cssi/SciSciGPT-SciSciNet huggingface dataset:
Inverse sequence similarity of proteins does not imply structural similarity

There is a debate on the folding of proteins with inverted sequences. Theoretical approaches and experiments give contradictory results. Many proteins in the Protein Data Bank (PDB) show conspicuous inverse sequence similarity (ISS) to each other. Here we analyze whether this ISS is related to structural similarity. For the first time, we performed a large scale three-dimensional (3-D) superposition of corresponding Calpha atoms of forwardly and inversely aligned proteins and tested the degree of secondary structure identity between them. Comparing proteins of less than 50% pairwise sequence identity, only 0.5% of the inversely aligned pairs had similar folds (99 out of 19073), whereas about 9% of forwardly aligned proteins in the same score and length range show similar 3-D structures (1731 out of 19248). This observation strongly supports the view that the inversion of sequences in almost all cases leads to a different folding property of the protein. Inverted sequences are thus suitable as protein-like sequences for control purposes without relations to existing proteins.
Super absorption of ultra-thin organic photovoltaic films

Abstract This article summarized our recent progress in theoretical designs for achieving super absorption in ultra-thin organic photovoltaic (OPV) films based on various planar OPV-on-metal and metal-OPV-metal structures. Three different structures were numerically simulated to demonstrate strongly enhanced optical absorption in ultra-thin OPV layers, which is polarization-independent and occurs over a wide range of incident angles in visible regime. Physical mechanisms associated with these super absorptive ultra-thin layers are analyzed and validated using numerical and analytical modeling.
A chomsky hierarchy of isotonic array grammars and languages

An array is a two-dimensional generalization of a string. Both sides of each rewriting rule of an isotonic array grammar have the same shape. In this paper we complete the Chomsky hierarchy of isotonic array grammars by introducing isotonic context-free array grammars. We obtain Chomsky and Greibach normal forms for context-free array grammars. We show that the one-dimensional (vertical or horizontal) isotonic regular and context-free array languages coincide and are closely related to the regular string languages. We also obtain a finite state recognizer characterization of regular array languages.
Non-concave dynamic programming

Abstract For the standard dynamic programming problem, this paper establishes results regarding the differentiability of the value function and the stability of a solution without assuming concavity of the single period return function.
Reconstructing the Image of an Industrial City

Abstract There is increasing competition between cities to attract investment. Older industrial cities have a particularly difficult time. It is in this context that there is an attempt to rewrite the meaning of the industrial city. Constructing a new, more positive picture includes the marketing of a new image, constructing a new environment, and reorienting a city's relatinship with its physical environment. The process involves many actors, from business leaders eager to stimulate investment to local citizens'groups seeking to reclaim community space. This paper examines these issues in Syracuse, New York, and documents the important changes in civic boosterism, the construction of a new inconography of the downtown, and the evolving discourse on environmental pollution.
Spectropolarimetric Imaging of Laser-Induced Fluorescence

A compact wavelength and polarization agile acoustooptic tunable filter (AOTF)-based imager is used to obtain both spectral and polarization signatures from laser-induced fluorescence in a solution for the first time. This imager covers the visible to near-IR region from 400 to 800 nm, with a 10-nm spectral resolution at 600 nm, it uses an electronically tunable TeO 2 AOTF as a bandpass filter, and a nematic liquid crystal variable retarder to change polarization to obtain two orthogonally polarized images at each spectral wavelength. In this experiment, a blocking filter for the laser was not used before the camera. Here we present fluorescence measurement results for a dilute solution of fluorescein in acetone, using a 532-nm laser. Our results showed that for the vertically polarized exciting light, the fluorescence has a spectropolarimetric dependence in agreement with literature. This imager provides a simpler yet powerful tool to facilitate such measurements remotely with ability to extract both spectral and polarization information at each pixel of an extended sample image.
Increasing FPGA resilience against soft errors using task duplication

Reconfigurable computing systems are becoming increasingly widespread as they bring the flexibility of programmable systems and approach the performance of ASICs. While the prior research on FPGAs mainly studied issues such as performance, power, and area optimization, reliability related issues have not taken much attention. However, with increasing soft error rates, providing resilience to soft errors in FPGA based embedded platforms is becoming an increasingly important issue. This paper proposes an OS-directed task duplication scheme for increasing reliability by providing resilience against soft errors. The idea is to exploit the unused portions of the FPGA space to schedule duplicates of active tasks. The outputs of the primary and duplicate tasks are compared to check for the existence of soft errors.
Predictors of Clinically Significant Radiographic Shoulder Pathology in the Emergency Department.

