify atherosclerosis. Results Compared to the PO group, mice fed BO, EO and FO had significantly lower plasma total and very low density lipoprotein (VLDL) cholesterol concentrations. EO and FO groups also had lower plasma triglyceride concentrations compare to PO and BO fed mice. Compared to the PO group, mice fed BO and EO had significantly reduced aortic CE, comparable to the FO group. However, lack of leukocyte GPR120 did not significantly affect plasma lipids or atherosclerosis severity within any diet group. Conclusion Atherogenic diets enriched in n-6 and n-3 PUFAs derived from botanical oils (BO and EO) were as atheroprotective as FO compared to a diet containing saturated/monounsaturated fat (PO). Furthermore, lack of leukocyte GPR120 had minimal effect on plasma lipid/lipoprotein profile and atherosclerosis, suggesting that n-3 as well as n-6 PUFA associated atheroprotection is primarily due to reduction of VLDL-cholesterol in LDLr-/- mice.
Coming to Terms with Europe: Konstantin Simonov and Oles’ Honchar’s Literary Conquest of East Central Europe at the End of World War II

This chapter explores how two Soviet writers, the Russian Konstantin Simonov and the Ukrainian Oleksandr Honchar, depicted the encounter of Soviet Soldiers with East Central Europe at the end of World War II. Both writers’ first postwar works—Simonov’s play Under the Chestnut-trees of Prague and Honchar’s trilogy The Standard-Bearers—examined the encounter of Soviet soldiers with East Central Europe as their subject matter. In these works, both authors tried to mitigate the “moral and psychological shock” and a sense of cultural inferiority that many Soviet citizens experienced during their encounter with East Central Europe during World War II. These Soviet people who traveled westward, often as soldiers, saw higher living standards, levels of education, urbanization and industrialization that superseded those of the USSR. The strategies that these major Soviet authors employed to restore the injured sense of pride to mass Soviet readers reflect the way in which literature mediated the complicated and contradictory process of consolidation of the “socialist second world” in the immediate postwar years.
Analysis of Dosimetry Measurements in EBR-II

Analyses of an extensive series of reaction-rate measurements done recently in the Experimental Breeder Reactor II (EBR-II) runs 50G and 50H were performed with transport theory and diffusion theor...
“Mobile” polymer brushes with self-adjusting tethering density - A theoretical treatment of thermodynamically stable single crystals of amorphous-crystalline diblock copolymers in various solvents

Abstract “Mobile” polymer brushes with self-adjustable tethering density can be found in the single crystals of amorphous-crystalline diblock copolymers in the thermodynamically stable state. In such a system, the amorphous blocks form polymer brushes on the surface of the single crystal of the crystalline blocks. Different from the common polymer brushes with fixed tethering density, of which polymers are attached either chemically or physically on a substrate, the polymer brushes tethered on the single crystal are “smart” and partially release the highly stretched conformation by “telling” the crystalline blocks to provide more surface area via forming higher folded chain single crystals. Such a polymer brushes system is treated theoretically using the Flory approximation. Thicknesses of the amorphous polymer brush layer (La) and the single crystal lamellae (Lc) are found to have different scaling relations with the degree of polymerization of the amorphous block (ra) in different types of solvents. The amorphous layer thickness, La, is proportional to the 2/3 power of ra in a poor solvent for the amorphous blocks, the 3/4 power in theta solvent, and the 4/5 power in good solvent. The scaled powers between La and ra of the “mobile” polymer brushes are all weaker than the normal polymer brushes, which scales with ra to the first power, indicating the partial releasing of the stretched nature. The crystal thickness, Lc, is proportional to the −1/3 power of ra in poor solvent for the amorphous blocks, the −1/2 power in theta solvent, and the −3/5 power in good solvent, clearly indicating that a folded chain single crystal possesses a larger number of folds at a large ra to facilitate the crowding of the amorphous chains on the surface.
Stress is associated with an increased risk of recurrent seizures in adults.

