cssi/SciSciGPT-SciSciNet huggingface dataset:
TextTree Construction for Parser and Treebank Development

TextTrees, introduced in (Newman, 2005), are skeletal representations formed by systematically converting parser output trees into unlabeled indented strings with minimal bracketing. Files of TextTrees can be read rapidly to evaluate the results of parsing long documents, and are easily edited to allow limited-cost treebank development. This paper reviews the TextTree concept, and then describes the implementation of the almost parser- and grammar-independent TextTree generator, as well as auxiliary methods for producing parser review files and inputs to bracket scoring tools. The results of some limited experiments in TextTree usage are also provided.
Reactivity patterns of class I HLA monoclonal antibodies that distinguish three species of macaques.

The reactivity of a panel of 40 monoclonal antibodies (mAb) specific for HLA class I antigens was assessed in 117 unrelated Macaca mulatta (Mm), with a standard microcytotoxicity assay, in order to compare phenotypic frequencies with those previously reported for M. fascicularis (Mfl) and M. nemestrina (Mn). Based on the reactivity with HLA typed human cell panels, the epitopes recognized by these mAb in macaques were classified as nonpolymorphic, polymorphic "public," and polymorphic "private." Nei's genetic identity (I) and distance (D) formulae were applied to estimate I and D between each of the macaque species and between each macaque species and humans. The HLA nonpolymorphic epitopes emerged as spcies-specific determinants, as all three macaque species showed clear differences from each other and from humans in the frequency of occurrence in population samples. From our previous serologic study and from published sequence data, it is evident that the major histocompatibility complex (MHC) is highly conserved in primate evolution. Ninety percent of the mAb reacted at a similar frequency in either two or three macaque species. With few exceptions, the mAb reacted at a greater frequency in humans than in macaques. Concerning private HLA class I epitopes, we have previously speculated that the human MHC class I polymorphisms probably predate the diversification of macaque-human lineages, and hence would be highly conserved. However, the inconsistent pattern of occurrence of human monomorphic epitopes among the macaque species suggests that a complex explanation is required. One possibility is that HLA monomorphic epitopes are invariant in humans because of their yet unknown functional role; however, this explanation loses some force because of the inconsistent pattern of occurrence among three closely related species of Macaca. However, we favor a second possibility, i.e., that the monomorphic epitopes in humans might be the result of the accumulated neutral mutations and are not subjected to functional constraints. This explanation seems to fit the inconsistent pattern of occurrence of these epitopes among macaques.
Crystal Structures and Bonding in Solids

Matter comes in three forms or phases: gases, liquids, and solids; the last two are called condensed systems. Semiconductors are crystalline solids. To understand their electrical properties we need a basic knowledge of their crystal structure.
Basing Point Pricing and Public Policy

I. Introduction: the nature of the problem, 289; alternative pricing systems, 292; standards of public policy, 293. — II. Pricing practices and the level and flexibility of margins, 294; and the level of costs, 297. — III. Pricing practices and the long run adaptation of capacity to demand, 300; the location of producers, 304; and the allocation of transport resources, 305. — IV. Pricing practices and capacity in relation to cyclical fluctuations in demand, 306; and the organization of the industry, 309. — V. Summary and conclusions, 313.
Reducing the time complexity of the fuzzy c-means algorithm

In this paper, we present an efficient implementation of the fuzzy c-means clustering algorithm. The original algorithm alternates between estimating centers of the clusters and the fuzzy membership of the data points. The size of the membership matrix is on the order of the original data set, a prohibitive size if this technique is to be applied to very large data sets with many clusters. Our implementation eliminates the storage of this data structure by combining the two updates into a single update of the cluster centers. This change significantly affects the asymptotic runtime as the new algorithm is linear with respect to the number of clusters, while the original is quadratic. Elimination of the membership matrix also reduces the overhead associated with repeatedly accessing a large data structure. Empirical evidence is presented to quantify the savings achieved by this new method.
Outcomes After Withholding Anticoagulation From Patients With Suspected Acute Pulmonary Embolism and Negative Computed Tomographic Findings: A Cohort Study

