cssi/SciSciGPT-SciSciNet huggingface dataset:
Identifying indicators of chemical, biological, radiological, and nuclear (CBRN) weapons development activity in sub-national terrorist groups

Data collected on known terrorist organizations allow intelligence agencies to build a statistical database of features for each group and an observed level of development of chemical, biological, radiological, or nuclear (CBRN) weapons. For the intelligence analyst, a statistical exploration of the structure of the multivariate data is helpful for determining which subset of features—and the relative contribution of each feature in the subset—best discriminate between levels of CBRN weapons development. The resulting function that is used to discriminate between CBRN development levels is called the ‘classifier’. Once the appropriate subset of indicators has been identified and a classifier developed, intelligence agencies will be better able to focus their information gathering and to assess the effect that changes in a terrorist group's features will have on their CBRN weapons development. Additionally, the classifier will enable the intelligence agency to predict the CBRN weapons development level of terrorist group where the feature set of the group is known but the level is unknown. In this analysis, we compare three approaches for building a classifier that best predicts CBRN weapons development levels using a training set with 45 observations; (1) heuristic pattern recognition approach that couples a weighted Minkowski distance metric with a nonparametric kernel-based classification method, (2) classification trees, and (3) discriminant analysis. Where possible, cross-validation is conducted on the data to ensure that the resulting classifier is not overly dependent on the training set. This initial analysis provides some interesting results and suggests a reasonable starting point for finding structure in the data as more observations are added.
Ionic mechanisms of cardiac arrhythmias

The heart pumps >2000 gallons of blood every day through the body's intricate vascular network. Each heartbeat is initiated and carefully regulated by specialized electrical impulses known as action potentials. These impulses are driven by electrical currents, which are composed of charged particles (ions) that flow in and out of individual cardiac myocytes. Ion currents mediate the contraction of individual cardiac myocytes and synchronize the electrical and contractile behavior of the heart; thereby, allowing its pumping function to remain efficient and highly coordinated. Disruption of normal impulse propagation throughout the heart interrupts the coordinated contraction of the cardiac chambers, and produces malignant, lethal rhythm disturbances (arrhythmias), which underlie the majority of sudden cardiac death cases in patients with heart disease. Here, we review our current understanding of normal and abnormal cardiac electrical behavior with emphasis on the ionic mechanisms of cardiac arrhythmias.
Parent-child Relationships, Parental Attitudes towards Sex, and Birth Outcomes among Adolescents

Abstract Study Objective To examine how parent-child relationships, parental control, and parental attitudes towards sex were related to pregnancy outcomes among adolescent mothers. Design Prospective cohort study. Parental report of relationship satisfaction, disapproval of adolescent having sex, discussion around sexual health, and sexual communication attitudes, and adolescent report of relationship satisfaction, parental control, and parental disapproval of sex were examined as predictors of self-reported birth outcomes. Weighted multivariable linear regression models were run incorporating interactions by race. Setting United States. Participants 632 females who participated in Waves I and IV of the National Longitudinal Study of Adolescent Health (Add Health), a nationally-representative sample of students enrolled in grades 7-12 in 1994-95 and followed up in 2007-2008. Main Outcome Measures Birthweight and gestational age. Results For Black adolescents, better parent-child relationship was associated with higher birthweight (0.14 kg, P Conclusion Parent-child relationships and attitudes about sex affect outcomes of pregnant adolescents.
Interpretations of an adjoint-derived observational impact measure

The measure developed by Langland and Baker to estimate and compare the utility of arbitrary sets of observations for reducing forecast error is re-derived here. The formula uses adjoints of both a forecast model and a data assimilation system. Although the final expression here is nearly identical to that developed by Langland and Baker, the third-order character of their measure is now explicitly presented. The appropriateness of going beyond first order is explained and a warning of the measure's nonlinearity possibly clouding its interpretation is offered.
Polarimetric imaging and radiometry in shallow waters

Imaging in scattering media with the purpose of object identification has always been a challenging task. In the ocean, and especially in coastal areas, the situation is one of the worst: absorption and scattering by suspended and dissolved particles take away most of the information and blur the image of the target to be identified. In addition, one has also to take into account the variability of the bottom which, being close to the surface, plays an important role in the resulting integrated light field. Our goal in this study is to gain insight into the effects of the variable environments on the complex polarized underwater realm. We analyze the polarized tridimensional underwater environment. The instruments deployed were an underwater hyperspectral and multi-angular polarimeter, whose accuracy and exactness of results have been previously validated by the means of different radiative transfer calculations; and a green band full-Stokes polarimetric video camera, enclosed in a custom made underwater housing. The results presented here were collected during the first field deployment of the imaging camera. An in-situ validation of the camera with the polarimeter has been obtained and the results have been used to validate the values of the Stokes elements in the images, both for the water column itself and for the underlying bottom. © (2012) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Turmoil in the Nile River Basin: Back to the Future?