Abstract Background Although there are no clinical decision rules for radiograph use among persons with shoulder pain, they are ordered for most patients. Previously published reviews have demonstrated that radiography is overutilized in evaluating emergency department (ED) patients with shoulder pain, and clinical factors might define patients in whom plain film radiography need not be performed. Objectives The objectives of this study were to identify predictors of clinically significant shoulder pain and develop a clinical decision radiograph-ordering rule for adult ED patients with shoulder pain. Methods Records from adult ED visits resulting in shoulder radiographs were reviewed. Potential predictors of clinically significant shoulder pain were then identified. Univariate screening was performed to find variables associated with injury and were subsequently included in a multivariable prediction model. Results Five of the predetermined factors were found to be associated with the likelihood of injury: history of trauma, range of motion, deformity, age, and duration of pain. Receiver operating characteristics revealed an area under the curve of 80%. Conclusions Despite accounting for multiple variables, the area under the curve was 80%. Based on these results it is not practical to develop clinical decision radiograph ordering rules for ED patients with shoulder pain.
Advances in apple culture worldwide

Over the last 60 years, planting densities for apple have increased as improved management systems have been developed. Dwarfing rootstocks have been the key to the dramatic changes in tree size, spacing and early production. The Malling series of dwarfing rootstocks (M.9 and M.26) have been the most important dwarfing rootstocks in the world but are poorly adapted in some areas of the world and they are susceptible to the bacterial disease fire blight and the soil disease complex, apple replant disease which limits their uses in some areas. Rootstock breeding programs in several parts of the world are developing improved rootstocks with resistance to fire blight, and replant disease, and improved cold hardiness and yield efficiency. A second important trend has been the increasing importance of new cultivars. New cultivars have provided opportunities for higher prices until they are over-produced. A new trend is the "variety club" in which variety owners manage the production and marketing of a new unique cultivar to bring higher prices to the growers and variety owners. This has led to many fruit growers being unable to plant or grow some new cultivars. Important rootstock and cultivar genes have been mapped and can be used in marker assisted selection of future rootstock and cultivar selections. Other important improvements in apple culture include the development of pre-formed trees, the development of minimal pruning strategies and limb angle bending which have also contributed to the dramatic changes in early production in the 2nd-5th years after planting. Studies on light interception and distribution have led to improved tree forms with better fruit quality. Simple pruning strategies and labor positioning platform machines have resulted in partial mechanization of pruning which has reduced management costs. Improved plant growth regulators for thinning and the development of a thinning prediction model based on tree carbohydrate balance have improved the ability to produce the optimum fruit size and crop load. Other new plant growth regulators have also allowed control of shoot growth, control of preharvest fruit drop and control of fruit softening in storage after harvest. As we look to the future, there will be continued incremental improvement in our understanding of plant physiology that will lead to continued incremental improvements in orchard management but there is likely to be dramatic changes in orchard production systems through genomics research and genetic engineering. A greater understanding of the genetic control of dwarfing, precocity, rooting, vegetative growth, flowering, fruit growth and disease resistance which will lead to new varieties and rootstocks which are less expensive to grow and manage.
Effect of Nasal Dilators on Perceived Odor Intensity

Subjects wearing nasal dilators rated olfactory stimuli as being more intense compared with ratings done without nasal expansion. The results support a perceptual constancy model in olfaction.
The reliability of embedded AI systems

An artificial intelligence (AI) software reliability model, which accounts for the trade-off between correctness and response time, fuzzy rather than binary output, faults in fundamental techniques used in AI programs, and the evolving database that AI programs rely on, is discussed. The model can be reduced to a simpler form for most applications, such as stand-alone expert systems and game-playing programs. In its full generality, it is applicable to real-time planning systems involving hardware and software. >
Influence of support structure on preparation and utilization of polymeric reagents

Polymer bound reagents have become established components of the repertoire of synthetic organic chemists. Recent advances in this field are reviewed with particular attention focused upon the nature of the polymer support. The application of condensation polymers as supports are highlighted. Techniques for chlormethylating polymers containing oxyphenylene repeat units with 1,4-bis [chloromethoxy] butane are presented and the properties of the new supports polymers are described. Aspects of site-site interaction of crosslinked polymer matrices are discussed. The review includes a summary of applications for polymer-bound transition metal catalysts, phase transfer catalysts and organic reagents. Finally, the future of polymeric reagents is examined.
Effects of a 6-week, individualized, supervised exercise program for people with bleeding disorders and hemophilic arthritis.

