cssi/SciSciGPT-SciSciNet huggingface dataset:
Interobserver Reliability of the Berlin ARDS Definition and Strategies to Improve the Reliability of ARDS Diagnosis

Background Failure to reliably diagnose ARDS may be a major driver of negative clinical trials and underrecognition and treatment in clinical practice. We sought to examine the interobserver reliability of the Berlin ARDS definition and examine strategies for improving the reliability of ARDS diagnosis. Methods Two hundred five patients with hypoxic respiratory failure from four ICUs were reviewed independently by three clinicians, who evaluated whether patients had ARDS, the diagnostic confidence of the reviewers, whether patients met individual ARDS criteria, and the time when criteria were met. Results Interobserver reliability of an ARDS diagnosis was "moderate" (kappa = 0.50; 95% CI, 0.40-0.59). Sixty-seven percent of diagnostic disagreements between clinicians reviewing the same patient was explained by differences in how chest imaging studies were interpreted, with other ARDS criteria contributing less (identification of ARDS risk factor, 15%; cardiac edema/volume overload exclusion, 7%). Combining the independent reviews of three clinicians can increase reliability to "substantial" (kappa = 0.75; 95% CI, 0.68-0.80). When a clinician diagnosed ARDS with "high confidence," all other clinicians agreed with the diagnosis in 72% of reviews. There was close agreement between clinicians about the time when a patient met all ARDS criteria if ARDS developed within the first 48 hours of hospitalization (median difference, 5 hours). Conclusions The reliability of the Berlin ARDS definition is moderate, driven primarily by differences in chest imaging interpretation. Combining independent reviews by multiple clinicians or improving methods to identify bilateral infiltrates on chest imaging are important strategies for improving the reliability of ARDS diagnosis.
Catheter-based endobronchial electroporation is feasible for the focal treatment of peribronchial tumors

Abstract Objective To evaluate the feasibility of catheter-based endobronchial electroporation for the treatment of peribronchial tumors and assess the incidence of treatment-related adverse events. Methods Cytotoxicity of electroporation with or without cisplatin or gefitinib was assessed in vitro with lung cancer and normal cell lines. A novel catheter was designed for endobronchial electroporation, and computer simulations were used to predict in vivo treatment effects. Electroporation with the test catheter was performed (2000 V, 70 pulses) in the main bronchus of 8 pigs at 11 locations. Computed tomography imaging was performed before they were killed at 4 hours (6 animals) or 4 weeks (2 animals) posttreatment. Treated airway and surrounding parenchyma were compared with sham treatment via gross and histopathology. Results Significant cell death due to electroporation and increased cytotoxicity in combination with cisplatin or gefitinib were observed in cancer cells only (P Conclusions Catheter-based endobronchial electroporation is a reproducible technique that can be used to treat peribronchial tumors in combination with cisplatin, without affecting patency of the treated bronchus.
Adapted Tango Dancing for Parkinson's Disease (PD) Can Be Safely Delivered in Community-Based Settings (P02.079)

OBJECTIVE: This study aimed to determine the feasibility and efficacy of delivering adapted tango for PD in the community. BACKGROUND: Adapted tango has improved mobility, balance and QOL in individuals with PD, when examined in controlled laboratory settings (Hackney et al, 2007, Hackney & Earhart 2009, 2010a, b). Community based programs are needed, but whether the adapted tango program can be delivered safely and effectively in such settings is unclear. DESIGN/METHODS: Four dance teachers without clinical qualifications trained in 15h of adapted tango methods. Thirty individuals with mild-moderate PD were assigned to 20, 1.5h lessons of tango (n=21, 10 female; age: 68(7.6)y; range: 55-81y, Hoehn Y age: 74(6.5)y; range: 61-82y, Hoehn Y Hackney). Disclosure: Dr. McKee has nothing to disclose. Dr. Hackney has nothing to disclose.
Laser Surgery for Head and Neck Cancer

Lasers have broad applications in otolaryngology. The myriad possible uses result from the combination of many different anatomic subsites, different types of pathology (both benign and malignant), and several different types of available lasers. A comparison of the KTP laser for hemorrhagic hereditary telangectasias of the nasal cavity, for instance, with photodynamic therapy for esophageal lesions reveals the wide range of applications for laser technology in the head and neck region. It is difficult, however, to make generalizations about laser use when one considers such disparate functions, sites, and pathology. This chapter, then, is limited to a discussion of lasers in the management of squamous cell carcinoma of the oral cavity, oropharynx, hypopharynx, and larynx.
Evaluating Practice: Assessment of the Therapeutic Process

In this article, the use of the Vanderbilt Psychotherapy Process Scale as a tool for evaluating clinical practice is offered as an addition to the use of single system designs of evaluation. An overview of the scale as a framework for teaching and evaluation of the therapeutic relationship is presented.
Alternative Kraftstoffe aus Biomasse