Since the end of the Cold War, the Nile co-basin states have been moving towards constructing a regional water governance regime. The focus has been on how to promote cooperative harmonization of the water needs and growth priorities of all basin countries. Unfortunately, the effort appears to have come to a screeching halt, resuscitating old fears of potential inter-riparian conflicts. This paper examines the evolution of contentious politics of hydrology in the Nile basin in light of the regional and international approaches that have hitherto been employed to bring the co-basin states together on the importance of peaceful utilization of Nile waters.
Robust High-Resolution Fine OCT Needle for Side-Viewing Interstitial Tissue Imaging

Fine optical coherence tomography (OCT) imaging needles that can be integrated with a standard biopsy needle have been developed with a new optics design to improve the optical quality and mechanical robustness, where a fiber-optic lens (that is spliced to a single-mode fiber) and a microreflector are encased within a microglass tube. The design also minimizes the cylindrical lens effect induced by the glass tube and eases the needle assembly process. Real-time cross-sectional OCT imaging of various tissue samples were performed ex vivo using the miniature-imaging needle along with a 1300-nm swept-source OCT system. The preliminary results demonstrate the improved mechanical and optical performance and suggest the potential of the fine OCT needle for minimally invasive interstitial imaging and image-guided biopsy.
Structure of (001)-, (110)-, and (111)-oriented Pb(Fe1/2Nb1/2)O3 epitaxial thin films on SrRuO3-buffered SrTiO3 substrates

We have studied the lattice structure of variously oriented lead iron niobate (PFN) thin films with thicknesses of 50 < t < 500 nm that were deposited by pulsed laser deposition (PLD). We have identified that (001)-, (110)-, and (111)-oriented PFN thin films have tetragonal, orthorhombic, and rhombohedral phases at room temperature, respectively. The change in phase stability, when deposited on substrates of different orientations, is discussed with respect to the influence of epitaxial stress.
Heats of mixing: Alcohol- aromatic binary systems at 25°, 35°, and 45°c.

A new isothermal calorimeter with no vapor space is described. It allows the accurate and rapid determination of heats of mixing of endothermic liquid systems. Data are presented for eighteen binary systems composed of a lower alcohol and a simple benzene derivative at 25°, 35°, and 45°C. Precise equations for representing these data are also presented.
Intragastric oxygen: experimental observations in newborn puppies.

SUMMARY Ten puppies delivered by cesarean section and paralysed with succinylcholine were given intragastric oxygen. There was no evidence of oxygen absorption from the stomach or gut as judged by the oxygen saturation of the portal vein or aortic blood. However, when the lungs were expanded and artificial ventilation applied, the oxygen levels rose rapidly. The pH fell and the PCO2 rose during asphyxiation at approximately the same rate in both the experimental group and a control group, irrespective of the administration of I.G. O2. The useof I.G. O2 was completely ineffective as a resuscitation procedure even though the oxygen requirements were minimized by paralysing the animals, and the ductus venosus, foramen ovale and ductus arteriosus were patent.
Propagation in rectangular tunnel with imperfectly conducting walls

An approximate formulation is presented for what is usually considered to be an intractable problem in waveguide theory. The essence is to show that a TM (transverse magnetic) class of modes will be an adequate representation even when all four walls are imperfectly conducting.
Robust Resource Allocation for Large-scale Distributed Shared Resource Environments

This paper presents a new formulation of the resource selection and binding problem and proposes a new algorithm called integrated selection and binding to solve this problem. Our insight is that a resource selection algorithm should consider binding failures. Consequently, the key idea of the integrated selection and binding approach is to decompose a resource collection request into components that can be bound and composed independently and to select multiple sets of resources for each component. The integrated approach is more efficient and effective than the separate approach for competitive access to federated resources
The challenge of collaborative learning in engineering and math

The CoWeb is a collaborative learning technology used in many classes (over 100) at Georgia Institute of Technology (Georgia Tech), USA. The authors present evidence of the success of the tool in supporting learning at a low cost. They also provide anecdotes about the active resistance they have received to use of the CoWeb in engineering, mathematics and some computer science classes. Evidence from interviews and questionnaires points to some of the sources for this resistance.
The safety of combined cardiac and vascular operations: how much is too much?

Objective: The purpose of this study was to identify factors correlating with a poor outcome following combined cardiac and vascular procedures. Methods: We reviewed 45 consecutive patients undergoing combined cardiac and vascular operations. These included cardiac/CEA (n=27), cardiac/AAA (n=13), cardiac/AAA/one other vascular reconstruction (n=4), and cardiac/renal artery bypass (n=1). Group I included all patients with no morbidity or mortality (n=41) and Group II included patients who died or suffered significant morbidity (stroke, renal failure) (n=4). Results: Overall mortality was 4.4% (2/45). These two patients underwent cardiac surgery combined with two additional vascular procedures (cardiac/AAA/other). In patients undergoing cardiac/CEA or cardiac/AAA, there were no deaths and one stroke (contralateral to CEA). Group II had significantly decreased ejection fraction (39%±6% vs 52%±1%) and an increased number of procedures (2.75 vs 2.04). Conclusions: Combined cardiac surgery and vascular reconstruction can be performed safely. However, multiple vascular reconstructions or the presence of decreased ejection fraction increased operative risk.
Cloning, expression, and DNA sequence analysis of genes encoding nontypeable Haemophilus influenzae high-molecular-weight surface-exposed proteins related to filamentous hemagglutinin of Bordetella pertussis.