SummaryObjective The literature is sparse on the complex interrelationships between stressors, depression, anxiety disorders, and epilepsy. We hypothesized that a relationship exists between stress and epilepsy. We evaluated whether markers of stress are associated with seizure recurrence in a low income community-based cohort of adults with single unprovoked seizure or newly diagnosed epilepsy. Methods We ascertained adult residents of Northern Manhattan and Harlem, New York City, with a first unprovoked seizure or newly diagnosed epilepsy, between December 2010 and January 2013. At enrollment, we collected information about seizure phenomenology, demographics, clinical information, and measures of stress (environmental stress, stressful life events, facets of allostatic load—i.e., the cumulative effect of adaptation to stress, psychiatric disorders, and low collective efficacy). Collective efficacy assesses neighborhood characteristics and incorporates social cohesion and informal social control. All subjects were followed for 2 years for further seizures. Cox proportional hazard regression models were used to estimate the hazard ratios of seizure recurrence during the 2 years of follow-up. Results We identified 52 subjects (64.2%) with a single unprovoked seizure and 29 (35.9%) with newly diagnosed epilepsy. Seizure recurrence was recorded in 38.5% (N = 20) of subjects with a single unprovoked seizure and in 69% of those with epilepsy (N = 20) (p = 0.01). In the overall sample, the hazard of seizure recurrence was increased by lifetime generalized anxiety disorder (3.0-fold) and by low collective efficacy (2.7-fold). In a second model, the hazard was increased by lifetime mood disorder (2.1-fold) and low collective efficacy (2.5-fold). Significance Markers of stress (i.e., low collective efficacy, lifetime mood disorder, and lifetime generalized anxiety disorder) were associated with an increased risk for seizure recurrence in adults with a single unprovoked seizure or newly diagnosed epilepsy. Stress-reducing interventions, such as mindfulness, may be a useful, safe, and inexpensive adjunctive treatment for epilepsy.
Glycomic and glycoproteomic analysis of glycoproteins—a tutorial

The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
Policy Readiness for Offshore Carbon Dioxide Storage in the Northeast

Reducing the amount of carbon dioxide in the atmosphere is vital to mitigate climate change. To date reduction efforts have primarily focused on minimizing the production of carbon dioxide during electricity generation, transport, and other activities. Going forward, to the extent that carbon dioxide continues to be produced, it will need to be captured before release. The captured carbon dioxide can then be utilized in some fashion, or it can be injected into underground geological formations – e.g., depleted oil and gas reserves, deep saline aquifers, or basalt rock reservoirs – where, it is hoped, it will remain permanently sequestered (“carbon capture and storage” or “CCS”). Research is currently being undertaken into the possibility of injecting carbon dioxide into the seabed. One study, involving researchers from Columbia’s Lamont-Doherty Earth Observatory, aims to identify possible injection sites in the seabed along the northeast coast of the U.S. It is anticipated that, following identification of suitable sites, a demonstration project will be undertaken to assess the feasibility of offshore CCS. This paper outlines key regulatory requirements for the demonstration project and any subsequent commercial operations.
Immigrants as Symbolic Assailants: Crimmigration and Its Discontents

Despite little evidence of an immigration-crime nexus, many American jurisdictions have adopted a punitive approach to undocumented immigrants and an increasingly restrictive and exclusive system o...
Anti-Gal Interaction With Trypanosoma , Leishmania , and Plasmodium Parasites