Die sich abzeichnenden Veranderungen auf dem Rohstoff- und Energiesektor bewirken ein Umdenken auf dem Gebiet der Kraftstofftechnologie. Die Forschung Energietechnik und Neue Technologien in der Volkswagenwerk AG befast sich daher intensiv mit Verfahren zur Herstellung von alternativen Kraftstoffen aus Biomasse. Die Alkohole Athanol und Methanol bieten gunstige Voraussetzungen fur einen Einsatz im Kraftfahrzeug. Unter Berucksichtigung landesspezifischer Voraussetzungen und bei Anwendung neuester Technologien kann die Herstellung von Alkoholen in verschiedenen Landern bald wirtschaftlich werden.
Using Attachment Theory When Placing Siblings in Foster Care

Attachment theory offers a useful model for determining if siblings removed from their birth parent's home and awaiting placement should remain together or be separated when placed in foster care. The paper draws from the attachment theory literature, social work literature, and the author's experience as an outpatient psychotherapist. Using the concept of a secure attachment environment, this paper argues that siblings can potentially contribute to, or detract from, a secure attachment environment. When siblings are supportive of each other they can contribute to it. When the sibling relationships are chronically abusive, the individual siblings within a sibling-set are precluded from achieving a secure attachment environment. In these cases the need for separation of the siblings is indicated, and must be considered.
Evolution of the SQUID and its Use in Biomagnetic Research

With benefit of several decades of hindsight, I think London’s hypothesis, that superconductivity is a state characterized by long-range phase coherence, must have required great intellectual courage. He suggested that the theory of wave-particle duality known as quantum theory, hitherto applied only to submicroscopic systems such as individual atoms and molecules, should now be applied to vastly larger systems, such as a one-kilometer loop of superconducting wire. He proposed this startling hypothesis as a trivially simple way of understanding the Meissner effect, the exclusion of magnetic field from a bulk material when it is cooled through the superconducting transition temperature. A consequence of the hypothesis was that if magnetic field is trapped inside a hole or imperfection in a piece of bulk superconductor, the total flux contained within the hole must be quantized. The flux within the hole must be an integral multiple of a basic value, denoted Фo. He suggested Фo = h/e (Planck’s constant divided by the electronic charge) as an obvious possibility for the magnitude of the quantum of flux. The quantity h/e had long been known as a factor in the magnetic effect in atomic spectra known as Zeeman splitting. In 1961, several years after London’s death, it was shown experimentally (and immediately confirmed theoretically, as Prof. Bill Little once put it) that the flux quantum is Фo = h/e (or 2.07 × 10−15 Wb), rather than h/e (Doll and Nabauer, 1961; Deaver and Fairbank, 1961). It was already known that the superconducting state involved electron pairing (with charge 2e), but it seems no one had thought to relate this to flux quantization.
Thermal analyses of polymers: XIV. Multiple melting phenomena in poly(ethylene terephthalate)☆

Abstract The observation of multiple melting phenomena in poly(ethylene terephtha- late) (PET) by DSC or DTA has been confirmed to arise from recrystallization by the changes in birefringence occurring in the thermal regime of the polymer. Isothermal birefringence changes illustrate the melting of crystallites around 230–248 °C, with the formation of more perfect and higher melting crystallites at temperatures of annealing above 248°C. The formation of diethylene glycol residues in the PET during solid state polymerization may be a cause of the higher melting endotherm occurring at lower temperatures when annealed under vacuum.
Esc4/Rtt107 and the control of recombination during replication.

When replication forks stall during DNA synthesis, cells respond by assembling multi-protein complexes to control the various pathways that stabilize the replication machinery, repair the replication fork, and facilitate the reinitiation of processive DNA synthesis. Increasing evidence suggests that cells have evolved scaffolding proteins to orchestrate and control the assembly of these repair complexes, typified in mammalian cells by several BRCT-motif containing proteins, such as Brca1, Xrcc1, and 53BP1. In Saccharomyces cerevisiae, Esc4 contains six such BRCT domains and is required for the most efficient response to a variety of agents that damage DNA. We show that Esc4 interacts with several proteins involved in the repair and processing of stalled or collapsed replication forks, including the recombination protein Rad55. However, the function of Esc4 does not appear to be restricted to a Rad55-dependent process, as we observed an increase in sensitivity to the DNA alkylating agent methane methylsulfonate (MMS) in a esc4Δ rad55Δ mutant, as well as in double mutants of esc4Δ and other recombination genes, compared to the corresponding single mutants. In addition, we show that Esc4 forms multiple nuclear foci in response to treatment with MMS. Similar behavior is also observed in the absence of damage when either of the S-phase checkpoint proteins, Tof1 or Mrc1, is deleted. Thus, we propose that Esc4 associates with ssDNA of stalled forks and acts as a scaffolding protein to recruit and/or modulate the function of other proteins required to reinitiate DNA synthesis.
Racial/ethnic differences in the utilization of chemotherapy among stage I-III breast cancer patients, stratified by subtype: Findings from ten National Program of Cancer Registries states.