Abstract A group of high-molecular-weight surface-exposed proteins of nontypeable Haemophilus influenzae are major targets of human serum antibody (S. J. Barenkamp and F. F. Bodor, Pediatr. Infect. Dis. J. 9:333-337, 1990). To further characterize these proteins, we cloned and sequenced genes encoding two related high-molecular-weight proteins from a prototype nontypeable Haemophilus strain. The gene encoding a 120-kDa Haemophilus protein consisted of a 4.4-kbp open reading frame, and the gene encoding a 125-kDa protein consisted of a 4.6-kbp open reading frame. The first 1,259 bp of the two genes were identical. Thereafter, the sequences began to diverge, but overall they were 80% identical, and the derived amino acid sequences showed 70% identity. A protein sequence homology search demonstrated similarity between the derived amino acid sequences of both cloned genes and the derived amino acid sequence of the gene encoding filamentous hemagglutinin, a surface protein produced by the gram-negative pathogen Bordetella pertussis. Antiserum raised against a recombinant protein encoded by the 4.6-kbp open reading frame recognized both the 120- and the 125-kDa proteins in the prototype strain as well as antigenically related high-molecular-weight proteins in 75% of a collection of 125 epidemiologically unrelated nontypeable H. influenzae strains. The antiserum directed against the recombinant protein also recognized purified filamentous hemagglutinin. A murine monoclonal antibody to filamentous hemagglutinin recognized both the 120-kDa and the 125-kDa protein in the prototype strain as well as proteins identical to those recognized by the recombinant-protein antiserum in 35% of the nontypeable H. influenzae strain collection. Thus, we have identified and partially characterized a group of highly immunogenic surface-exposed proteins of nontypeable H. influenzae which are related to the filamentous hemagglutinin of B. pertussis.
Radio Frequency Identification Applications in Hospital Enviroments

Radio frequency identification (RFID) technology has recently begun to receive increased interest from practitioners and academicians. This interest is driven by mandates from major retailers such ...
KGF prevents oxygen-mediated damage in ARPE-19 cells.

PURPOSE. Oxidative stress has been implicated in a variety of diseases of the eye. In several other tissues, keratinocyte growth factor (KGF) has been shown to prevent negative cellular changes associated with oxidative insult, such as permeability increases and nuclear DNA damage. In this study, we looked at whether KGF provided these same protective effects to cultured human retinal pigmented epithelial (RPE) cells (ARPE-19). METHODS. Reverse transcriptase–polymerase chain reaction (RT-PCR) using a published primer pair sequence followed by restriction endonuclease digestion with AvaI and HincII was used to look for the KGF receptor message in ARPE-19 cells. Cellular response to KGF was verified through proliferation assays and Western blot analysis for mitogen-activated protein kinase (MAPK). Single-cell gel electrophoresis was used to assess DNA damage, Western blot analysis was used to assay actin cytoskeletal changes, and electrical resistance and tracer experiments with Transwell tissue plates were used to assess permeability changes. Immunostaining was used to verify the existence of the tight junction protein occludin. RESULTS. It was verified through RT-PCR that the ARPE-19 cell line exhibited the message for FGFR2-IIIb, otherwise known as KGFR. KGF was also shown to increase cellular proliferation and activated the MAPK p44/p42 cascade. KGF ameliorated nuclear DNA damage and cytoskeletal rearrangement caused by oxidative stress through the addition of exogenous hydrogen peroxide but was unable to prevent permeability changes. CONCLUSIONS. KGF was shown to significantly reduce DNA damage and cytoskeletal rearrangement caused by oxidative stress in cultured ARPE-19 cells. This result may be useful in targeting future therapies to combat a multitude of diseases of the eye that result from increases in reactive oxygen species. (Invest Ophthalmol Vis Sci. 2005;46:3435–3442) DOI:10.1167/
Hermite Methods for Aeroacoustics: Recent Progress

We present recent developments on Hermite methods for aeroacoustic simulations including time-stepping methods, hybridization with discontinuous Galerkin methods for handling of boundary conditions and adaptive implementations. By scaling studies reported below we show that the features unique to Hermite methods have promise to enable efficient exploitation of modern petascale architectures. We also present preliminary computations of turbulent jet noise obtained with the current implementation of our compressible Navier-Stokes solver.
Geometrical structure and thermal phase transition of the dilute s-state Potts and n-vector model at the percolation threshold

A new relation is given in percolation theory from which follows that the backbone of the incipient infinite cluster is made of singly-connected links and “blobs”, the number of links diverge with an universal exponent 1. It is also shown that this exponent characterizes the crossover exponent of the dilute s-state Potts model while for the n-vector model is given by the low density resistivity exponent.
AN ANALYSIS OF THE 1990–1992 TERM LIMITATION ELECTIONS