Objective To determine the outcome of withholding anticoagulation from patients with suspected acute pulmonary embolism in whom computed tomographic (CT) findings are interpreted as negative for pulmonary embolism. Patients and Methods This retrospective cohort study included 1512 consecutive patients referred from August 7, 1997, to November 30, 1998, for CT because of clinically suspected acute pulmonary embolism. All patients were examined by electron beam CT, and scanning was performed in a cephalocaudad direction from the top of the aortic arch to the base of the heart with 3-mm collimation, 2-mm table incrementation, and an exposure time of 0.2 second (130 peak kV, 620 mA, and standard reconstruction algorithm). Contrast material was infused at a rate of 3 to 4 mL/s through an antecubital vein with an automated injector. Findings on CT were interpreted as either positive or negative. The main outcome measures were deep venous thrombosis, pulmonary embolism, and vital status within 3 months after the CT scan and the cause of death based on medical record review, mailed patient questionnaires, and telephone interviews. Results In 1010 patients (67%) CT scans were interpreted as negative for acute pulmonary embolism. Seventeen patients were excluded because they received anticoagulation. Of the remaining 993 patients, deep venous thrombosis or pulmonary embolism developed in 8; 118 patients died, 3 of pulmonary embolism. Nineteen patients were known to be alive, but additional clinical information could not be obtained. The 3-month cumulative incidence of overall deep venous thrombosis or pulmonary embolism was 0.5% (95% confidence interval, 0.1%-1.0%) and of fatal pulmonary embolism, 0.3% (95% confidence interval, 0.0%-0.7%). Conclusions The incidence of (1) overall deep venous thrombosis or pulmonary embolism or (2) fatal pulmonary embolism among patients with suspected acute pulmonary embolism, negative CT results, and no other evidence of venous thromboembolism is low. Withholding anticoagulation in these patients appears to be safe.
Exploring a Strategy to Enhance Quality and Patient Safety in U.S. Hospitals through Nurse and Physician Coleadership

Poster Presentation Objective To explore the factors that hindered or enhanced the role development of the partners and the nature and dynamics of the working relationships of coleaders. Design Qualitative inquiry was used to obtain evidence from practice. Setting A large, urban hospital located in the Midwest United States. Sample Eight nurse and physician coleaders were interviewed individually about their shared roles and responsibilities and their collaborative work within a coleadership structure. Methods A deductive content analysis approach was used. Coding started with nine categories that were derived from an extensive review of the literature on coleadership in business, education, and health care. Cross case analysis revealed 40+ subcategories. Results Nurse/physician coleadership is a form of plural leadership in which two formal leaders lead a hospital unit, share power to build a more democratic process, and take back power and influence from diffuse sources of power commonly found in the hospital setting. Two essential themes, the Shared Role Space: Moving from I to We and Partnered Leadership: Dynamic Interplay of Complementary Competencies , emerged from the data to describe the experience, and a conceptual framework was proposed. Numerous factors were revealed that enhanced or hindered the role development of coleaders. The dynamic interplay of the work of coleaders was portrayed. Conclusion/Implications for Nursing Practice Coleadership is different than interprofessional collaboration or teamwork. Clinicians and administrators are offered a toolkit to help ensure successful development of the nurse/physician coleadership model in hospitals. This plural leadership model is a strategy worth exploring to address the challenges of successfully implementing quality and patient safety innovations in hospitals.
Think About It: The Misbegotten Promise of Positive Thinking Discourse

This article, historical and critical in scope, explores self-help literature’s positive thinking discourse, through which key concepts of selfhood, self-transformation, and society are textually c...
A dynamic security association control scheme for efficient authentication in wireless networks

In this paper, we present a dynamic security association control scheme to improve system performance during authentication in wireless networks. First, a new architecture composed of licensed authentication centers (LACs) for inter-domain authentication is introduced, in which security associations (SAs) are created and modified on demand, thus reducing the number of SAs and dynamically adjusting the lifetime of an SA. Then, a dynamic SA (DSA) control scheme is developed to determine an optimal threshold time for DSAs by using a utility function for maximizing the bandwidth efficiency. Simulation results reveal the effectiveness of the proposed scheme in terms of the improvement in authentication latency, bandwidth efficiency, and the number of SAs.
Endothelium-derived relaxing and contracting factors.

Endothelium-dependent relaxation of blood vessels is produced by a large number of agents (e.g., acetylcholine, ATP and ADP, substance P, bradykinin, histamine, thrombin, serotonin). With some agents, relaxation may be limited to certain species and/or blood vessels. Relaxation results from release of a very labile non-prostanoid endothelium-derived relaxing factor (EDRF) or factors. EDRF stimulates guanylate cyclase of the vascular smooth muscle, with the resulting increase in cyclic GMP activating relaxation. EDRF is rapidly inactivated by hemoglobin and superoxide. There is strong evidence that EDRF from many blood vessels and from cultured endothelial cells is nitric oxide (NO) and that its precursor is L-arginine. There is evidence for other relaxing factors, including an endothelium-derived hyperpolarizing factor in some vessels. Flow-induced shear stress also stimulates EDRF release. Endothelium-dependent relaxation occurs in resistance vessels as well as in larger arteries, and is generally more pronounced in arteries than veins. EDRF also inhibits platelet aggregation and adhesion to the blood vessel wall. Endothelium-derived contracting factors appear to be responsible for endothelium-dependent contractions produced by arachidonic acid and hypoxia in isolated systemic vessels and by certain agents and by rapid stretch in isolated cerebral vessels. In all such experiments, the endothelium-derived contracting factor appears to be some product or by-product of cyclooxygenase activity. Recently, endothelial cells in culture have been found to synthesize a peptide, endothelin, which is an extremely potent vasoconstrictor. The possible physiological roles and pathophysiological significance of endothelium-derived relaxing and contracting factors are briefly discussed.
Systematic development and exploration of service-oriented software architectures