Background People with bleeding disorders may develop severe arthritis due to joint hemorrhages. Exercise is recommended for people with bleeding disorders, but guidelines are vague and few studies document efficacy. In this study, 65% of people with bleeding disorders surveyed reported participating in minimal exercise, and 50% indicated a fear of exercise-induced bleeding, pain, or physical impairment. Objective The purpose of this study was to examine the feasibility, safety, and efficacy of a professionally designed, individualized, supervised exercise program for people with bleeding disorders. Design A single-group, pretest-posttest clinical design was used. Methods Thirty-three patients (3 female, 30 male; 7–57 years of age) with mild to severe bleeding disorders were enrolled in the study. Twelve patients had co-existing illnesses, including HIV/AIDS, hepatitis, diabetes, fibromyalgia, neurofibromatosis, osteopenia, osteogenesis imperfecta, or cancer. Pre- and post-program measures included upper- and lower-extremity strength (force-generating capacity), joint range of motion, joint and extremity circumference, and distance walked in 6 minutes. Each patient was prescribed a 6-week, twice-weekly, individualized, supervised exercise program. Twenty participants (61%) completed the program. Results Pre- and post-program data were analyzed by paired t tests for all participants who completed the program. No exercise-induced injuries, pain, edema, or bleeding episodes were reported. Significant improvements occurred in joint motion, strength, and distance walked in 6 minutes, with no change in joint circumference. The greatest gains were among the individuals with the most severe joint damage and coexisting illness. Limitations Limitations included a small sample size with concomitant disease, which is common to the population, and a nonblinded examiner. Conclusions A professionally designed and supervised, individualized exercise program is feasible, safe, and beneficial for people with bleeding disorders, even in the presence of concomitant disease. A longitudinal study with a larger sample size, a blinded examiner, and a control group is needed to confirm the results.
Vibrational analysis of peptides, polypeptides, and proteins. I. Polyglycine I.

Synopsis A force field has been refined for the antiparallel chain-rippled sheet structure of polyglycine I. Transition dipole coupling and hydrogen bonding are explicitly taken into account. Amide I and amide I1 mode splittings are well accounted for, the latter also providing a quantitative explanation of the amide A and amide B mode frequencies and intensities. In addition to predicting other features of the vibrational spectrum of polyglycine I, this force field is completely transferable to other 6 polypeptides, even though these have the antiparallel chainpleated sheet structure.
Analysis: Desirable Attributes of Insulin Injection Pens That Drive Patient Preference and Compliance

Insulin pens are used by approximately half of worldwide insulin users. Insulin pens have made insulin injections easier compared to traditional vial and syringe injections. In an article in this issue of Journal of Diabetes Science and Technology, Dr. Asakura discusses several important design parameters, which are considered during refillable insulin-injection pen design. Ease of cartridge replacement, insulin-dose setting dial use, injection, and prominence of audible clicks can all affect overall dose accuracy and user friendliness of insulin pens in patients suffering from diabetes and related comorbidities. These parameters, along with patient introduction from prescribing physicians and level of training provided, drives patient pen selection and injection-regimen compliance to control their blood sugar.
Ultrastructure of the vestibular sensory areas in experimental lathyrism.

The effects of β-aminopropionitrile (BAPN), a lathyrogenic substance, on the vestibular sensory areas of the rat were studied by means of electron microscopy. Degenerative changes occurred in both the type I and type II hair cells, with swelling of mitochondria, numerous large laminated inclusions, vacuolization and protrusion of the supranuclear cytoplasm. The nerve endings showed only mild degeneration. In the connective layer, numerous large membranous whorls were seen enclosing lipid droplets and smooth vesicles. It is suggested that these lesions are primarily due to a disturbance in protein metabolism. The study is a further example of ototoxicity and indicates that lesions in the vestibular end organs play a role in the pathogenesis of experimental lathyrism.
A Blocker-Vigilant Channel-Select Filter with Adaptive IIP3 and Power Dissipation

A dynamic biasing scheme that reduces the average dc power of channel-select filters is presented. An adaptive IIP3, 5th-order Butterworth low-pass filter is implemented in a 0.18mum CMOS process with a 1.8V supply voltage. The filter quiescent current is 1.2mA, with a -5dBV out-of-channel IIP3. With a blocker level of -13dBV, the supply current increases to 2.7mA and the IIP3 increases to +20dBV
The Pharmacogenetics of Alcohol Use Disorder

Background Annually, the use and abuse of alcohol contributes to millions of deaths and billions of dollars in societ al costs. To determine the impact of genetic variation on the susceptibility to the disorder and its response to treatment, studies have been conducted to assess the contribution of a variety of candidate genetic variants. These variants, which we review here, were chosen based upon their observed or hypothesized functional relevance to AUD risk or to the mechanism by which medications used to treat the disorder exert their effects.
Intelligent power allocation strategies in an unlicensed spectrum

We consider power allocation strategies for radios operating in unlicensed bands. Since each radio's power allocation is a source of interference for other radios sharing the same spectrum, we seek to develop "intelligent" power allocation strategies that not only greedily optimize performance, but also tend toward socially optimal solutions. Radio interaction is modeled as a two-player repeated game where players develop "reputations" based on previous actions. Bad behavior can result in punishment meted out by other players while socially acceptable behavior could be rewarded. The space of possible radio strategies is explored using genetic algorithms and we find that there are identifiable strategy features shared by all good policies. We conclude with a brief discussion of the possible applicability of our strategies and algorithms, depending on the operating environment and computational complexity at hand
Run-time detection in parallel and distributed systems: application to safety-critical systems