This paper examines 18 statewide term-limitation elections held between 1990 and 1992 in 16 states. Three basic explanations of the term-limit vote are considered: partisanship, race, and alienation. The results suggest that whites are more likely to support term limits than minorities, and Republicans are more likely to do so than Democrats. Measures of alienation yielded mixed results. An income-based measure of the concept was inconclusive. Nevertheless, a connection between the constituencies of the term-limitation movement and Ross Perot's presidential bid is apparent. The results also reveal that media framing of the term-limitation issue may have affected the outcome in the early term-limitation elections by intensifying voters' distrust of government institutions.
Decomposition of Benzoate Ester Radical Anions

La reduction electrochimique des esters d'acide benzoique en milieu aprotique conduit a des radicaux anioniques relativement stables, qui se decomposent pour redonner des produits electrochimiquement inactifs, suivant un mecanisme EC. Cependant dans le cas de concentrations plus elevees l'ester d'acide benzoique presente un comportement mecanistique plus complique
Performance Evaluation of a Novel Direct Table Lookup Method and Architecture with Application to 16-bit Integer Functions

We describe several integer function properties which in combination allow direct lookup tables to be reduced in size and structure to simpler lookup trees. Our principal result is a novel table lookup method based on a mapping of a lookup tree to a row-by-column ROM with pre and post processing logic substantially reducing the table size. Our lookup architecture allows common 16-bit integer functions such as multiplicative inverse, square, and the discrete log to be realized with table size of order 2-8 Kbytes, in comparison to the 128 Kbyte size of an arbitrary 16-bits-in 16-bits-out function table. The lookup methodology is illustrated with specific development of the 16-bit integer discrete-log function. Implementation for both unnormalized and normalized indices are synthesized into standard cell netlists and performance and area results are given that demonstrate their effectiveness.
TERATOMAS OF THE TONGUE PRESENT AT BIRTH

A large teratoma of the tongue, present at birth, was successfully removed at 32 h of age. It contained immature neural tissue consisting of a loose neurofibrillary matrix with primitive neurons, rossettes, and papillary tissue. Serum alpha fetoprotein was present at 8 days of age, as reported in some patients with malignant teratomas. Our case, however, had no histologic evidence of malignancy, no serum alpha fetoprotein at 7 months of age, and no recurrence at 1 years. The four glossal tumors reported in the literature, including one with immature neural elements, were all present at birth. In 1 case, another teratoma of the tongue was found 5 months after removal of the congenital one. It may not have been a recurrence, as the mass was located in a different area of the tongue. It appears that congenital teratomas of the tongue do not behave in a malignant fashion, at least in the 5 known cases.
EFFECTS OF FEMALE IMMIGRANTS ON DEMOGRAPHY AND SOCIAL ORGANIZATION OF PRAIRIE VOLE (MICROTUS OCHROGASTER) POPULATIONS

We experimentally investigated effects of female immigrants on demography and social organization of prairie vole (Microtus ochrogaster) populations. We tested the hypothesis that increased immigrant pressure by unrelated adult females would decrease the survivorship of juveniles and indirectly decrease the proportion of communal groups in the populations. We established prairie vole populations in 8 enclosures (32 � 32 m). Four populations were supplemented with adult female immigrants, and the other 4 served as control populations in which no females were introduced. The results showed that adult female immigrants reduced the proportion of females and the proportion of juveniles in resident populations but did not change the social organization. We concluded that adult female immigrants did negatively affect resident populations. However, the direct numerical input and subsequent reproduction by immigrants would compensate for their negative effect on resident populations.
Electronic Ordering System Improves Postoperative Pain Management After Total Knee or Hip Arthroplasty.

Objectives: The authors investigated the impact of computerized provider order entry (CPOE) on the delivery times of analgesia and subsequent patient outcomes. We hypothesized that patients would report less pain and use less pain medications compared with the previous paper-based system. Methods: Two groups of patients after a total hip (THA) or knee arthroplasty (TKA) were retrospectively compared: one comprising 106 patients when the paper-based ordering system was in effect (conventional group), and one comprising 96 patients after CPOE was installed (electronic group). All patients received a regional anaesthetic at surgery (combined spinal-epidural). TKA patients also received a single-injection femoral nerve block. After transfer to the postoperative anaesthesia care unit (PACU), a patient-controlled epidural analgesia (PCEA) infusion was initiated. The following data was collected from the PACU record: time to initiation of analgesia, visual analog scale (VAS) pain scores at initiation of analgesia and hourly for the first postoperative day (POD), volume of pain medication used, length of stay (LOS) in the PACU and the hospital. Results: The time to initiation of analgesia from arrival in the PACU was significantly lower in the electronic group compared to the conventional group (24.5 ± 28.3 minutes vs. 51.1 ± 26.2 minutes; mean ± SD, p < 0.001), as were VAS pain scores (0.82 ± 1.08 vs. 1.5 ± 1.52, p < 0.001) and the volume of PCEA needed to control pain (27.9 ± 20.2 ml vs. 34.8 ± 20.3 ml, p = 0.001) at 4 hours postoperatively. PACU LOS and hospital LOS did not significantly differ in the two groups. Conclusions: After implementation of CPOE, patients received their postoperative analgesia faster, had less pain, and required less medication.
Freud Still Matters to Nursing: A Response to Sandra P. Thomas.