The notion of service is becoming increasingly popular as a means for implementing large-scale distributed, reactive systems. Systematic development approaches and modeling notations for services are still largely missing from the literature. We introduce an architecture definition language for service-oriented software architectures. It provides modeling elements for interaction patterns defining services, as well as for mapping sets of services to target component configurations. We also present a comprehensive software development process that considers services as first class modeling elements. By decoupling the modeling of services from their implementation on target component configurations this process enables exploration of multiple architectures implementing the same set of services. We substantiate our view of services as cross-cutting architectural aspects by providing a mapping from services to aspects in AspectJ. We illustrate applicability of our approach by modeling service-oriented architectures for portions of the Center TRACON automation system as a running example.
Role of preoperative palliation of jaundice in pancreatic cancer.

Recent studies suggest that there is no significant benefit and that there may be significantly higher morbidity rates in pancreatic cancer patients who undergo preoperative plastic stent placement for obstructive jaundice. This review attempts to define the role of stenting in patients with pancreatic cancer and malignant obstructive jaundice. The latter includes patients unresectable for cure, those who are too frail to withstand an operation, the occasional patient who presents with cholangitis, and those patients who will have a significant delay in surgery because of preoperative neoadjuvant therapy. Literature review. A therapeutic endoscopy team member of a multidisciplinary team which evaluates and treats >250 pancreatic cancer patients yearly. There are 5 historical randomized controlled trials (RCTs) and 1 current RCT demonstrating no significant benefit in preoperatively decompressing jaundiced patients with pancreatic malignancy with percutaneously placed tubes or endoscopically inserted plastic stents. There are 5 RCTs defining a longer patency rate with self-expandable metal stents (SEMS) compared to plastic prostheses suggesting that in the setting of palliation as well as the use of neoadjuvant therapy for resectable or borderline resectable patients, SEMS placement is preferable. Despite data demonstrating lack of efficacy and potential harm in decompressing the biliary tree as opposed to early surgery in jaundiced patients with pancreatic malignancy, endoscopic retrograde cholangiopancreatography with SEMS insertion remains an invaluable palliative modality in non-resectable patients as well as those in whom contemplated resection is delayed in order to give neoadjuvant therapy.
Bounds on power savings using runtime dynamic voltage scaling: an exact algorithm and a linear-time heuristic approximation

Dynamic voltage/frequency scaling (DVFS) has been shown to be an efficient power/energy reduction technique. Various runtime DVFS policies have been proposed to utilize runtime DVFS opportunities. However, it is hard to know if runtime DVFS opportunities have been fully exploited by a DVFS policy without knowing the upper bounds of possible energy savings. We propose an exact but exponential algorithm to determine the upper bound of energy savings. The algorithm takes into consideration the switching costs, discrete voltage/frequency voltage levels and different program states. We then show a fast linear time heuristic can provide a very close approximate to this bound.
The golf ball-on-tee sign.

The collecting tubules within the medullary pyramid come together to form the papillary ducts that penetrate the papillary tip and drain into a calyx. Normally, individual collecting tubules are not visualized; rather, the normal papilla has a distinctive blush that fades with time. In papillary necrosis, however, central necrosis and sloughing of the papilla create a cavity, which is occasionally large, that fills with contrast material and communicates with the calyceal concavity. Thus, the golf ball–on-tee sign is created, indicating necrosis.
Applying a One-Dimensional Mass Transport Model Using Groundwater Concentration Data

One-dimensional analytical mass transport models are familiar to environmental professionals because they are typically used as learning devices in undergraduate groundwater courses. The application of the models requires relatively certain knowledge of contaminant release to the saturated zone. However, release data are typically not reliably known at sites with uncontrolled contaminant releases. A mass balance approach has been developed to calculate contaminant release parameters based on site-specific groundwater concentration data. Standard numerical calibration and sensitivity analysis techniques were modified for use with the one-dimensional spreadsheet model. A groundwater concentration dataset from a Superfund site was used to evaluate three schemes for calculating the model initial concentration. The site application demonstrates how the spreadsheet model could be used for preliminary remediation system comparisons including restoration time estimating. The use of the spreadsheet model may reduce the effort associated with subsequent numerical modeling typically required for remedial design. The spreadsheet application highlights the importance of collecting physical data with groundwater concentration data.
Evidence of Lattice Relaxation in Platinum-Doped Silicon