There is growing interest in run-time detection as parallel and distributed systems grow larger and more complex. This work targets run-time analysis of complex, interactive scientific applications for purposes of attaining scalability improvements with respect to the amount and complexity of the data transmitted, transformed, and shared among different application components. Such improvements are derived from using database techniques to manipulate data streams. Namely, by imposing a relational model on the data streams, constraints on the stream may be expressed as database queries evaluated against the data events comprising the stream. The application in the paper is to a safety-critical system. The paper also presents a tool, dQUOB, Dynamic QUery OBjects, which: (1) offers the means for dynamic creation of queries and for their application to large data streams; (2) permits implementation and runtime use of multiple "query optimization" techniques; and (3) supports dynamic reoptimization of queries based on streams' dynamic behavior.
Glycosylation of Pilin and Nonpilin Protein Constructs by Pseudomonas aeruginosa 1244

PilO is an oligosaccharyl transferase (OTase) that catalyzes the O-glycosylation of Pseudomonas aeruginosa 1244 pilin by adding a single O-antigen repeating unit to the β carbon of the C-terminal residue (a serine). While PilO has an absolute requirement for Ser/Thr at this position, it is unclear if this enzyme must recognize other pilin features. To test this, pilin constructs containing peptide extensions terminating with serine were tested for the ability to support glycosylation. It was found that a 15-residue peptide, which had been modeled on the C-proximal region of strain 1244 pilin, served as a PilO substrate when it was expressed on either group II or group III pilins. In addition, adding a 3-residue extension culminating in serine to the C terminus of a group III pilin supported PilO activity. A protein fusion composed of strain 1244 pilin linked at its C terminus with Escherichia coli alkaline phosphatase (which, in turn, contained the above-mentioned 15 amino acids at its C terminus) was glycosylated by PilO. E. coli alkaline phosphatase lacking the pilin membrane anchor and containing the 15-residue peptide was also glycosylated by PilO. Addition of the 3-residue extension did not allow glycosylation of either of these constructs. Site-directed mutagenesis of strain 1244 pilin residues of the C-proximal region common to the group I proteins showed that this structure was not required for glycosylation. These experiments indicate that pilin common sequence is not required for glycosylation and show that nonpilin protein can be engineered to be a PilO substrate.
A Faustian Foreign Policy from Woodrow Wilson to George W. Bush: Dreams of Perfectibility

A Faustian Foreign Policy from Woodrow Wilson to George W. Bush critiques U.S. foreign policy during this period by showing how moralistic diplomacy has increasingly assumed Faustian overtones, especially during the Cold War and following September 11. The ideological components of American diplomacy, originating in the late 18th and 19th centuries, evolved through the 20th century as U.S. economic and political power steadily increased. Seeing myth making as essential in any country's founding and a common determinant of its foreign policy, Professor Joan Hoff reveals how the basic belief in its exceptionalism has driven America's past and present attempts to remake the world in its own image. She expands her original concept of 'independent internationalism' as the modus operandi of U.S. diplomacy to reveal the many unethical Faustian deals the United States entered into since 1920 to obtain its current global supremacy.
Role of spin fluctuations in the conductivity of CrO 2

We present a time-resolved terahertz spectroscopic study of the half-metallic ferromagnet ${\mathrm{CrO}}_{2}$. The ultrafast conductivity dynamics excited by an optical pump displays very short (several picoseconds) and a very long (several hundred picoseconds) characteristic time scales. We attribute the former to the electron-phonon relaxation and the latter to the spin-lattice relaxation. We use this distinction to quantify the relative contribution of the scattering by spin fluctuations to the resistivity of ${\mathrm{CrO}}_{2}$: We find that they contribute less than one half of all scattering events below room temperature. This contribution rises to $\ensuremath{\sim}70%$ as the temperature approaches ${T}_{C}=390$ K. The small effect of spin fluctuations on the resistivity is unexpected in light of the proposed double-exchange nature of the electronic and magnetic properties of ${\mathrm{CrO}}_{2}$.
Pattern rejection