Abstract Background The study aimed to examine racial/ethnic differences in chemotherapy utilization by breast cancer subtype. Methods Data on female non-Hispanic white (NHW), non-Hispanic black (NHB), and Hispanic stage I-III breast cancer patients diagnosed in 2011 were obtained from a project to enhance population-based National Program of Cancer Registry data for Comparative Effectiveness Research. Hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) were used to classify subtypes: HR+/HER2-; HR+/HER2+; HR-/HER2-; and HR-/HER2 + . We used multivariable logistic regression models to examine the association of race/ethnicity with three outcomes: chemotherapy (yes, no), neo-adjuvant chemotherapy (yes, no), and delayed chemotherapy (yes, no). Covariates included patient demographics, tumor characteristics, Charlson Comorbidity Index, other cancer treatment, and participating states/areas. Results The study included 25,535 patients (72.1% NHW, 13.7% NHB, and 14.2% Hispanics). NHB with HR+/HER2- (adjusted odds ratio [aOR] 1.22, 95% CI 1.04–1.42) and Hispanics with HR-/HER2- (aOR 1.62, 95% CI 1.15–2.28) were more likely to receive chemotherapy than their NHW counterparts. Both NHB and Hispanics were more likely to receive delayed chemotherapy than NHW, and the pattern was consistent across each subtype. No racial/ethnic differences were found in the receipt of neo-adjuvant chemotherapy. Conclusions Compared to NHW with the same subtype, NHB with HR+/HER2- and Hispanics with HR-/HER2- have higher odds of using chemotherapy; however, they are more likely to receive delayed chemotherapy, regardless of subtype. Whether the increased chemotherapy use among NHB with HR+/HER2- indicates overtreatment needs further investigation. Interventions to improve the timely chemotherapy among NHB and Hispanics are warranted.
'Seeing' Strain in Soft Materials.

Several technologies can be used for measuring strains of soft materials under high rate impact conditions. These technologies include high speed tensile test, split Hopkinson pressure bar test, digital image correlation and high speed X-ray imaging. However, none of these existing technologies can produce a continuous 3D spatial strain distribution in the test specimen. Here we report a novel passive strain sensor based on poly(dimethyl siloxane) (PDMS) elastomer with covalently incorporated spiropyran (SP) mechanophore to measure impact induced strains. We have shown that the incorporation of SP into PDMS at 0.25 wt% level can adequately measure impact strains via color change under a high strain rate of 1500 s−1 within a fraction of a millisecond. Further, the color change is fully reversible and thus can be used repeatedly. This technology has a high potential to be used for quantifying brain strain for traumatic brain injury applications.
Executive Summary: Heart Disease and Stroke Statistics—2013 Update A Report From the American Heart Association

Author(s): Go, Alan S; Mozaffarian, Dariush; Roger, Veronique L; Benjamin, Emelia J; Berry, Jarett D; Borden, William B; Bravata, Dawn M; Dai, Shifan; Ford, Earl S; Fox, Caroline S; Franco, Sheila; Fullerton, Heather J; Gillespie, Cathleen; Hailpern, Susan M; Heit, John A; Howard, Virginia J; Huffman, Mark D; Kissela, Brett M; Kittner, Steven J; Lackland, Daniel T; Lichtman, Judith H; Lisabeth, Lynda D; Magid, David; Marcus, Gregory M; Marelli, Ariane; Matchar, David B; McGuire, Darren K; Mohler, Emile R; Moy, Claudia S; Mussolino, Michael E; Nichol, Graham; Paynter, Nina P; Schreiner, Pamela J; Sorlie, Paul D; Stein, Joel; Turan, Tanya N; Virani, Salim S; Wong, Nathan D; Woo, Daniel; Turner, Melanie B; American Heart Association Statistics Committee and Stroke Statistics Subcommittee
Prospective teachers’ noticing and mathematical decisions to respond: using technology to approximate practice

In recent years, teacher professional noticing has become more prevalent internationally. One common definition to distinguish professional noticing from everyday noticing includes the three interr...
A Smart Home Lab as a Pedagogical Tool

Active learning engages students in the development of knowledge and skills within a supportive environment. The domain of ”Smart Homes” creates such a setting for this experiential learning. Smart Homes are intended to anticipate and meet inhabitant’s needs as they unobtrusively adapt to changing preferences and goals. The vision is to create the optimal balance between current inflexible, limited systems and powerful, but complicated and unproven, pervasive systems. Finding this balance involves investigating approaches for decision making, adaptation, knowledge representation, new user interfaces, and more. Within this rich and realistic domain, students are motivated to actively explore and learn. In this chapter, we describe our experiences with students over the past decade. We argue that one must move from virtual reality simulations to more physical environments, which we call real virtuality.
Investigating the role of the innate immune response in relapse or blast crisis in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is characterized by expression of the tyrosine kinase oncogene, Bcr–abl. Tyrosine kinase inhibitors (TKI) induce prolonged remission in CML, and therapy discontinuation is an accepted approach to patients with reduction in Bcr–abl transcripts of four logs or greater. Half such individuals sustain a therapy free remission, but molecular mechanisms predicting relapse are undefined. We found relative calpain inhibition in CML cells with stabilization of calpain substrates, including βcatenin and Xiap1. Since the Survivin gene is activated by βcatenin, this identified two apoptosis-resistance mechanisms. We found that Survivin impaired apoptosis in leukemia stem cells (LSCs) and Xiap1 in CML granulocytes. Consistent with this, we determined treatment with an inhibitor of Survivin, but not Xiap1, prevented relapse during TKI treatment and after therapy discontinuation in a murine CML model. By transcriptome profiling, we identified activation of innate immune response pathways in murine CML bone marrow progenitors. This was increased by TKI treatment alone, but normalized with addition of a Survivin inhibitor. We found that activation of the innate immune response induced rapid blast crisis in untreated CML mice, and chronic phase relapse during a TKI discontinuation attempt. These results suggest that extrinsic stress exerts adverse effects on CML-LSCs.
“Their wounds are our wounds”: a case for affective solidarity between Palestine and Kashmir