The natural anti-Gal antibody binds to several protozoan parasites, including Trypanosoma , Leishmania , and Plasmodium . The binding is to α-gal-like epitopes presented by these parasites mostly on glycoinositol phospholipids and glycoproteins. These epitopes further stimulate the immune system of infected individuals to produce anti-Gal at elevated titers. In vitro studies with sera from infected patients and in vivo studies in GT-KO mice producing anti-Gal demonstrated complement-dependent and independent lysis and neutralization of Trypanosoma and Plasmodium parasites. These observations suggest that anti-Gal may con­tribute to natural protection against infections by these parasites. The high rates of infections suggest, however, that in a substantial proportion of populations in endemic regions, protective activity of the natural anti-Gal antibody is insufficient. Thus, significant numbers of infecting parasites succeed in evading the antibody by invading RBC or nucleated cells where they are protected from anti-Gal. Moreover, shedding of Trypanosoma cell membranes in the chronic phase of Chagas’ disease may cause anti-Gal-mediated autoimmune-like phe­nomena that could be lethal, in particular, because of heart failure. In view of these consid­erations, it may be of interest to determine whether constant elevation of anti-Gal activity in individuals in endemic regions may contribute to protection against such infections. It is not clear whether immunization with vaccines inducing increased production of anti-Gal may be helpful because anti-Gal activity usually returns to the preimmunization level, within few months post immunization. It may be possible that providing nonpathogenic bacteria (e.g., as food supplement) that elevate anti-Gal production, and which become an integral part of the microbiome, will result in continuous increase in anti-Gal titers to levels that enable effective destruction of invading parasites, thus increasing protection against such infections.
Distributive residuated frames and generalized bunched implication algebras

We show that all extensions of the (non-associative) Gentzen system for distributive full Lambek calculus by simple structural rules have the cut elimination property. Also, extensions by such rules that do not increase complexity have the finite model property, hence many subvarieties of the variety of distributive residuated lattices have decidable equational theories. For some other extensions, we prove the finite embeddability property, which implies the decidability of the universal theory, and we show that our results also apply to generalized bunched implication algebras. Our analysis is conducted in the general setting of residuated frames.
SECURING BLUETOOTH LOW ENERGY LOCKS FROM UNAUTHORIZEDACCESS AND SURVEILLANCE

This chapter describes several vulnerabilities that affect commercial and residential Bluetooth Low Energy security devices and outlines methods for exploiting plaintext, obfuscated and hard-coded passwords, brute forcing passwords and hashes, fuzzing commands and performing man-in-the-middle attacks. Evaluations reveal that 75% of the tested security and access control systems have vulnerabilities that grant unauthorized access. In addition to obtaining access, malicious actors can extract sensitive information that can be used to develop patterns of human behavior. This chapter discusses five solutions for preventing or mitigating Bluetooth Low Energy security breaches, most of which involve minimal implementation overhead on the part of developers.
Developmental biology: A cellular view of regeneration.

How the salamander regrows an entire limb after injury has flummoxed the wisest of scientists. A closer look at the cells involved in limb regeneration shows that remembering past origins may be crucial for this feat.
Demographic, Clinical and Histopathological Features of Oral Neural Neoplasms: A Retrospective Study.

Intraoral neural neoplasms though unusual may be clinically significant. The aim of this study was to categorize and evaluate oral neural tumors in a large oral pathology biopsy service. With IRB approval, a retrospective search of all neural neoplasms of the oral cavity in the archives of the University of Florida Oral Pathology Biopsy Service spanning from 1994 to 2015 was performed. Extraoral cases as well as cases with insufficient patient information were excluded. A total of 340 out of 164,578 submitted specimens in a 22 year period (0.2%) were included with a mean age of 43.3 years (range: 6–89), and 44% male and 56% female. The most commonly affected locations were: tongue (37.5%), palate (22%), lip (19%), and gingiva (14%). The microscopic diagnoses rendered, in descending order of frequency were: neurofibromas (NFs): 123 (36%), granular cell tumor (GCT): 108 (32%), schwannomas: 61 (17%), palisaded encapsulated neuromas: 39 (11%), benign neural lesion not otherwise specified: 8 (2%), and mucosal neuroma c/w multiple endocrine neoplasia type 2B (MEN 2B): 1 (< 0.5%). Six cases of NF reported a history of neurofibromatosis Type 1 (NF 1). Four cases showed multifocal lesions. Immunohistochemical staining was performed on equivocal cases (25% of the lesions) and all were confirmed by their S-100 positivity. Intraoral neural neoplasms, though uncommon should be in the differential diagnosis of oral soft tissue entities and specific consideration to syndromal linkage is paramount as this may impact patient management.
Engineering Proton Transfer in Photosynthetic Oxygen Evolution: Chloride, Nitrate, and Trehalose Reorganize a Hydrogen-Bonding Network

