cssi/SciSciGPT-SciSciNet huggingface dataset:
Interaction of the RecA Protein of Escherichia coli with Single-stranded Oligodeoxyribonucleotides

The RecA protein of Escherichia coli performs a number of ATP-dependent, in vitro reactions and is a DNA-dependent ATPase. Small oligodeoxyribonucleotides were used as DNA cofactors in a kinetic analysis of the ATPase reaction. Polymers of deoxythymidilic acid as well as oligonucleotides of mixed base composition stimulated the RecA ATPase activity in a length-dependent fashion. Both the initial rate and the extent of the reaction were affected by chain length. Full activity was seen with chain lengths > or = 30 nt. Partial activity was seen with chain lengths of 15-30 nt. The lower activity of shorter oligonucleotides was not simply due to a reduced affinity for DNA, since effects of chain length on KmATP and the Hill coefficient for ATP hydrolysis were also observed. The results also suggested that single-stranded DNA secondary structure frequently affects the ATPase activity of RecA protein with oligodeoxyribonucleotides.
The Historical Development of an Evolutionary Archaeology

Increasingly in the last several years there has been a growing number of archaeologists who are beginning to take note of the fact that Darwinian evolution offers a powerful means of explaining variation in the material record. The approach has been variously termed evolutionary, or selectionist, archaeology, and though it is still in a formative stage, there are clear signs of future growth and development. Although Darwinian evolutionary archaeology has not enjoyed the meteoric rise seen in the overnight sensation of the 1960s, processual archaeology, there are now in preparation or in press several edited books on the subject (e.g., Teltser 1995; O’Brien 1996), as well as numerous evolutionarily focused articles in leading archaeological journal (e.g., Dunnell 1978a, 1980; Leonard and Jones 1987; Rindos 1989; O’Brien and Holland 1990, 1992; Neff 1992; O’Brien et al 1994) and monographs (e.g., Feathers 1989; Braun 1990; Dunnell 1992, 1995; O’Brien and Holland 1995a,b).
Avoiding deadlock avoidance

The evolution of processor architectures from single core designs with increasing clock frequencies to multi-core designs with relatively stable clock frequencies has fundamentally altered application design. Since application programmers can no longer rely on clock frequency increases to boost performance, over the last several years, there has been significant emphasis on application level threading to achieve performance gains. A core problem with concurrent programming using threads is the potential for deadlocks. Even well-written codes that spend an inordinate amount of effort in deadlock avoidance cannot always avoid deadlocks, particularly when the order of lock acquisitions is not known a priori. Furthermore, arbitrarily composing lock based codes may result in deadlock - one of the primary motivations for transactional memory. In this paper, we present a language independent runtime system called Sammati that provides automatic deadlock detection and recovery for threaded applications that use the POSIX threads (pthreads) interface - the de facto standard for UNIX systems. The runtime is implemented as a pre-loadable library and does not require either the application source code or recompiling/relinking phases, enabling its use for existing applications with arbitrary multi-threading models. Performance evaluation of the runtime with unmodified SPLASH, Phoenix and synthetic benchmark suites shows that it is scalable, with speedup comparable to baseline execution with modest memory overhead.
Principles of constructing a timeliness-guaranteed kernel and time-triggered message-triggered object support mechanisms

One of the major components required for the construction of future complex real-time computer systems (RTCS) needed in safety-critical applications is a timeliness-guaranteed operating system. A model of an operating system kernel called the DREAM kernel that can support both conventional real-time processes and new-style real-time objects has been formulated. The key emphasis in formulating the DREAM kernel was in the realization of guaranteed timely responses to the service requests from supported client programs. This paper presents a summary of the main structuring principles that were exploited to realize guaranteed timely service capabilities while maintaining the modular and easily expandable structure in the DREAM kernel. Implementation of real-time processes and real-time objects involves designing various calls to DREAM kernel services. A library of functions, called the DREAM library and providing user-friendly interfaces to the DREAM kernel, has been developed in the authors' laboratory. This library consists of a collection of specific C++ classes. A 32-bit prototype version of the DREAM kernel, version D3.0, encapsulated by the DREAM library that supports well-structured real-time application programming in C++ has been implemented. This prototype version has been used in efficient development of several real-time object structured applications including a non-trivial defense C/sup 3/ system, a steel factory control system, and an advanced traffic management system.
Tear Osmolarity — A New Gold Standard?