The photoionization cross section of the platinum-acceptor level in silicon was measured (in relative units) as a function of photon energy. Capacitance transients due to electron emission from this level were studied in a p+n gated photodiode at temperatures of 40, 60, and 80 K. Measurements were made over the wavelength range of 2 to 5 µm with light from a prism monochromator with a constant bandpass of 10 meV. The platinum density in the diode was about 1014 cm−3, providing a ratio of deep to shallow (phosphorus) levels of about 0.1. The data are in good agreement with the Ridley-Amato lattice-coupling model when a Huang-Rhys parameter of S = 0.3 is used, corresponding to a Frank-Condon shift of 15 meV if an average phonon energy of 50 meV is assumed. The electronic energy of the acceptor level was 226 ± 5 meV below the conduction band, independent of temperature and in agreement with previous studies of thermal ionization. The present results provide the first clear experimental evidence of lattice relaxation associated with a deep level in silicon. However, the observed Huang-Rhys parameter is smaller than the theoretical estimates of Lowther (S ≅ 1), suggesting that multiphonon emission may not be the only mechanism for carrier recombination involving this level.
Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain

Previous single-molecule fluorescence resonance energy transfer (smFRET) studies in which the second and sixth ankyrin repeats (ARs) of IκBα were labeled with FRET pairs showed slow fluctuations as if the IκBα AR domain was unfolding in its native state. To systematically probe where these slow dynamic fluctuations occur, we now present data from smFRET studies wherein FRET labels were placed at ARs 1 and 4 (mutant named AR 1-4), at ARs 2 and 5 (AR 2-5), and at ARs 3 and 6 (AR 3-6). The results presented here reveal that AR 6 most readily detaches/unfolds from the AR domain, undergoing substantial fluctuations at room temperature. AR 6 has fewer stabilizing consensus residues than the other IκBα ARs, probably contributing to the ease with which AR 6 "loses grip". AR 5 shows almost no fluctuations at room temperature, but a significant fraction of molecules shows fluctuations at 37 °C. Introduction of stabilizing mutations that are known to fold AR 6 dampen the fluctuations of AR 5, indicating that the AR 5 fluctuations are likely due to weakened inter-repeat stabilization from AR 6. AR 1 also fluctuates somewhat at room temperature, suggesting that fluctuations are a general behavior of ARs at ends of AR domains. Remarkably, AR 1 still fluctuates in the bound state, but mainly between 0.6 and 0.9 FRET efficiency, whereas in the free IκBα, the fluctuations extend to <0.5 FRET efficiency. Overall, our results provide a more complete picture of the energy landscape of the native state dynamics of an AR domain.
X-irradiation induces ER stress, apoptosis, and senescence in pulmonary artery endothelial cells

AbstractPurpose: The use of clinical radiation for cancer treatment is limited by damage to underlying normal tissue including to the vascular endothelium. We investigated the mechanisms of X-ray-induced cell damage to endothelial cells.Methods: We evaluated necrosis, apoptosis, cellular senescence, and the contribution of endoplasmic reticulum (ER) stress in pulmonary artery endothelial cells (PAEC) irradiated with X-rays (2–50 Gray [Gy]).Results: Clonogenic assays showed that 10 Gy induced ∼99.9% loss of cell viability. No necrosis was detected using lactate dehydrogenase assays, but a low population underwent extrinsic and intrinsic apoptosis, as indicated by the activation of caspases 3, 8, and 9 as well as by neutral comet assay. A majority of PAEC underwent accelerated senescence, as indicated by morphological changes, increased 21 kD cyclin-dependent kinase inhibitor (p21/waf1), decreased sirtuin 1 (SIRT1), and elevated senescence-associated β-galactosidase (SA-β-gal). ER stress was detected by ass...
Design of an Adaptive Scanning Optical Microscope for Simultaneous Large Field of View and High Resolution

In microsystems applications from micro-assembly to biological observation and manipulation, the optical microscope remains one of the most important tools. However, it suffers from the well known trade-off between resolution and field of view. Traditional solutions involve moving the sample under the microscope using a moving stage or moving the microscope itself, and switching between low and high magnification objective lenses. In this paper, we present a new optical microscope design that uses a 2-dimensional high speed, high precision steering mirror system to scan the sample. By stitching the images together as a mosaic, we have the potential to achieve both high resolution and large field of view. Working in coordination with a deformable mirror, this arrangement offers certain advantages over the current state of the art in demanding spatial-temporal observations. We describe the theory of operation, our design methodology, and present a preliminary simulated design. A reduced functionality experimental prototype has been constructed to demonstrate the basic efficacy of the concept and we demonstrate with both biological and micro-assembly examples.
Molecular mechanisms of resistance to heat and oxidative damage