Edited byMona M. Shattell, PhD, RN, FAANDePaul University, School of Nursing, Chicago, Illinois, USAEdited byMichelle Cleary, PhD, RNUniversity of Western Sydney, School of Nursing and Midwifery, S...
Worldwide Paper Company

This case is based on an actual investment decision made by a major paper-products company and is primarily designed to be a straightforward exercise in assessing cash flows, cost of capital, and net present value of a capital-investment decision. The case works well for all audiences who are learning the basics of discounted cash flow and investment analysis, including the estimation of relevant cash flows (both cost savings and increased revenues), the effect of taxes on cost savings and revenues, the change in net working capital as a cash flow, and the weighted average cost of capital as the discount rate for the average investment.
Improving Social Skills of Adults With Autism Spectrum Disorder Through Physical Activity, Sports, and Games: A Review of the Literature

Socialization skill deficiencies among adults with autism spectrum disorder (ASD) can lead to depression, anxiety, aggression, and physical health problems. Clinical interventions must treat primary deficiencies and prevent secondary conditions. A treatment model emphasizing the integration of physical activity with social intervention strategies for adults with ASD is proposed.
Insulin a possible inducer of the biosynthesis of rat liver insulinase.

SummaryInsulinase activity was determined by quantitating the degradation of insulin 131I substrate by rat liver homogenates. Plasma insulin was determined by a two-antibody radioimmunoassy procedure. In rats fasted for 1-4 days, insulin levels were 30% at 1 day and 10% at 4 days. Insulinase activity decreased less rapidly, being 80% at 1 day, 60% at 2 days, 35% at 3 days, and 25% at 4 days. On refeeding, insulin levels rose to normal promptly; whereas, insulinase activity did not return to normal until the third day. Refed animals treated with actinomycin D had only 48% of normal insulinase activity after 3 days of refeeding. Actinomycin D also inhibited the renewal of insulinase activity in insulin treated alloxan diabetic rats. These results are compatible with the hypothesis that insulin is an inducer of insulinase biosynthesis.
Retroperitoneal leiomyoma: a case report.

Background Retroperitoneal leiomyomata are rare neoplasms. These masses can be asymptomatic or can cause pelvic discomfort, urinary frequency, abdominal fullness or back pain. Case A 28-year-old, nulliparous female presented with worsening dysmenorrhea and bulk symptoms from fibroids. MRI revealed an exophytic anterior lower uterine segment fibroid with internal degeneration. During surgery the fibroid was discovered to be retroperitoneal in location, contrary to preoperative imaging findings. Pathology confirmed a benign leiomyoma. Conclusion The treatment for these masses is complete excision. The retroperitoneal location of this fibroid was not evident on preoperative ultrasound and MRI. Imaging can be used only as a guide for operative planning and does not always represent the anatomy accurately. Surgical excision is required, and only at surgery will the exact anatomical location of the fibroid be ascertained.
Collectivism and individualism in Latino recovery homes

ABSTRACTResearch indicates that Latinos underutilize substance abuse interventions; cultural variables may contribute to difficulties accessing and completing treatment for this group. As a result, there is a need to understand the role of cultural constructs in treatment outcomes. The purpose of this study was to investigate how levels of collectivism (COL) and individualism (IND) relate to length of stay and relapse outcomes in self-run recovery homes. We compared Latinos in several culturally modified recovery Oxford Houses to Latinos in traditional recovery Oxford Houses. By examining COL and IND in the OH model, we explored whether aspects of COL and IND led to longer lengths of stay and better substance use outcomes. We hypothesized that higher levels of COL would predict longer stays in an Oxford House and less relapse. COL did not have a main effect on length of stay. However, COL had a significant interaction effect with house type such that COL was positively correlated with length of stay in tr...
Enterovesical Cystoplasty for Bladder Closure in Cloacal Exstrophy

Successful bladder closure was accomplished in 4 infants with cloacal exstrophy by enterocystoplasty. Two patients were operated upon as newborns, and 2 were 3 and 8 months old, respectively. Three patients are alive and all are incontinent awaiting secondary bladder neck reconstruction. The surgical technique and results are described.
Perceptual Evidence Against Internal Structure in American Sign Language Syllables

Syllables in spoken languages have been argued to have an internal structure which may cluster the consonants and vowels into subgroups. The most commonly used subgroups are the Onset (initial cons...
Evaluating Teacher Preparation Using Graduates’ Observational Ratings