The efficiency of pattern recognition is particularly crucial in two scenarios; whenever there are a large number of classes to discriminate, and, whenever recognition must be performed a large number of times. We propose a single technique, namely, pattern rejection, that greatly enhances efficiency in both cases. A rejector is a generalization of a classifier, that quickly eliminates a large fraction of the candidate classes or inputs. This allows a recognition algorithm to dedicate its efforts to a much smaller number of possibilities. Importantly, a collection of rejectors may be combined to form a composite rejector, which is shown to be far more effective than any of its individual components. A simple algorithm is proposed for the construction of each of the component rejectors. Its generality is established through close relationships with the Karhunen-Loeve expansion and Fisher's discriminant analysis. Composite rejectors were constructed for two representative applications, namely, appearance matching based object recognition and local feature detection. The results demonstrate substantial efficiency improvements over existing approaches, most notably Fisher's discriminant analysis.
Cooperative decay rate and cooperative Lamb shift from a nanospherical configuration of two adjoining atomic species

The eigenmodes of a nanosphere configuration where the core is an ensemble of two-level atoms with resonance frequency ${\ensuremath{\omega}}_{C}$, and the shell is an ensemble of two-level atoms but with shifted resonant frequency ${\ensuremath{\omega}}_{B}$ are obtained for different values of the ratio of the core radius to the shell outer radius as function of $({\ensuremath{\omega}}_{C}\ensuremath{-}{\ensuremath{\omega}}_{B})$. I show that the eigenmodes belong to one of two branches. The dominant decay mode for superradiant emission may belong to either branch, depending on the system's parameters. In instances of configurations where the cooperative decay rate values for the two branches become equal, the cooperative exponential amplification (decay) is accompanied by temporal oscillations.
Determination of Ephedrine Hydrochloride Inn Zhiketangjiang by HPLC

Objective To establisb method for determining ephedrine hydrochoride in Zhiketangjiang by RP-HPLC.MethodsThe Agilent Extend C_(18) column with acetonitrile-0.1% H_3PO_4(5∶95) as the mobile phase was used.The flow rate at 1.0 ml/min and the detective wavelength was at 206 nm.ResultsThe calibration curve was linear at a range of 0.020 28～1.011 04 μg for the ephedrine hydrochloride(r=0.999 9).The average recovery was 97.69% and RSD was 0.9%(n=6).ConclusionThe method is accurate with a good reproducibility and can be used as a quantitative analysis for this preparation.
Engagement within occupational trainees: Individual difference predictors and commitment outcome

Abstract The present study examines occupational entrants' experiences of their vocational training, its relation with relevant internal characteristics, and its proposed impact on commitment to the profession. Particular focus is paid to trainees' engagement, hypothesizing motivation and self-efficacy as predictors, and occupational commitment as a distal outcome. Data were from 247 recent entrants into professional degree programs (architecture, engineering). All hypothesized predictive relations were supported, such that motivation (as both a composite and as solely intrinsic) and self-efficacy are predictive of engagement, and engagement is predictive of occupational commitment among early-stage trainees. Further, engagement partially mediated the relation between self-efficacy and commitment, and fully mediated the relation between motivation and commitment. Squared multiple correlations for endogenous variables indicated substantial variance in engagement and commitment accounted for by their respective predictors. Moreover, two structural equation models were examined and compared, proposing more holistic nomological nets for how these constructs fit together. A respecified model accounting for a sole focus on intrinsic motivation and a direct path between motivation and commitment was an excellent fit, superseding a competing model conceptualizing motivation as a composite and only an indirect motivation–commitment path. Finally, need for achievement moderated the relation between motivation and engagement such that the relation is stronger for individuals high in need for achievement than it is for those low in the desire to grow in their profession. The study contributes to our understanding of how early occupational trainees' experiences of work and individual characteristics impact their commitment to their intended profession.
Cosmic-ray astrophysicists close in on nearby supernova source

The "standard theory" of cosmic rays – high-energy particles that continually bombard the Earth from space – postulates that the rays, actually charged nuclei, are accelerated by supernova remnants. This was first suggested in the early 1960s by Ginzburg and Syrovatskii, who estimated that the conversion of just 1% of the kinetic energy of the expanding remnant would supply all of the galactic cosmic rays. Supernova remnants (SNR) can expand with velocities in excess of 10000 km s-1 and the acceleration is thought to occur at shocks in the expanding shell of the remnant. Although this model can explain the acceleration of nuclei with energies of up to at least 1014 eV, our Galaxy is believed to produce all of the cosmic rays up to 1018–1019 eV. (Higher energy particles are thought to come from extra-galactic sources.)
Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types

Identification and analysis of recurrent combinatorial patterns of multiple chromatin modifications provide invaluable information for understanding epigenetic regulations. Furthermore, as more data becomes available, it is computationally expensive and unnecessary to study combinatorial patterns of all modifications. A novel framework is proposed to investigate recurrent combinatorial patterns of a subset of quantitatively selected chromatin modifications. The framework is based on heirarchical clustering and selects subsets of chromatin modifications that form distinct recurrent patterns at regulatory regions. The identified recurrent combinatorial patterns can be further utilized to discover novel regulatory regions. Data is in the form of genome wide maps of histone acetylations, methylations, and histone variant of human skeletal muscular and B-lymphocyte cells both derived from the ENCODE project. A case study conducted at promoter regions is presented: four out of twelve chromatin modifications were selected, eight different promoter states were identified and the identified patterns of active promoters were further utilized to discover novel promoter regions. Several previously un-annotated promoters were discovered, further investigations confirm their promoter functions. This framework is approproiately general and could lead to better understanding of epigenetic regulations by discovering previously unknown regulatory regions.
An approach to infer putative disease-specific mechanisms using neighboring gene networks.