Both Palestine and the Indian held Kashmir have become hallmarks of a postcolonial siege manifest in heavy militarisation, illegal occupation, human rights violations, and an excruciating love born...
Applying Real Options and Game Theory to Information System Decision Making: The Application Software Provider Case

Due to the rapid progress and adoption of information technologies, the decision making for technology investments has become very complex. Also, after the burst of the investment on information technologies (IT) bubble in 2000, companies and investors now require information systems decisions be based on demonstrable value creation that is aligned with the business mission and goals. In this context, it is essential for the IT community to adopt better models for decision-making regarding investments and projects. In this paper, we made a literature review of applying Real Options and Game Theory models for information system decisionmaking. Specifically, we formulate some research questions to analyze the delivery of software applications over the Internet on demand and on a variable pay as-you-go basis. Under this model of delivery, that is starting to be offered by Application Service Providers (ASP) like IBM and Oracle, the customer pays the software as a utility, similar to telephone or energy services. We describe how the combination of Real Option and Game Theory helps Information Systems managers to adopt an optimal strategy for the decision-making process of selecting ASP services. This extended abstract is organized as follows: first we present an overview of ASP and Real Options. Second, we explain an application of Real Options to analyzing ASP software delivery model (Techopitayakul, Johnson, 2001). Third, we consider the new research trends that extend the real option model with game theory to analyze the information system decision-making process under competition. Finally, to do a summary and we present some research questions
Computationally Guided Design of BCR-ABL Tyrosine Kinase Inhibitors

ABSTRACT BCR-ABL tyrosine kinase inhibitors (TKI) are used to treat the chronic myeloid leukemia (CML). Many TKI have been developed as the primary treatment to the CML. Imatinib, a first generation TKI, directly targets BCR-ABL with effective results. As the disease becomes more advanced, patients start to develop resistance to imatinib. Due to this effect it is necessary to generate novel treatments for advanced stage CML. Computational tools can predict new drug candidates to target BCR-ABL. We have designed two new drug candidates with different levels of modification, based on the predicted structure activity relationships with BCR-ABL. These new drug candidates are predicted to have better binding affinities with BCR-ABL than imatinib, which can be more potent treatments of the disease.
Pax2a regulates angiogenesis to facilitate mmp2-dependent basement membrane remodeling of the optic fissure

ABSTRACT Vertebrate retinal development requires timely and precise fusion of the optic fissure (OF). Recent studies have suggested hyaloid vasculature to be involved in optic fissure fusion. In order to examine this link, we analyzed OF fusion and hyaloid vasculogenesis in the zebrafish pax2anoi mutant line. We determined that OF basement membrane (BM) remodeling, normally preceded by F-actin accumulation is mis-regulated in pax2a−/− embryos. Comparing transcriptomic profiles of pax2a−/− and wildtype eyes we discovered a novel connection between regulation of angiogenesis and fusion. Pax2a−/− eyes exhibited a significant reduction of talin1 expression, a regulator of hyaloid vasculature, in addition to increased expression of an anti-angiogenic protease, adamts1. Using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a−/− embryos. Additionally, pharmacological inhibition of VEGF signaling or adamts1 mRNA overexpression phenocopied the pax2a−/− vasculature, F-actin and BM remodeling phenotypes. Finally, we show that hyaloid vasculature expresses mmp2 which is necessary for remodeling the fissure BM. Taken together we propose a pax2a driven mechanism that restricts anti-angiogenic activity of adamts1 enabling hyaloid vasculature invasion of the OF and delivery of the BM remodeler mmp2.
Dual antiplatelet therapy may prevent coronary ischemic events beyond one year—the case for extended treatment

Abstract Platelet inhibition is one of the cornerstones of treatment for coronary artery disease. Aspirin and a P2Y12 receptor antagonists such as clopidogrel, prasugrel, or ticagrelor potently inhibit platelets and create the combination commonly referred to as dual antiplatelet therapy (DAPT). Essential in the acute setting after percutaneous coronary intervention and in the months that follow, but controversial when used years after intervention, DAPT—and the optimal duration for use—has been the subject of many studies. In this chapter, we review the evidence and make the case for extended treatment for patients who are particularly vulnerable to recurrent ischemic events.
Medulla glutamatergic neurons control wake-sleep transitions