Spore heat resistance can be predicted within reasonable limits from knowledge of optimal growth temperature of the sporeformer, the temperature of sporulation, water content of the spore protoplast, cortex size, total mineralization and specific mineralization. The molecular mechanisms by which dehydration and mineralization act to stabilize spores against heat damage are unknown. A major need for further progress is to identify the principal targets for lethal damage. In this review the hypothesis was explored that heat killing may be related to oxidative killing. The proposed common denominator for the two is the formation of radicals able to react with, and irreversibly damage, spore polymers such as proteins or DNA.
CAPTURE OF ANASTREPHA SPECIES (DIPTERA: TEPHRITIDAE) WITH MULTILURE TRAPS AND BIOLURE ATTRACTANTS IN GUATEMALA

Abstract Two trapping systems were compared in a study in Guatemala during the wet season, May through Dec 2001. Trap/lure combinations consisting of green or yellow-based plastic McPhail-like traps baited with a synthetic 2-component lure (putrescine and ammonium acetate) and 300 mL of propylene glycol antifreeze as a preservative were compared to the traditional glass McPhail baited with torula yeast/borax and 300 mL of water. Both systems captured several key Anastrepha species including Anastrepha ludens Loew, A. obliqua, Macquart, A. serpentina Weidemann, A. striata Schiner, A. distincta Greene, A. fraterculus Weidemann as well as Ceratitis capitata Weidemann. Additionally, 13 other Anastrepha spp. were captured with the synthetic lure. The plastic traps captured more key flies than the McPhail trap except for A. distincta where there were no significant differences between the yellow-based plastic trap and the McPhail trap and no significant differences between any trap and lure for trapping A. frat...
Effect of nucleation on transformation toughening

A simple model is presented to account for the effect of martensitic nucleation in ZrO2 particles on theoretical predictions of toughness enhancement during transformation toughening. The model allows for shear and volumetric strain contributions during nucleation, whereas only volumetric strain contributes to toughness enhancement. It is predicted that toughness enhancement results for both stationary and growing cracks. The predicted toughness enhancement exceeds the theoretical prediction for the case when only volumetric strain is allowed to operate. The important material property is identified to be the ratio of volumetric to shear strain during nucleation of the martensitic product in the transformation from tetragonal to monoclinic symmetry of the ZrO2 particles.
ON THE REPRESENTATION OF BELIEFS BY PROBABILITIES

This paper explores two axiomatic structures of subjective expected utility assuming a finite state-space and state-dependent, connected, topological outcome-spaces. Building on the work of Karni and Schmeidler (1981) the analytical framework includes, in addition to the preference relation on acts, introspective preferences on hypothetical lotteries that are linked to the preference relation on acts by consistency axioms. The two models accommodate state-dependent preferences and yield subjective probabilities that correctly represent the decision-maker's beliefs. State-independent preferences are a special case.
Stabilizing scheduling policies for a single machine system

A generic manufacturing environment is considered. The emphasis is on the small-lot, discrete and asynchronous type of manufacturing systems rather than high volume and continuous type manufacturing. Two classes of scheduling policies are proposed to render the machine stable. The policies are of feedback type. The new scheduling policies are based on the current buffer conditions of the part types. In the first class, the decision is made based on the current overall buffer level of all part types. In the second class, the decision is based on the processing time of the part types. The decision is made in real time and online. >
Diagnostics for causes of packet loss in a high performance data transfer system

Summary form only given. As computational grids become an increasingly dominant force in the high-performance computing arena, the problem of efficiently transferring very large data sets, across geographically distributed computing resources, becomes increasingly difficult and important. Current approaches view the problem largely, if not exclusively, as a network-level problem. Thus all packet loss is interpreted and treated as a network congestion event, limiting the ability to detect or react to changes in the end-to-end system. We believe that a new approach to this problem is worth pursuing, and we are investigating techniques that can differentiate between data loss caused by contention in the network and loss caused by contention for shared CPU resources at the communication endpoints. The approach is to collect and analyze what we term packet-loss signatures that describe the patterns of packet-loss in the current transmission window. We analyze these signatures using Fourier analysis and symbolic dynamics, and present a simple set of experiments demonstrating the effectiveness of this approach.
Blue Light Cystoscopy with Cysview: The USC Experience

Abstract Introduction: Blue light cystoscopy (BLC) using hexaminolevulinic acid has been shown to improve the detection of nonmuscle invasive bladder cancer (NMIBC) during transurethral resection of bladder tumors.1–3 Although the FDA has not yet approved BLC for the detection of carcinoma in situ (CIS), both the European Association of Urology and the International Consultation on Urological Diseases recommend it based on the evidence from clinical trials. Despite the lack of recommendation for repeat use or re-resection, a number of trials have shown the significant improvement in detection of recurrent papillary tumors.2 BLC results in lower recurrence rate and a better recurrence-free survival, but no study, to date, has shown a progression benefit.4 Overall, the false-positive proportion rate of BLC is 12% while it was 10% with white light (WL) alone. In this video, we demonstrate the use of Cysview® for the detection of different stages of urothelial carcinoma, its role in detection of cancer in the...
Opportunities and challenges for TCR mimic antibodies in cancer therapy.