Motivation The ultimate goal of any experiment is to understand the biological phenomena underlying the condition investigated. This process often results in genes network through which a certain biological mechanism is explained. Such networks have been proven to be extremely useful, for the prediction of mechanisms of action of drugs or the responses of an organism to a specific impact (e.g. a disease, a treatment, etc.). Here, we introduce an approach able to build a network that captures the putative mechanisms at play in the given condition, by using datasets from multiple experiments studying the same phenotype. This method takes advantage of known interactions extracted from multiple sources such as protein-protein interactions and curated biological pathways. Based on such prior knowledge, we overcome the drawbacks of snap-shot data by considering the possible effects of each gene on its neighbors. Results We show the effectiveness of this approach in three different case studies and validate the results in two ways considering the identified genes and interactions between them. We compare our findings with the results of two widely-used methods in the same category as well as the classical approach of selecting differentially expressed (DE) genes in an investigated condition. The results show that 'neighbor-net' analysis is able to report biological mechanisms that are significantly relevant to the given diseases in all the three case studies, and performs better compared to all reference methods using both validation approaches. Availability and implementation The proposed method is implemented as in R and will be available an a Bioconductor package. Supplementary information Supplementary data are available at Bioinformatics online.
Prevention of Sexually Transmitted Diseases in HIV-Infected Individuals

Prevention of sexually transmitted infections (STIs) is an important part of the care of the HIV-infected individual. STIs have been associated with increased risk of transmission and acquisition of HIV. Among HIV-infected persons, treatment failures and high recurrence rates of some STIs are more common. Despite the recognized importance of prevention and discussion of sexual health, rates of screening for STIs are suboptimal. Moreover, rates of STIs such as syphilis continue to increase particularly in men who have sex with men (MSM). This review focuses on the most common STIs seen among HIV-infected individuals and recommendations for screening and prevention.
Reasons for non-participation and ways to enhance participation in health examination surveys—the Health 2011 Survey

High-participation rates to the health examination surveys are needed to obtain representative information about population health. This study aimed to examine reasons for non-participation and factors that could enhance participation using data from the Health 2011 Survey, conducted in 2011-12 in Finland (N = 8135). The most common reason for non-participation was unsuitable timing or location of the health examinations. Older persons also reported that they were too sick to participate. Flexibility on selection of examination times and places and getting feedback on the measurements were most often mentioned as factors which would increase willingness to participate in the future.
Perspective and epistemic state ascriptions

This article explores whether perspective taking has an impact on the ascription of epistemic states. To do so, a new method is introduced which incites participants to imagine themselves in the position of the protagonist of a short vignette and to judge from her perspective. In a series of experiments (total N=1980), perspective proves to have a significant impact on belief ascriptions, but not on knowledge ascriptions. For belief, perspective is further found to moderate the epistemic side-effect effect significantly. It is hypothesized that the surprising findings are driven by the special epistemic authority we enjoy in assessing our own belief states, which does not extend to the assessment of our own knowledge states.
Invasive Species: Vectors and Management Strategies. Gregory M. Ruiz and James T. Carlton, eds. 2003. Island Press, Washington, DC. 518 pp. $75 hardcover, $40 paperback.

Invasive Species consists of 18 chapters contributed by different authors, all directed at an overview of “vectors” that transport species to new regions in which the organisms are not indigenous. ...
The Status of Probability in the Elementary and Lower Secondary School Mathematics Curriculum: The Rise and Fall of Probability in School Mathematics in the United States

Probability is no longer featured as an important domain of study in the elementary and lower secondary school mathematics curriculum in the United States. The majority of U.S. states have adopted a mathematics curriculum that has eliminated probability as a topic of study in the elementary grades and narrowed its focus in the lower secondary grades. I illustrate the decline of probability via an overview of the various standards documents that have guided mathematics curriculum and instruction for the past 25 years. This situation is not unique to the United States; many other countries around the world do not include probability in the mathematics curriculum for students under the age of 11. I discuss the implications of this curricular decision and raise questions for the consideration of the research community.
Phase II Study of Maintenance Pembrolizumab in Patients with Extensive-Stage Small Cell Lung Cancer (SCLC)