SUMMARY Sleep is a ubiquitous behavior in animal species. Yet, brain circuits controlling sleep remain poorly understood. Previous studies have identified several brain structures that promote sleep, but whether these structures are involved in sleep initiation or sleep maintenance remains largely unknown. Here we identified a population of glutamatergic neurons in the medulla that project to the preoptic area (POA), a prominent sleep-promoting region. Chemogenetic silencing of POA-projecting medulla neurons disrupts the transitions from wakefulness to Non-Rapid Eye Movement (NREM) sleep, whereas chemogenetic activation of these neurons promotes NREM sleep. Moreover, we show that optogenetic activation of medulla glutamatergic neurons or their projections in the POA reliably initiates long-lasting NREM sleep in awake mice. Together, our findings uncover a novel excitatory brainstem-hypothalamic circuit that controls the wake-sleep transitions.
Pediatric Orthotopic Heart Transplant Requiring a Novel Cardiectomy with Anastomoses at the Atrioventricular Groove

Introduction Transplantation is the definitive treatment of choice for congenital heart disease not amenable to further surgical repair. Many patients present with complex surgical histories, thus implantation of an orthotopic heart is challenging and preoperative planning imperative. We present a novel cardiectomy technique followed by a bi-atrial to bi-ventricular anastomoses Case Report To avoid taking down the calcified venous baffles, we performed a cardiectomy similar to that for a total artificial heart. An incision was made on the ventricular side of the right ventricular AV groove, which was extended anteriorly across the right ventricular outflow tract just proximal to the pulmonary valve. Posteriorly this was extended across the interventricular septum onto the left ventricular side of the AV groove leaving some residual anterior mitral leaflet and aortic valve tissue in situ. The atrial cuff consisted of approximately 1cm of residual muscle. The donor heart was prepared so that the atria would be anastomosed at the level of the corresponding AV groove. CPB, cross-clamp and ischemic time were 194, 99 and 218 minutes respectively. Post-operative ECHO showed excellent biventricular function, no evidence of mitral valve stenosis or insufficiency, and only mild tricuspid valve insufficiency. Summary This complex case demonstrates the critical need to carefully delineate the technical strategy to adequately plan for complex recipient anatomy in congenital heart patients undergoing transplantation. Utilizing advanced imaging modalities in coordination with pre-operative surgical planning is paramount to successful outcomes of novel transplantation techniques.
Advancing nature-based solutions by leveraging Engineering With Nature® strategies and landscape architectural practices in highly collaborative settings.

The US Army Corps of Engineers (USACE)'s Engineering With Nature® (EWN®) initiative consistently promotes the use of collaboration for identifying innovative, nature-based solutions (NBS) that lead to more resilient communities and water-based infrastructure. In recent years, EWN researchers, in partnership with landscape architects (LAs) affiliated with the Dredge Research Collaborative (DRC), have championed an innovative, collaborative strategy that offers traditional planners an opportunity to participate in visioning exercises during the initial phases of coastal storm risk management projects. This has resulted in the identification, development, and incorporation of design concepts that prioritize NBS and the placement of natural and nature-based features (NNBF). These concepts, and their development process, have been documented in reports for the use of both the participating planners and other audiences interested in innovative NNBF. Upon observing these favorable outcomes, it has become clear that the integration of disciplines-landscape architecture, applied science, and engineering-has increased our ability to process, utilize, and communicate complex information. Both groups (i.e., DRC's LAs and EWN engineers and scientists) have considerable experience related to infrastructure design and performance; they elucidate ways to achieve functional engineering criteria while also maximizing ecological value and/or promoting more recreational opportunities. However, this partnership also produces a complementary set of uniquely acquired skills and expertise, which advances the development of NBS through accelerated and more meaningful communications. This study will offer insight into the partnership, collaborative techniques, and resulting products that have fostered innovation as well as advocacy for more sustainable infrastructure. Integr Environ Assess Manag 2021;00:1-7. © 2021 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
Auto-encoding brain networks with applications to analyzing large-scale brain imaging datasets

There has been huge interest in studying human brain connectomes inferred from different imaging modalities and exploring their relationship with human traits, such as cognition. Brain connectomes are usually represented as networks, with nodes corresponding to different regions of interest (ROIs) and edges to connection strengths between ROIs. Due to the high-dimensionality and non-Euclidean nature of networks, it is challenging to depict their population distribution and relate them to human traits. Current approaches focus on summarizing the network using either pre-specified topological features or principal components analysis (PCA). In this paper, building on recent advances in deep learning, we develop a nonlinear latent factor model to characterize the population distribution of brain graphs and infer the relationships between brain structural connectomes and human traits. We refer to our method as Graph AuTo-Encoding (GATE). We applied GATE to two large-scale brain imaging datasets, the Adolescent Brain Cognitive Development (ABCD) study and the Human Connectome Project (HCP) for adults, to understand the structural brain connectome and its relationship with cognition. Numerical results demonstrate huge advantages of GATE over competitors in terms of prediction accuracy, statistical inference and computing efficiency. We found that structural connectomes have a stronger association with a wide range of human cognitive traits than was apparent using previous approaches.
Integrating single-cell transcriptomics and microcircuit computer modeling.