Photosystem II oxidizes water at a Mn4CaO5 cluster. Oxygen evolution is accompanied by proton release through a 35 A hydrogen-bonding network to the lumen. The mechanism of this proton-transfer reaction is not known, but the reaction is dependent on chloride. Here, vibrational spectroscopy defines the functional properties of the proton-transfer network using chloride, bromide, and nitrate as perturbative agents. As assessed by peptide C═O frequencies, bromide substitution yields a spectral Stark shift because of its increase in ionic radius. Nitrate substitution leads to more complex spectral changes, consistent with an overall increase in hydrogen-bonding interactions with the peptide backbone. The effects are similar to spectral changes previously documented in site-directed mutations in a putative lumenal pathway. Importantly, the effects of nitrate are reversed by the osmolyte, trehalose. Trehalose is known to alter hydrogen-bonding interactions in proteins. Trehalose addition also reverses a shift i...
Molecular Dissection of the Cell Cycle

There are essentially three approaches to the identification of genes that play a major regulatory role in the control of proliferation in animal cells: 1) the identification of proto-oncogenes, i.e. the cellular equivalents of retroviral transforming genes; 2) the molecular cloning of the wild-type alleles complementing temperature-sensitive (ts) defects in cell cycle specific ts mutants, and 3) the identification by differential screening of cDNA libraries of growth regulated genes, i.e. genes that are inducible by growth factors or are cell cycle regulated. Introduction of these genes under the control of appropriate promoters can influence the growth characteristics of the cells so that they can be grown in the absence of defined growth factors.
On Mercer's Theorem for (C, 2) - Means.

A direct proof is given for the following theorem, contained as a special case in a more general result ofPolniakowski:Theorem. Denote σn the Cesaro-means of order 2 of the sequenceS1, S2, ... ,α any real number satisfying 0<α<=1. Then\(\mathop { \lim }\limits_{n \to \infty } (\alpha S_n + ((1 - \alpha )\sigma _n ) = S\) implies\(\mathop { \lim }\limits_{n \to \infty } S_n = S\)
Secondary causes of hyperlipidemia