Abstract Objective The aim of this study was to assess the efficacy of maintenance pembrolizumab in patients with extensive-stage SCLC after treatment with platinum and etoposide. Methods Patients with extensive-stage SCLC with a response or stable disease after induction chemotherapy were eligible. Pembrolizumab at a dose of 200 mg administered intravenously every 3 weeks was initiated within 8 weeks of the last cycle of chemotherapy. The primary end point of the study was progression-free survival (PFS) from study registration, with overall survival (OS) as a key secondary end point. Available tumor tissue was assessed for expression of programmed death ligand 1 (PD-L1) both in the tumor cells and in the surrounding stroma. Blood for circulating tumor cells was collected before the first, second, and third cycles of pembrolizumab. Results Of the 45 patients enrolled, 56% were male and 22% had treated brain metastases. The median PFS was 1.4 months (95% confidence interval [CI]: 1.3–2.8), with a 1-year PFS of 13%. The median OS was 9.6 months (95% CI: 7.0–12), with a 1-year OS of 37%. Of the 30 tumors that could be assessed, three had PD-L1 expression (≥1%) in the tumor cells. A total of 20 tumors could be assessed for PD-L1 expression in the stroma. The median PFS in the eight patients with tumors positive for expression of PD-L1 at the stromal interface was 6.5 months (95% CI: 1.1–12.8) compared with 1.3 months (95% CI: 0.6–2.5) in 12 patients with tumors negative for this marker. No unexpected toxicities were observed. Conclusion Maintenance pembrolizumab did not appear to improve median PFS compared with the historical data. However, the 1-year PFS rate of 13% and OS rate of 37% suggest that a subset of patients did benefit from pembrolizumab.
Resilient Modulus Estimation System for Fine-Grained Soils:

A software tool was developed to estimate the resilient modulus of fine-grained subgrade soils. The subgrade resilient modulus is a key factor for use in mechanistic–empirical pavement design methods. However, for routine design use, the test method is too expensive and difficult to perform. Resilient modulus estimation software was developed with expert system approaches. Information entered by the user is first examined for reasonableness and accuracy. Then, data searching processes are initiated, and more than 30 estimation models can be invoked, depending on the availability of input data. All results were evaluated on the basis of certainty rules, such as how well data meet limitations existing during the model’s original development environment. The user is given four alternate methods on which to base the choice of a resilient modulus that is most appropriate for the site: one based on certainty rules and three based on statistical methods.
Autoantigen (64000-Mr) expression in coxsackievirus B4-induced experimental diabetes.

Extensive epidemiologic observations (GAMBLE et al. 1969; GAMBLE 1980; BARRET-CONNOR 1985), many case reports, and animal studies (CRAIGHEAD 1975; NOTKINS 1977) have associated group B coxsackieviruses in the etiology of type 1, insulin-dependent diabetes mellitus (IDDM). IDDM in human patients is rare until 9 months of age and has peaks of onset at 5–8 years and again at 10–14 years of age (GAMBLE 1977). These observations are consistent with epidemiological patterns of many infections, which are prevented by maternal immunity and have peaks at the time of entry into school and at early puberty.
National Implementation of a Trauma-Informed Intervention for Intimate Partner Violence in the Department of Veterans Affairs: First Year Outcomes

The U.S. Department of Veterans Affairs (VA) has recently implemented a comprehensive national program to help veterans who use or experience intimate partner violence (IPV). One important component of this plan is to implement Strength at Home (SAH), a 12-week cognitive-behavioral and trauma-informed group treatment designed to reduce and end IPV use among military and veteran populations. The present study describes initial patient and clinician findings from the first year of a training program tasked with implementing SAH at 10 VA medical centers. Results from 51 veterans who completed both pre- and post-treatment assessments indicate SAH was associated with significant pre- to post-treatment reductions in the proportion of veterans who reported using physical and psychological IPV toward a partner, the types of IPV used, and posttraumatic stress disorder symptoms. Overall, veterans reported high satisfaction with the quality and nature of services received, and with the program materials. In addition, 70% of sites and 34% of the 79 clinicians trained were successful in launching the program in the first year. The mean number of days between site training and initiation of the first group session was 135.86 (SD = 63.16, range 72–252). Results suggest that the training and implementation program was successful overall. However, average length of time between in-person training and initiation of group services was longer than desired and there were three sites that did not successfully implement the program within the first year, suggesting a need to reduce implementation barriers and enhance institutional support.
Augmenting Medical Decision Making With Text-Based Search of Teaching File Repositories and Medical Ontologies: Text-Based Search of Radiology Teaching Files