Abstract Biophysically realistic computer modeling of neuronal microcircuitry has served as a testing ground for hypotheses related to the structure and function of different brain microcircuits. Recent advances in single-cell transcriptomics provide snapshots of a neuron's molecular state and have demonstrated that cell-specific genetic markers engineer the electrophysiological properties of a neuron. Integrating these molecular details with biophysical modeling can allow unprecedented mechanistic insights. In this opinion review, we consider systems biology–based strategies involving statistical deconvolution and gene ontology to integrate the two approaches. We foresee that this integration will infer the nonlinear interactions between the transcriptomically detailed neurons in different brain states. For an initial assessment of these integrative strategies, we recommend testing them on a penetrant phenotype such as epilepsy or a basic organism model such as Caenorhabditis elegans.
Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil.

Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, epre-, which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence epre- states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. Solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.
Was Carl Menger a Neoclassical Economist

The title of this paper was chosen both for pedagogic and for rhetorical reasons. On the face of it, the title makes little sense. For "everyone knows" that the three great neoclassical economists were Jevons, Menger and Waliras. Their joint contribution was the development of marginal analysis. Walras specifically emphasized general equilibrium analysis. Marshall synthesized the new econoiid.cs, or neoclassical economics, with the insights of Ricardian orthodoxy, and developed a new orthodox that reigned in the Anglo-Saxon world until the thirties, when Hicks and Alien reintroduced Walraslan and Paretian ideas.
Ten years of "body packers" in New York City: 50 deaths.

We reviewed all 50 body packer deaths in New York City from 1990 to 2001. The majority (37/50) of deaths were caused by acute intoxications due to open or leaking drug packets in the gastrointestinal tract. The number of packets recovered ranged from 1 to 111 (average 46). The weight of the combined packets ranged from 9.4 to 1200 g (average of 377). The age ranged from 19 to 57 years (mean 37.1). The decedents were: 82% male, 66% Hispanic, 24% Black, and 10% White. The manners of death were 47 accidents, 1 homicide, 1 natural, and 1 undetermined. The causes of death included 42 acute intoxications, 5 intestinal obstructions/bowel perforations, 1 gunshot wound, 1 intracerebral hemorrhage due to hypertensive disease, and 1 undetermined. Of the 50 decedents, 42 were transporting opiates, 4 cocaine, and 4 both opiates and cocaine. There were 9 deaths from 1990–1995 and 41 from 1996–2001. Of the 41 deaths between 1996 and 2001, only 6 involved cocaine. In New York City there has been an increase in body packer deaths from the early 1990s to the late 1990s. Along with this increase is a marked predominance of opiate body packer deaths with few cocaine deaths.
Cooperating SQL Dataflow Processes for In-DB Analytics

Pushing data-intensive analytics down to database engines is the key to high-performance and secured execution; however, the existent SQL framework is unable to express general graph-based dataflow processes, and unable to orchestrate multiple dataflow processes with inter-operation data dependencies. In this work we extend SQL to Functional Form-SQL (FF-SQL) based on a calculus of queries, to declaratively express complex dataflow graphs. A FF-SQL query is constructed from conventional queries using Function Forms (FFs). While a conventional SQL query represents a dataflow tree, a FF-SQL query represents a more general dataflow graph. Further, with FF-SQL, a group of SQL dataflow processes with data dependency among their operations can be specified as a single, integrated FF-SQL definition, and executed cooperatively inside the database engine without repeated data retrieval, duplicated computation and unnecessary data copying. A novel extension to the PostgreSQL query engine is made to support FF-SQL dataflow processes.
On the Existence of Our Metals-Based Civilization I. Phase-Space Analysis

The stability of the barrier layers of bilayer passive films that form on metal and alloy surfaces, when in contact with oxidizing aqueous environments, is explored within the framework of the Point Defect Model (PDM) using phase-space analysis (PSA), in which the rate of growth of the barrier layer into the metal, (dL{sup +}/dt), and the barrier layer dissolution rate, (dL{sup -}/dt), are plotted simultaneously against the barrier layer thickness. A point of intersection of dL{sup -}/dt with dL{sup +}/dt indicates the existence of a metastable barrier layer with a steady state thickness greater than zero. If dL{sup -}/dt > (dL{sup +}/dt){sub L=0}, where the latter quantity is the barrier layer growth rate at zero barrier layer thickness, the barrier layer cannot exist, even as a metastable phase, as the resulting thickness would be negative. Under these conditions, the surface is depassivated and the metal may corrode at a rapid rate. Depassivation may result from a change in the oxidation state of the cation upon dissolution of the barrier layer, such that the dissolution rate becomes highly potential dependent (as in the case of transpassive dissolution of chromium-containing alloys, for example, in which the reaction Cr{sub 2}O{sub 3} + 5H{sub 2}O {yields} 2CrO{sub 4}{sup 2-} + 10H {sup +} + 6e{sup -} results in the destruction of the film), or by the action of some solution-phase species (e.g., H{sup +}, Cl{sup -}) that enhances the dissolution rate to the extent that dL{sup -}/dt > (dL{sup +}/dt){sub L=0}. The boundaries for depassivation may be plotted in potential-pH space to develop Kinetic Stability Diagrams (KSDs) as alternatives to the classical Pourbaix diagrams for describing the conditions under which metals or alloys exist in contact with an aqueous environment. The advantage of KSDs is that they provide kinetic descriptions of the state of a metal or alloy that is in much closer concert with the kinetic phenomenon of passivity and depassivation than are equilibrium thermodynamic diagrams. Thus, KSDs more accurately account for the limits of passivity in highly acidic systems, where acid depassivation occurs, and at high potentials, where transition to the transpassive state may occur in some systems. In any event, phase space analysis of the PDM permits specification of the conditions over which reactive metals will remain passive in contact with aqueous systems and hence of the conditions that must be met for the existence of our metals-based civilization.
Competition between Cable Television and Direct Broadcast Satellite - It's More Complicated than You Think