ABSTRACTIntroduction: Monoclonal antibodies (mAbs) are potent cancer therapeutic agents, but exclusively recognize cell-surface targets whereas most cancer-associated proteins are found intracellularly. Hence, potential cancer therapy targets such as over expressed self-proteins, activated oncogenes, mutated tumor suppressors, and translocated gene products are not accessible to traditional mAb therapy. An emerging approach to target these epitopes is the use of TCR mimic mAbs (TCRm) that recognize epitopes similar to those of T cell receptors (TCR).Areas covered: TCRm antigens are composed of a linear peptide sequence derived from degraded proteins and presented in the context of cell-surface MHC molecules. We discuss how the nature of the TCRm epitopes provides both advantages (absolute tumor specificity and access to a new universe of important targets) and disadvantages (low density, MHC restriction, MHC down-regulation, and cross-reactive linear epitopes) to conventional mAb therapy. We will also dis...
Current status of estrogen therapy for prostatic carcinoma.

Studies reevaluating the effects of estrogen in treating prostatic carcinoma have shown that while estrogen usually increases the duration and quality of survival, it appears to be associated with an increase in fatal and nonfatal thromboembolic complications. Findings also show that 1.0 mg of diethylstilbestrol daily is probably as effective against metastatic cancer of the prostate as 5.0 mg, and is associated with a lower incidence of cardiovascular complications.
Bioethics--problems for today.

1. Susan J Leclair, PhD CLS(NCA) 1. is the Focus: Bioethics guest editor. She is chancellor professor, Department of Medical Laboratory Science, University of Massachusetts Dartmouth, 285 Old Westport Road, Dartmouth MA 02747-2300. (508) 999-8786. (sleclair{at}umassd.edu) After completing the articles in Focus: Bioethics , the reader should be able to: 1. compare the Kantian view of ethics and utilitarianism as tools for medically-related decision-making. 2. compare and contrast autonomy and beneficience as tools for medically-related decision-making. 3. justify the use of these ethical theories in each of the three settings. 4. assess the philosophical theory used by a facility in situations concerning decision making. 5. assess the philosophical theories used by a facility in situations concerning informed consent. For millennia, all aspects of medicine were viewed as sacred trusts given by the gods for the benefit of humanity. Their word was unquestioned. From Imhotep who was raised to the status of a god in ancient Egypt and Galen whose work was supported by the Emperor Marcus Aurelius, physicians and their associates were held in reverence. They brought hope and solace. The loss of scientific thought and the arrival of the black death in medieval Europe caused that comfort to be replaced by fear and quackery.1,2 With the return of scientific investigation though the work of Erhlich, Pasteur, Gram, Koch, etc., medicine regained much of its former reputation as treatments for infections, diabetes, heart disease and so many more afflictions became possible in the mid-twentieth century. This continued explosive increase in scientific knowledge and medical treatment brought us to the point of asking, “If we can do something, must we?” Before there was treatment for serious diseases, there was no need for a discussion about the side effects of that treatment. Before there was life after certain diagnoses, there was no need for a discussion about the quality of that life. Before there was large scale experimentation on humans, there was no need for informed consent. Before there was laboratory or medical imaging studies to provide scientific support for diagnosis, there was no need for a discussion of the role of those practitioners in the ethical decision-making process. Before there were medically or scientifically based ethical dilemmas, there was… After completing the articles in Focus: Bioethics , the reader should be able to: 1. compare the Kantian view of ethics and utilitarianism as tools for medically-related decision-making. 2. compare and contrast autonomy and beneficience as tools for medically-related decision-making. 3. justify the use of these ethical theories in each of the three settings. 4. assess the philosophical theory used by a facility in situations concerning decision making. 5. assess the philosophical theories used by a facility in situations concerning informed consent.
Scalp Psoriasis: Clinical Features and Assessment

Many patients with psoriasis have involvement of the nails. Nail psoriasis can range from asymptomatic, limited involvement to being physically and functionally debilitating. Psoriatic lesions affecting the nail matrix can lead to pitting, leukonychia, red spots on the lunula, and nail plate crumbling. Moreover, nail bed lesions may result in onycholysis, splinter hemorrhages, oil drop discoloration, or nail bed hyperkeratosis. Clinical assessment of disease severity can be performed through various tools and may help clinicians track progress and response to treatment.
Paleoecology and Geoarchaeology at El Palmar and the El Zotz Region, Guatemala