Despite growing calls for more accountability of teacher education programs (TEPs), there is little consensus about how to evaluate them. This study investigates the potential for using observational ratings of program completers to evaluate TEPs. Drawing on statewide data on almost 9,500 program completers, representing 44 providers (183 programs) in Tennessee across 3 years, we investigate multiple models to estimate TEP quality. Results suggest that using observational ratings to evaluate TEPs has promise. We were able to detect significant and meaningful differences between TEPs, which were fairly robust across modeling approaches. Moreover, TEP rankings based on observational ratings were positively and significantly related to rankings based on student achievement gains.
Abstract 904: Heterozygous ATG7 inhibition enhances endocrine therapy responsiveness through regulation of damage associated molecular patterns and priming the immune system in ER+ breast tumors

Breast cancer is the most prevalent cancer in women, with over 230,000 new cases diagnosed annually. The most common type of breast cancer, comprising over 70% of all cases, express the estrogen receptor (ER); these tumors are usually treated with an endocrine therapy such as an antiestrogen or aromatase inhibitor. Unfortunately, many of these tumors develop resistance, or in some instances express de novo resistance, which limits the curative potential of these therapies. Autophagy, a cellular process of “self-eating”, is implicated as possible contributor to endocrine therapy resistance in breast cancer. We previously showed that inhibiting autophagy through low-dose chloroquine treatment reversed antiestrogen therapy resistance in ER+ orthotopic breast tumors. We now show that heterozygous deletion of ATG7 decreased breast tumor multiplicity and increased endocrine targeting therapy sensitivity in a DMBA-model of ER+ mammary carcinogenesis. Knockdown of ATG7 through RNAi increased cytoplasmic to nuclear high-mobility group binding protein B1 (HMGB1) protein ratio, suggesting targeting ATG7 promotes damage associated molecular patterns (DAMP) signaling. Heterozygous deletion of ATG7 also increased cytoplasmic HMGB1 protein expression in tumor epithelial cells indicating targeting ATG7 promotes DAMP signaling in vivo. Furthermore, tumors from ATG7 heterozygous mice displayed increased CD68 staining indicating elevated macrophage infiltration. Corroborating previous literature showing the critical role of autophagy in T-cell maturation, splenic CD8+ T-cells were significantly reduced in tumor bearing ATG7 heterozygous mice. However, ATG7 heterozygous mice displayed increased tumor CD8+ T-cell population. These data suggest that while targeting ATG7 reduces overall circulating T-cell populations, inhibiting ATG7 enhances tumoral cytotoxic T-cell recruitment. Tumors from ATG7 heterozygous mice also showed a significant decrease in foxp3+ cells, indicating targeting ATG7 reduces immuno-suppressive T-reg population. Serum from ATG7 heterozygous mice showed increased circulating MDC, MCP-1, IL-6, and eotaxin cytokines. Taken together, these data suggests that ATG7 inhibition promotes an anti-tumor pro-inflammatory cytokine profile to enhance tumoral immune cell recruitment and promote endocrine therapy responsiveness. Citation Format: Robert Clarke, Pamela A.G. Clarke, Anni Warri, Katherine L. Cook. Heterozygous ATG7 inhibition enhances endocrine therapy responsiveness through regulation of damage associated molecular patterns and priming the immune system in ER+ breast tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 904.
Assessment of a project-based curriculum for algorithm design and NP-completeness centered on the traveling salesperson problem

Algorithms and complexity are fundamental to Computer Science (CS). This paper describes the evaluation of an NSF-funded, project-based curriculum for algorithm design that includes strategies for intractable problems. This curriculum is a sequence of laboratory projects comprising increasingly sophisticated solvers for a single intractable problem. The curriculum is designed to integrate into existing, one-term, undergraduate courses that teach algorithm design and/or intractability. Three versions of the curriculum have been developed to facilitate its sustained adoption, each centered on a well-known problem: Traveling Salesperson (TSP), Satisfiability (SAT) and Sudoku. Over the past decade, the authors have adopted many versions of the curriculum to teach the Design and Analysis of Algorithms course that is required for CS majors at their institution. In the fall semester of 2014, they adopted and assessed a version of the TSP curriculum. The data shows that the curriculum enables the CS2013 core tier-1 and core tier-2 learning outcomes on Algorithms and Complexity. Additionally, the curriculum enables the CS2013 learning outcomes on Advanced Computational Complexity and some learning outcomes in Advanced Data Structures, Algorithms and Analysis. Thus, the curriculum enables students to engage with intractability and learn about NP-Completeness, while also learning the content of traditional undergraduate courses on algorithms.
Longitudinal Viral Dynamics in Semen During Early HIV Infection.