Direct Broadcast Satellite (DBS) is often considered a substitute for basic cable service, but current cable subscribers may face substantial switching costs to move from cable to DBS services. We use aggregate firm-level price data and other related demographic variables to examine the cost of switching from cable to DBS and vice versa. We find some firm-specific attributes and demographic variables that influence consumer choice and switching costs that appear to affect consumers' desire to switch from one service to another. We then use observation-specific dummy variables that stratify cable price based on changes in the level of cable prices between two periods to examine whether consumer behavior varies depending on the size of price change. We find that when quality-adjusted prices for basic cable services increase substantially, subscribers will switch from cable to DBS, presumably at the point at which the price change is larger than the cost of switching.
Optimization of multigrid based elliptic solver for large scale simulations in the FLASH code

FLASH is a multiphysics multiscale adaptive mesh refinement (AMR) code originally designed for simulation of reactive flows often found in Astrophysics. With its wide user base and flexible applications configuration capability, FLASH has a dual task of maintaining scalability and portability in all its solvers. The scalability of fully explicit solvers in the code is tied very closely to that of the underlying mesh. Others such as the Poisson solver based on a multigrid method have more complex scaling behavior. Multigrid methods suffer from processor starvation and dominating communication costs at coarser grids with increase in the number of processors. In this paper, we propose a combination of uniform grid mesh with AMR mesh, and the merger of two different sets of solvers to overcome the scalability limitation of the Poisson solver in FLASH. The principal challenge in the proposed merger is the efficiency of the communication algorithm to map the mesh back and forth between uniform grid and AMR. We present two different parallel mapping algorithms and also discuss results from performance studies of the two implementations. Copyright © 2012 John Wiley & Sons, Ltd.
Two-particle-resonance pairing mechanism of oxide superconductivity

The oxide superconductors La/sub 2-//sub x/Sr/sub x/CuO/sub 4/ and YBa/sub 2/Cu/sub 3/O/sub 6.5+//sub y/ are treated as strongly correlated electron systems consisting of Cu ions with an on-site electron-electron interaction U of order 10 eV interacting via oxygen bands. Pairing occurs via scattering of quasiparticles into the two-particle resonance at energy U. The model is expressed in a slave-boson formalism and solved in mean field. The results explain the observed scaling of T/sub c/ with hole concentration and is consistent with other data.
A Numerical Study of Pulsed Turbulent Pipe Flow

A numerical study of fully developed turbulent pipe flow due to a sinusoidally varying (with respect to time) axial pressure gradient was carried out using a nonlinear three-dimensional model. Pseudospectral methods were used to solve the model equations. The pulsation frequency was characteristic of the wall region eddies in steady turbulent flow. Attention was focused on the viscous wall region, and it was found that the mean profiles of axial velocity, fluctuation intensities, and turbulence production rate were essentially the same as in steady flow. The fluctuation intensities and the turbulence production rate showed a definite phase relationship to the pressure gradient. The turbulence production rate was the largest at the time in the pulsation cycle at which the largest adverse pressure gradient existed.
Allogeneic Splenocyte Transfer and Lipopolysaccharide Inhalations Induce Differential T Cell Expansion and Lung Injury: A Novel Model of Pulmonary Graft-versus-Host Disease

Background Pulmonary GVHD (pGVHD) is an important complication of hematopoietic cell transplant (HCT) and is thought to be a consequence of the HCT conditioning regimen, allogeneic donor cells, and posttransplant lung exposures. We have previously demonstrated that serial inhaled lipopolysaccharide (LPS) exposures potentiate the development of pGVHD after murine allogeneic HCT. In the current study we hypothesized that allogeneic lymphocytes and environmental exposures alone, in the absence of a pre-conditioning regimen, would cause features of pGVHD and would lead to a different T cell expansion pattern compared to syngeneic cells.
Existence of a Flat Phase in Red Cell Membrane Skeletons