A new paleoecology record from the El Palmar Cival adds to the emerging geoarchaeological record of El Zotz, Guatemala. El Palmar's 3 m stratigraphic record began in the Archaic period before 1500 B.C. at or just before initial Maya impacts. From the lowest level, Late Archaic organic deposition, with evidence for diverse tropical forest and a steady water table, transitioned to Early Preclassic clay deposition, decreased forest taxa, three known food taxa, and more economic species. Clay deposition continued through the Preclassic, with occasional organic and high charcoal deposition, increasing maize, and other possible economic pollen. Classic El Palmar saw a new land use type with continued disturbance evidence but diverse and greater forest cover. Human impacts continued, leaving high amounts of disturbance taxa, charcoal, and the highest maize pollen level, concomitant with lower deposition rates, δ13C evidence of increased, diverse tropical forest taxa and organic sediments. El Zotz Aguada's Early Classic to Postclassic sediment record overlaps this, with maize and squash pollen evidence changing to Classic period copal tree pollen dominance. Both records indicate the maximum quantity of C4 taxa derived organic matter was about 40%, leaving at least half from C3 taxa such as tropical forest species.
Modeling the Free Carrier Recombination Kinetics in PTB7:PCBM Organic Photovoltaics

Currently the exact recombination mechanism of free carriers in organic photovoltaic (OPV) devices is poorly understood. Often a reduced Langevin model is used to describe the decay behavior of electrons and holes. Here we propose a novel, simple kinetic model that accurately describes the decay behavior of free carriers in the PTB7:PCBM organic photovoltaic blend. This model needs to only take into account free and trapped holes in the polymer, and free electrons in the fullerene, to accurately describe the recombination behavior of free carriers as measured by time-resolved microwave conductivity (TRMC). The model is consistent for different PTB7:PCBM blend ratios and spans a light intensity range of over 3 orders of magnitude. The model demonstrates that dark carriers exist in the polymer and interact with photoinduced charge carriers, and that the trapping and detrapping rates of the holes are of high importance to the overall carrier lifetime.
Hypoplastic left anterior descending coronary artery as the cause of inducible myocardial ischemia in a 46-year-old man

Hypoplasia of the left anterior descending (LAD) coronary artery in the absence of other congenital cardiac anomalies is quite rare and presents a real therapeutic challenge. Few cases of this type coronary anomaly have been reported in children and young adults. We present a middle-aged man with clinical, electrocardiographic, and dobutamine stress echocardiographic evidence of myocardial ischemia caused by a hypoplastic distal LAD coronary artery originating from a septal perforator. Diagnostic and therapeutic challenges posed by this rare condition are discussed. The following core competencies are addressed in this article: Medical knowledge, Patient care
Actual Innocence and Wrongful Convictions

In response to wrongful convictions, there has been a revolution in criminal procedure and in research in law and science. Scholars have increasingly studied the characteristics of known wrongful conviction cases and they have conducted interdisciplinary research designed to assess potential changes to procedures used in criminal cases. Scientific bodies have made important recommendations based on this research, and in response, a wide range of jurisdictions have adopted noteworthy changes designed to safeguard crucial types of evidence, such as confession, forensic, and eyewitness evidence, during police investigations and at trial. As a result, both law and science have come together to produce tangible improvements to criminal justice.
Explanation in Computational Neuroscience: Causal and Non-causal

AbstractThis article examines three candidate cases of non-causal explanation in computational neuroscience. I argue that there are instances of efficient coding explanation that are strongly analo...
Spontaneous rupture of the ascending aorta.

Background Nontraumatic, spontaneous rupture of the ascending aorta is rare and the etiology is largely unknown. Methods We reviewed seven patients from our institution, with no known aortic disease or hereditary connective tissue disorder that presented with spontaneous ascending aortic rupture from 2012 to 2017. Results Most patients presented with non-radiating chest pain along with hypertension (71.4%). The mean ascending aortic diameter at rupture was 4.60 ± 0.62 cm. The median door-to-operating room time was 2.58 h, resulting from effective implementation of an aortic emergency protocol. There were no operative mortalities. Conclusions In patients with ascending aortic rupture, aortic diameter may not always correlate with the risk of rupture. Rapid diagnosis combined with a multidisciplinary approach is vital for the successful management of these high-risk patients.
Validation of Patient Reported Outcomes Measurement Information System (PROMIS) Computer Adaptive Tests (CATs) in the Surgical Treatment of Lumbar Spinal Stenosis.

Study Design.Prospective, cohort study.Objective.Demonstrate validity of Patient reported outcomes measurement information system (PROMIS) physical function, pain interference, and pain behavior computer adaptive tests (CATs) in surgically treated lumbar stenosis patients.Summary of Background Data.
Heat Exchanger Performance Impacts on Optimum Cost Conditions in Thermoelectric Energy Recovery Designs