Author(s): Morris, Sheldon R; Zhao, Mitchell; Smith, Davey M; Vargas, Milenka V; Little, Susan J; Gianella, Sara | Abstract: BackgroundMultiple viruses coinfect the male genital tract, influencing each other’s replication and perhaps affecting human immunodeficiency virus (HIV) pathogenesis and disease progression.MethodsThis study included 453 longitudinal seminal samples from 195 HIV-infected men from the San Diego Primary Infection Resource Consortium and 67 seminal samples from HIV-negative healthy controls. Seminal HIV RNA and DNA from 7 human herpesviruses (HHVs) were measured by real-time polymerase chain reaction. Longitudinal shedding rates were determined by Kaplan-Meier survival analysis. Predictors of viral shedding were determined using backwards selection in a multivariable generalized estimating equation model.ResultsHIV-infected participants presented significantly increased rates of seminal HHV shedding compared with HIV-uninfected controls. Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) were the most commonly detected HHV in semen of HIV-infected participants. Persistent shedding was more common for CMV and EBV when compared to other HHVs. With exception of HHV-7, HHV shedding was not significantly influenced by HIV RNA levels, CD4+ cell counts, or antiretroviral therapy. Presence of CMV, EBV, and herpes simplex virus (HSV) were independent predictors of genital HIV RNA shedding after adjusting for plasma HIV RNA and longitudinal measurements.ConclusionsSeminal replication of multiple HHVs is common in our HIV primary infection cohort. Genital replication of CMV and EBV was the most common and was significantly associated with seminal HIV RNA shedding. Prevalence of HSV shedding was lower and mostly intermittent, but its association with seminal HIV RNA was the strongest. Understanding the complex viral milieu in semen is important for HIV transmission but might also play a role in HIV pathogenesis and disease progression.
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology

The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions. We developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .
Assessing the Safety and Clinical Impact of Thoracoscopic Lung Biopsy in Patients with Interstitial Lung Disease.

Introduction The clinical relevance of surgical lung biopsy in Interstitial Lung Disease (ILD) is supported in the literature. Yet most reports reflect institutional or personal bias. Aim To evaluate the validity of radiologic diagnosis and clinical impact of lung biopsy to help clarify which patient benefit most from biopsy. Materials and methods We performed a retrospective analysis of a prospectively managed database. All patients who had a surgical lung biopsy for ILD within a period of four year (2009 to 2013) were included. Data included patient demographics, peri-operative variables and outcomes. Preoperative Computed Tomography (CT) imaging was reviewed by a thoracic radiologist blinded to the original report and pathologic information. Results A total of 47 patients were included. Lung tissue was obtained via a thoracoscopic approach in all but two that had mini-thoracotomy. Mean operating time was 51.1 minutes (18-123), median hospital stay was two days (1-18). Most (87.2%) of the patients were discharged within 72 hours. Thirty day mortality for elective surgery was 4.5% (2/44). Post-operative complications occurred in about one third of the patients. Complications in elective procedures included pneumothorax (10.4%), re-intubation (5.4%) and prolonged intubation (2.7%). Full concordance of radiographic diagnosis with the final diagnosis was significantly higher when reviewed by a cardiothoracic radiologist (60.5% vs. 21.3%). The preoperative clinical diagnosis was fully concordant with the final diagnosis in only 28.2% of cases. In 13.0% of patients the preoperative diagnosis was incorrect. Malignancy was the final diagnosis in two (4.3%) patients. In 51.1% of the patients, results of the biopsy did alter therapy. Conclusion Diagnosis of specific ILD by a cardiothoracic radiologist is more specific and accurate and will probably lead to more appropriate therapy. Elective thoracoscopic surgical lung biopsy is a safe procedure, leads to a more accurate diagnosis of ILD and impacts therapy.
Global brain metabolic quantification with whole‐head proton MRS at 3 T

Total N-acetyl-aspartate + N-acetyl-aspartate–glutamate (NAA), total creatine (Cr) and total choline (Cho) proton MRS (1H–MRS) signals are often used as surrogate markers in diffuse neurological pathologies, but spatial coverage of this methodology is limited to 1%–65% of the brain. Here we wish to demonstrate that non-localized, whole-head (WH) 1H–MRS captures just the brain's contribution to the Cho and Cr signals, ignoring all other compartments. Towards this end, 27 young healthy adults (18 men, 9 women), 29.9 ± 8.5 years old, were recruited and underwent T1-weighted MRI for tissue segmentation, non-localizing, approximately 3 min WH 1H–MRS (TE/TR/TI = 5/10[1]/940 ms) and 30 min 1H–MR spectroscopic imaging (MRSI) (TE/TR = 35/2100 ms) in a 360 cm3 volume of interest (VOI) at the brain's center. The VOI absolute NAA, Cr and Cho concentrations, 7.7 ± 0.5, 5.5 ± 0.4 and 1.3 ± 0.2 mM, were all within 10% of the WH: 8.6 ± 1.1, 6.0 ± 1.0 and 1.3 ± 0.2 mM. The mean NAA/Cr and NAA/Cho ratios in the WH were only slightly higher than the “brain-only” VOI: 1.5 versus 1.4 (7%) and 6.6 versus 5.9 (11%); Cho/Cr were not different. The brain/WH volume ratio was 0.31 ± 0.03 (brain ≈ 30% of WH volume). Air-tissue susceptibility-driven local magnetic field changes going from the brain outwards showed sharp gradients of more than 100 Hz/cm (1 ppm/cm), explaining the skull's Cr and Cho signal losses through resonance shifts, line broadening and destructive interference. The similarity of non-localized WH and localized VOI NAA, Cr and Cho concentrations and their ratios suggests that their signals originate predominantly from the brain. Therefore, the fast, comprehensive WH-1H-MRS method may facilitate quantification of these metabolites, which are common surrogate markers in neurological disorders.
Sample Size Calculation for Differential Expression Analysis of RNA-Seq Data