Biomolecular membranes display rich statistical mechanical behavior. They are classified as liquid in the absence of shear elasticity in the plane of the membrane and tethered (solid) when the neighboring molecules or subunits are connected and the membranes exhibit solid-like elastic behavior in the plane of the membrane. The spectrin skeleton of red blood cells was studied as a model tethered membrane. The static structure factor of the skeletons, measured by small-angle x-ray and light scattering, was fitted with a structure factor predicted with a model calculation. The model describes tethered membrane sheets with free edges in a flat phase, which is a locally rough but globally flat membrane configuration. The fit was good for large scattering vectors. The membrane roughness exponent, zeta, defined through h alpha L zeta, where h is the average amplitude of out-of-plane fluctuations and L is the linear membrane dimension, was determined to be 0.65 +/- 0.10. Computer simulations of model red blood cell skeletons also showed this flat phase. The value for the roughness exponent, which was determined from the scaling properties of membranes of different sizes, was consistent with that from the experiments.
The response patterns of single receptors in the crustacean statocyst.

The behaviour of single receptors in the statocyst of the lobster Homarus americanus was studied by moving single receptor hairs or the statolith with a micro-needle while recording the electrical activity from single sensory neurons innervating these hairs. After removing the statolith, the sensory hairs formerly in contact with it assume an angle of about 40 degrees from the cyst floor and in this resting position the associated sensory neuron discharges spontaneously. Movement of a statolith hair toward the vertical causes an increase in frequency during the first 15 degrees, however further displacement in this dirction causes the frequency to drop until it is blocked entirely at a vertical deflexion of 40 degrees from the resting position. The block is reversible and the discharge returns as the hair is moved back toward its resting position. The hair has a peak position where discharge frequency reaches a maximum. Deflexion away from the peak position in either direction decreases the rate of discharge. The hairs may be set below their peak position thus resulting in the bell-shaped response curve observed with stimulation of this receptor type. These receptors function as static position receptors by firing at different non-adapting rates corresponding to specific degrees of hair deflexion. The threshold displacement of the statolith hair nerve terminal is approximately 0$\cdot $5 $\mu $. Different statolith hair receptors are set at various points within their response range by their relation to the sand mass. This provides a means for resolving the ambiguity inherent in the bell-shaped response curve of the single receptor and points to the importance of the multiplication of sensory channels within a single modality. The thread hairs, which are responsible for acceleration sensitivity, increase in frequency with either posterior or ventral deflexion and decrease during either anterior or dorsal deflexion. This differential response to movement accounts for the burst-depression type of coding obtained from acceleration receptors in the intact organ. It is argued that duplication of sensory channels is necessary to retain sensitivity and reliability in a sensory system where the response is superimposed upon an aperiodic background discharge.
Low-Temperature Solar Thermal Systems: An Untapped Energy Resource in the United States

The number of buildings appropriate for solar depends in part on population density and climate. The actual market penetration depends on many factors, including among others first and lifecycle cost, availability, customer preference, and local building and plumbing codes and standards. For the sake of argument, assume a market penetration of 50% of current electric water heaters and 20% of gas water heaters optimistic but achievable goals. A reasonable estimate of the average solar fraction of these systems the fraction of the energy provided by solar with the remainder supplied by the current energy source is 0.5. With this assumed scenario, solar water heaters would displace about 88 billion kWh 0.3 quadrillion BTU of the primary electricity and natural gas in residential buildings. The consequent reduction in greenhouse emissions would be 6.7 million metric tons of carbon 6. If commercial water heating is treated in the same manner, an additional 50 billion kWh 0.17 quadrillion BTU of primary energy consumption could be avoided with a carbon reduction of 2.7 million metric tons. The total projected carbon savings is equivalent to removing 7 million passenger cars from the road 7. Note
On the algebra of Dirac bispinor densities: Factorization and inversion theorems

The algebraic system formed by Dirac bispinor densities ρi≡ψΓiψ is discussed. The inverse problem—given a set of 16 real functions ρi, which satisfy the bispinor algebra, find the spinor ψ to which they correspond—is solved. An expedient solution to this problem is obtained by introducing a general representation of Dirac spinors. It is shown that this form factorizes into the product of two noncommuting projection operators acting on an arbitrary constant spinor.
REVIEW OF U.S. ENVIRONMENTAL PROTECTION AGENCY RESEARCH IN OIL-WATER SEPARATION TECHNOLOGY

ABSTRACT The U.S. Environmental Protection Agency has sponsored two separate research contracts in the field of oil-water separation for the fiscal year 1974. One project, with Pollution Abatement Research, Inc., of Dallas, Texas, concerns the development of a chemically assisted, back-washable coalescer with chemically assisted backwash solids scrubber. This device is designed for use on offshore oil production platforms, although it has a wide potential of applicability. Preliminary tests made with large-volume samples of produced water from an offshore oil production platform yielded very promising results with less than 10 ppm produced oil in the effluent water. The second project, with the Ben Holt Company of Pasadena, California, is to develop a new concept of adsorption of oil-contaminated water onto a regenerable coked surface. The project is aimed at chemically stabilized emulsions and dissolved oils. A bench-scale device has been built, and testing has proven the feasibility of the concept. The ...