Cost is just as important as power density or efficiency for the adoption of waste heat recovery thermoelectric generators (TEG). Prior work [1] has shown that the system design that minimizes cost (e.g., the $/W value) can be close to the designs that maximize the system’s efficiency or power density, however, it is important to understand the relationship between those designs to optimize TEG performance-cost compromises. Expanding on recent work [1, 2, 3] the impact of heat exchanger conditions on the optimum TEG fill factors and cost scaling of a waste heat recovery thermoelectric generator with a detailed treatment of the hot side exhaust heat exchanger has been investigated further. The effect of the heat lost to the environment and updated relationships between the hot-side and cold-side conductances [4] that maximize power output are considered. The optimum fill factor to minimize TEG energy recovery system costs is strongly dependent on the heat leakage fraction, σ, the mass flow rate of the exhaust, the hot-side heat exchanger effectiveness, heat exchanger UAh, and heat flux. These relationships are explored and characterized for typical exhaust gas-flow conditions to show the inherent design complexities. The heat exchanger costs often dominate the TEG cost equation and it is critical to fully understand the tradeoff between heat exchanger performance, optimum TEG fill factors, and cost to establish potentially optimum design points within the cost-performance design space. This work will explore the design tradeoffs and relationships within the cost-efficiency-power density design space for a typical thermoelectric energy recovery system application. The interplay between optimum TEG fill factors and heat exchanger design can impact system footprint, volume, and mass in weight-sensitive applications. Less-effective, low-cost heat exchangers may outperform higher cost alternatives from a market adoption perspective. This shift of emphasis acknowledging the interdependence of optimum TEG fill factors and heat exchanger performance has significant implications on thermoelectric waste heat recovery systems designs and their operation. In addition, preferred TEG design regimes exist that accommodate reasonable compromises in TE performance and cost. This effort highlights how the optimum fill factor–heat exchanger performance relations couple to these optimum TEG performance-cost domains based on TEG-system-level analyses and provides a focus for future system research and development efforts.
Electrical Conductivity Methods for Measuring and Mapping Soil Salinity

Publisher Summary This chapter reviews the various electrical conductivity methods for measuring soil salinity together with compatible ways for mapping it, including establishing the locations of measurement sites. Advantages and limitations of the alternative methods are discussed and a practical integrated mobile system for measurement/monitoring/mapping is described. Measurement of the electrical conductivity of saturated soil paste extracts can be accurately predicted from measurements of the electrical conductivity and saturation percentage of the soil paste, with substantial savings in time. The measurement of bulk soil electrical conductivity (EC,), made using both four-electrode and electromagnetic induction techniques, can be used to even greater advantage for salinity appraisal. Soil salinity can be determined from EC, directly in the field without requiring laboratory analysis. Alternatively, limited ground-truth techniques involving limited laboratory analysis can be used to predict salinity from the more easily and quickly made measurements of EC,. Both of these salinity assessment techniques have been shown to be reliable and practical. Commercial instrumentation is available for measuring EC, using both four-electrode and electromagnetic induction methodology. These equipment and methodologies have been shown to be useful for purposes of measuring, monitoring, and mapping field salinity, for detecting the presence of shallow water tables, and for assessing the adequacies of leaching and drainage practices for soil salinity control.
Vortex-Induced Vibration Structural Response under Parametric Excitation

A model for calculating response associated with vortex-induced vibrations of a cylinder is proposed. The model considers the periodic wake as a nonlinear oscillator interacting nonlinearly with the body oscillator. For studying structural response, parametric excitation is taken as the driving mechanism. The nonlinear stiffness considered in the model arises out of the vortex-structure interaction and the nonlinear fluid damping is due to higher-order fluctuations. This model represents the mechanism of vortex-induced vibration that includes lock-in motion over a bandwidth, zones of instability for various frequency ratios, phase jump and hysteresis in structural response. Mathematical analysis of the model shows that there are two distinct levels of response. A significant phase jump during the mode transition is also observed. The study for structural response shows a hysteretic behavior at both ends of the lock-in zone due to parametric excitation and high amplitude nonlinear damping resembling experimentally observed free vortex-induced vibrations of cylinders. This study suggests that the structural response due to vortex-induced vibration is nonlinear and parametric.
EMNets: A Convolutional Autoencoder for Protein Surface Retrieval Based on Cryo-Electron Microscopy Imaging

Protein surface shape plays an essential role in various function of proteins. In order to efficiently investigate protein function and evolutionary history, we introduce a global protein surface shape representation called EMNets. EMNets provides an effective and accurate way of protein surface representation and similarity search, and thus contributes to biomedical research. The method uses a Convolutional Autoencoder (CAE) neural network to learn the geometric information of three-dimensional (3D) density maps in a data-driven manner. Our method effectively represents a 3D cryo-electron microscopy density map by using a descriptor consists of only 256 numeric variables which is called EMNets descriptor. Based on EMNets descriptor, we are able to retrieve similar protein surfaces using k-nearest-neighbor algorithm in real-time. The search results of protein surface represented with the EMNets descriptor has shown high agreement with the existing Combinatorial Extension (CE) algorithm of sequence and structure similarity search. Overall, EMNets is a powerful tool in comparing 3D protein structures obtained by cryo-electron microscopy.