The Holy Grail of precision medicine is the comprehensive integration of patient genotypic with phenotypic data to develop personalized disease prevention and treatment strategies. Next-generation sequencing technologies (NGS) and other types of high-throughput assays have exploded in popularity in recent years, thanks to their ability to produce an enormous volume of data quickly and at relatively low cost compared to more traditional laboratory methods. The ability to generate big data brings us one step closer to the realization of precision medicine; nevertheless, across the life cycle of such data, from experimental design to data capture, management, analysis, and utilization, many challenges remain. In this paper, we reviewed and discussed several statistical methods to estimate sample size based on the Poisson and Negative Binomial distributions for RNAseq experimental design.
Stability Properties of Feynman's Operational Calculus for Exponential Functions of Noncommuting Operators

Stability properties of Feynman's operational calculus are addressed in the setting of exponential functions of noncommuting operators. Applications of some of the stability results are presented. In particular, the time-dependent perturbation theory of nonrelativistic quantum mechanics is presented in the setting of the operational calculus and application of the stability results of this paper to the perturbation theory are discussed.
Polymers for Thin Film Capacitors: Energy Storage – Li Conducting Polymers

This chapter summarizes the fundamentals of film capacitors and presents a general review of recent efforts on the development of dielectric polymers with high-energy density, with emphasis on polymer structures, dielectric properties, energy densities, and more importantly the correlation between these elements. These developments include biaxially oriented polypropylenes, poly(vinylidene fluoride) - based ferroelectric polymers, high-performance aromatic polymers, and polymer nanocomposites. The chapter concludes with a discussion of scientific issues that remain to be address as well as an outlook for the future polymer capacitors.
Saccular Impairment in Alzheimer's Disease Is Associated with Driving Difficulty.

Background/Aims: Patients with Alzheimer’s disease (AD) experience increased rates of vestibular loss. Recent studies suggest that saccular impairment in mild cognitive impairment (MCI) and AD patients is associated with impaired spatial cognitive function. However, the impact of saccular impairment on everyday behaviors that rely on spatial cognitive function is unknown. Methods: We recruited 60 patients (21 MCI and 39 AD) from an interdisciplinary Memory Clinic. Saccular function was measured, and a visuospatial questionnaire was administered to assess whether participants experienced impairments in terms of driving difficulty, losing objects, falls, and fear of falling. Results: In multiple logistic regression analyses, MCI and AD patients with bilateral saccular impairment had a significant, greater than 12-fold odds of driving difficulty (OR 12.1, 95% CI 1.2, 117.7) compared to MCI and AD patients with normal saccular function, and the association appears to be mediated by spatial cognition as measured by the Money Road Map Test. Conclusion: This study suggests a novel link between saccular impairment and driving difficulty in MCI and AD patients and demonstrates that driving difficulty may be a real-world manifestation of impaired spatial cognition associated with saccular impairment.
Coccolith dissolution within copepod guts affects fecal pellet density and sinking rate.

The most common biomineral produced in the contemporary ocean is calcium carbonate, including the polymorph calcite produced by coccolithophores. The surface waters of the ocean are supersaturated with respect to calcium carbonate. As a result, particulate inorganic carbon (PIC), such as calcite coccoliths, is not expected thermodynamically to dissolve in waters above the lysocline (~4500-6000 m). However, observations indicate that up to 60-80% of calcium carbonate is lost in the upper 500-1000 m of the ocean. This is hypothesized to occur in microenvironments with reduced saturation states, such as zooplankton guts. Using a new application of the highly precise 14C microdiffusion technique, we show that following a period of starvation, up to 38% of ingested calcite dissolves in copepod guts. After continued feeding, our data show the gut becomes increasingly buffered, which limits further dissolution; this has been termed the Tums hypothesis (after the drugstore remedy for stomach acid). As less calcite dissolves in the gut and is instead egested in fecal pellets, the fecal pellet sinking rates double, with corresponding increases in pellet density. Our results empirically demonstrate that zooplankton guts can facilitate calcite dissolution above the chemical lysocline, and that carbon export through fecal pellet production is variable, based on the feeding history of the copepod.
Natural History of a Forgotten American Grassland

Taking a break from after-dinner email, I stroll into the family room, glass of cabernet in hand, to find my family watching the Discovery Channel on TV. I almost never watch television, so I do not know what to expect when I encounter one of these strange machines. This time I see a view from a lowflying aircraft of a beautiful green prairie landscape somewhere in the Great Plains of North America. The low undulating hills and soft, waving grass roll into the distant horizon. It is an inviting and comforting sight, a verdant scene once common in the center of our continent but now hard to find due to conversion of millions of acres of prairie to agriculture. The narrator, a well-known actress who, my daughter informs me, has battled aliens in movies, repeats a well-worn refrain: “Grasslands occur where there is too much rain for desert, but not enough rain to support forest.”