Secondary causes of hyperlipidemia are important to recognize. In fact, hyperlipidemia may be a clue to the presence of an underlying systemic disorder. It may greatly heighten the risk of atherosclerosis with a raised LDL-c, triglyceride-rich lipoprotein excess, and increased lipoprotein(a) as well as lowered HDL-c. The search for secondary causes may provide a clue as to why patients with primary lipid disorders suddenly develop worsening lipid profiles. The point is a crucial one because some acquired causes of hyperlipidemia, such as alcohol, estrogens, steroids, or pregnancy, when superimposed on a primary familial form of hypertriglyceridemia can result in a saturated removal system and a buildup of chylomicrons, which can lead to life-threatening pancreatitis. A convenient way to remember secondary causes is to think of the four D's of diet, drugs, disorders of metabolism, and diseases. Although diets rich in saturated fats and cholesterol are a common cause of the mild hypercholesterolemia seen in our society, alcohol excess and weight gain can explain much of the tendency toward hypertriglyceridemia. Interestingly anorexia nervosa has long been associated with severe but reversible hypercholesterolemia. Several classes of drugs need to be considered as common causes of altered lipid profiles. Glucocorticoids and estrogens elevate triglycerides and raise levels of HDL-c. Anabolic steroids taken orally markedly reduce levels of HDL-c in contrast to injectable testosterone, which does not adversely affect the LDL-to-HDL ratio. Oral contraceptives affect atherosclerotic risk depending on the kind and doses of progestin/estrogen. In those with an underlying primary hypertriglyceridemia and associated obesity, estrogenic medications can depress triglyceride removal mechanisms, leading to the chylomicronemia syndrome and pancreatitis. Antihypertensives have variable effects on lipids and lipoproteins. Although short-term thiazide usage raises cholesterol, triglycerides, and LDL-c, long-term usage is not necessarily associated with significant alterations in lipid levels. Alpha blockers may cause an increase in HDL-c, whereas beta blockers raise triglycerides and lower HDL-c. Sympatholytics, angiotensin converting enzyme inhibitors, and calcium channel blockers are essentially lipid neutral. Retinoids can be associated with increased LDL-to-HDL ratios and occasionally striking elevations in triglycerides. Cyclosporine raises LDL-c and lipoprotein(a). Classes of drugs that may raise HDL-c include cimetidine, antiepileptic drugs, and tamoxifen, but the effect may be seen primarily in women. Hypothyroidism is the most common secondary cause of hyperlipidemia after dietary causes are considered. A thyroxine and TSH level should be obtained on all new cases of clinically important hyperlipidemia.(ABSTRACT TRUNCATED AT 400 WORDS)
Chapter 13: Environmental Valuation: The Sum of Specific Damages Approach

This is chapter 13 of Environmental Economics: An Integrated Approach and deals with the "sum of specific damages" valuation method (sometimes called the "health effects model").
How Does the Adult Surgeon Learn

Both the breadth of knowledge and range of technical skills that residents are now expected to master prior to graduation have grown exponentially. A unique challenge that sets surgical education apart from medical education is that surgery as a specialty requires not only the mastery of complex physiology, anatomy, and disease processes but also the ability to interpret and apply that knowledge in the operating room. To be effective educators, it is imperative to understand the theoretic foundation of how adults learn.
Adjust: runtime mitigation of resource abusing third-party online ads

Online advertising is the most critical revenue stream for many Internet companies. However, showing ads on websites comes with a price tag. Since website contents and third-party ads are blended together, third-party ads may compete with the publisher contents, delaying or even breaking the rendering of first-party contents. In addition, dynamically including scripts from ad networks all over the world may introduce buggy scripts that slow down page loads and even freeze the browser. The resulting poor usability problems lead to bad user experience and lower profits. The problems caused by such resource abusing ads are originated from two root causes: First, content publishers have no control over third-party ads. Second, publishers cannot differentiate resource consumed by ads from that consumed by their own contents. To address these challenges, we propose an effective technique, AdJust, that allows publishers to specify constraints on events associated with third-party ads (e.g., URL requests, HTML element creations, and timers), so that they can mitigate user experience degradations and enforce consistent ads experience to all users. We report on a series of experiments over the Alexa top 200 news websites. The results point to the efficacy of our proposed techniques: AdJust effectively mitigated degradations that freeze web browsers (on 36 websites), reduced the load time of publisher contents (on 61 websites), prioritized publisher contents (on 166 websites) and ensured consistent rendering orders among top ads (on 68 websites).
Diagnosis, Prognosis, and Management of Breast Cancer in an 81-Year-Old Male Patient.

Due to the lower rate of breast cancer in men compared to women, there are fewer studies on which to base the treatment of a male patient with breast cancer; and this is further complicated when the patient is part of the elderly population. We report the case of an 81-year-old male who came in for imaging of pulmonary nodules and had an incidental finding of abnormal growth in the breast. Further imaging was performed, and biopsy was completed, confirming invasive ductal carcinoma. Eventually, the patient was treated with a modified radical mastectomy. In this report, we also engage in a discussion of the treatment considerations for patients of male sex and older age group.