Teaching files are widely used by radiologists in the diagnostic process and for student education. Most hospitals maintain an active collection of teaching files for internal purposes, but many teaching files are also publicly available online, some linked to secondary sources. However, public sources offer very limited and ad-hoc search capabilities. Based on the previous work on data integration and text-based search, the authors extended their Integrated Radiology Image Search IRIS 1.1 engine with a new medical ontology, SNOMED CT, and the ICD10 dictionary. IRIS 1.1 integrates public data sources and applies query expansion with exact and partial matches to find relevant teaching files. Using a set of 28 representative queries from multiple sources, the search engine finds more relevant teaching cases versus other publicly available search engines.
Designing biofuel supply chains while mitigating harmful algal blooms with treatment wetlands

Abstract Preventing harmful algal blooms (HAB) in water bodies is an urgent environmental challenge across the world. This is a side effect from the supply chain of products from agricultural biomass, and renders many bio-based products environmentally unsustainable. Most existing efforts for designing sustainable supply chains aim to reduce the life cycle environmental impact, while ignoring nature’s role in absorbing the emissions. Using the framework of techno-ecological synergy (TES), this work explicitly accounts for the role of wetlands in absorbing farm runoff to design environmentally sustainable biofuel supply chains. Application to a twenty-one county region of Northwest Ohio, which is largely responsible for HABs in Lake Erie, indicates opportunities for designing techno-ecological supply networks that are economically and ecologically superior to conventional techno-centric networks. Using the TES framework also provides counterintuitive solutions that encourage intensive agriculture with higher phosphorus runoff if there is enough land available for conversion into wetland ecosystems.
Misidentified Clovis-age fish bone at Shawnee-Minisink and the problem with single case studies in Late Pleistocene archaeology

Abstract Paleoindians in North America are often described as specialized big game hunters. Over the years a few sites that show evidence of diversity in subsistence pursuits have been used to argue that Paleoindians were generalized foragers. In this paper, we provide new information on the fish remains reported from the Shawnee-Minisink Clovis site in Pennsylvania, USA. This site has long been touted as an example of generalized foraging by Paleoindians. Through detailed Scanning Electron Microscope (SEM) analyses and energy-dispersive X-ray spectroscopy, we demonstrate that the previous reported fish bone from the Shawnee-Minisink site is not bone but a modern contaminant. We briefly summarize these findings and other published results to show that this single site can no longer be used as an example of foraging diversity by Paleoindians. Based on these findings we caution traditional approaches to identifying calcined bone and the use of single case studies to characterize Early Paleoindian lifeways.
A Highly Stretchable Polyacrylonitrile Elastomer with Nanoreservoirs of Lubricant Using Cyano-Silver Complexes

Stretchable materials are indispensable for applications such as deformable devices, wearable electronics, and future robotics. However, designs for new elastomers with high stretchability have undergone only limited research. Here we have fabricated highly stretchable Ag+/polyacrylonitrile elastomer with nanoreservoirs of lubricant using cyano-silver complexes. The prepared products feature nanoconfinement structures of lubricant surrounded by polymer chains with coordination bond through chelates of cyano-silver, resulting in an enhanced stretchability of more than 600% from 2%. The elastomeric properties were investigated, and a mechanical response model was proposed, which explained the structural evolution including the polymer chain fluidity under external deformation. Also, the easy breakage and dynamic reformation of cyano-silver coordination complexes promises a strain recovery under various stretching conditions. This elastomer itself can directly work as sensors and open paths to alternative substrates for soft electronics development.
An Incomplete Masterpiece

The recent wave of popular and academic commentary on Masterpiece Cakeshop sounded a common theme: disappointment, even frustration. Masterpiece was held out as a case that was finally going to explain and resolve the conflicts between free expression, free exercise, and discrimination that were coming up again and again in the lower courts. But Justice Kennedy, the critical consensus went, avoided reaching many of the main First Amendment issues in the case and had instead ruled narrowly, giving us a prime example of"judicial minimalism:• This assessment may be far too generous. In our short Article, we make the case that Masterpiece is a flawed decision because of its fundamental incompleteness, not its minimalism. Despite being held out as an opinion on religious liberty, Kennedy's decision is cursory on the baker's religious beliefs and how they have been burdened-a perhaps forgivable sin-but then simply omits any discussion of whether the state interest might outweigh the baker's religious freedom-a less forgivable sin. The failure to do any balancing makes the religious liberty aspect in Masterpiece unfinished. Indeed, Masterpiece fails to follow the steps that Justice Kennedy himself had set out in his previous opinions on religious liberty. And this leads us to surmise that Masterpiece may not be a religious liberty decision at all, but one about the violation of the baker's due process rights. If this was the case, however, the correct resolution would be not a win for the baker, but a remand for a new hearing (as Justice Kennedy had himself suggested in other opinions): a procedural remedy for a procedural flaw .. But Kennedy doesn't take this route, either. In essence, Masterpiece is not a narrow or minimalist opinion, but rather a collection of false starts, none of which ofter much insight or illumination on the areas of law they purport to address.