The purpose of this presentation is to propose tear osmolality measurement as a new gold standard for the diagnosis of keratoconjunctivitis sicca. Agreement on the diagnostic criteria is needed in order to permit meaningful comparisons of scientific results obtained from varying patient populations. The method employed is a review of previous studies of clinical symptoms, signs and diagnostic tests employed in making a diagnosis of keratoconjunctivitis sicca. Data from previous studies are reviewed and the results of individual and combinations tests are compared in regard to sensitivity, specificity and overall efficiency in establishing accurate diagnoses. The results are that the measurement of tear osmolality measurement provides the greatest sensitivity, specificity and overall efficiency of a single test. Adding either the Schirmer test without anesthetic or tear lactoferrin measured by the Lactoplate™ method in parallel to tear osmolality measurement did not increase the sensitivity of diagnotic testing beyond 90% which was obtained by using tear osmolality measurement alone. The specificity of such combination diagnostic testing was increased only from 95% to 100%. The simplicity of tear osmolarity measurement and its established reliability supports the conclusion that this test is a reasonable candidate for a new international gold standard in the diagnosis of keratoconjunctivitis sicca.
Additional observations on Rhynchosperma quinnii (Medullosaceae): a permineralized ovule from the Chesterian (Upper Mississippian) Fayetteville Formation of Arkansas

New ovules from the Fayetteville Formation (Upper Mississippian) of Arkansas expand our knowledge of the morphology and anatomy of Rhynchosperma and suggest it was produced by a medullosan seed fern. Rhynchosperma has been described as radially symmetrical with a two-layered integument and vascularization in the integument only. The apical portion of the integument is ribbed; the nucellus is fused to the integument and apically differentiated into a dome-shaped pollen chamber. The vascular system is incompletely known and apparently restricted to the base of the integument. The new specimens are like Rhynchosperma in external shape, size, number of ribs, and numerous histological features. However, new data reveal that the nucellus is vascularized by a sheath of tracheids, the integument is vascularized by discrete bundles, the pollen chamber has a nucellar beak, and the nucellus is attached to the integument for a variable distance from the base. In addition, the integument is tripartite with an elaborate apical region; ribs formed by the integument are more pronounced at the apex; and internally open, hollow lobes form a stellate micropylar canal. The presence of a tripartite integument, the nature of the vascular system, the nucellus-integument attachment, the pollen chamber structure, symmetry, and the association with medullosan vegetative remains suggest medullosan affinity for these ovules and strengthens the evidence for the origin of the family before the end of the Lower Carboniferous.
The incidence of diagnostic error in medicine

A wide variety of research studies suggest that breakdowns in the diagnostic process result in a staggering toll of harm and patient deaths. These include autopsy studies, case reviews, surveys of patient and physicians, voluntary reporting systems, using standardised patients, second reviews, diagnostic testing audits and closed claims reviews. Although these different approaches provide important information and unique insights regarding diagnostic errors, each has limitations and none is well suited to establishing the incidence of diagnostic error in actual practice, or the aggregate rate of error and harm. We argue that being able to measure the incidence of diagnostic error is essential to enable research studies on diagnostic error, and to initiate quality improvement projects aimed at reducing the risk of error and harm. Three approaches appear most promising in this regard: (1) using ‘trigger tools’ to identify from electronic health records cases at high risk for diagnostic error; (2) using standardised patients (secret shoppers) to study the rate of error in practice; (3) encouraging both patients and physicians to voluntarily report errors they encounter, and facilitating this process.
Direct Reduction of Alkyl Monohalides at Silver in Dimethylformamide: Effects of Position and Identity of the Halogen

Electrochemical reduction of primary (1-halodecane), secondary (2-halohexane and cyclohexyl halide), and tertiary halides (tert-butyl halide) at a silver cathode in dimethylformamide (DMF) containing 0.050 M tetramethylammonium perchlorate (TMAP) was investigated with the aid of cyclic voltammetry and controlled-potential (bulk) electrolysis for iodides, bromides, and chlorides. Selected reductions were probed in dried DMF–TMAP and DMF containing tetra-n-hexylammonium perchlorate (THAP). Cyclic voltammograms reveal that the number of cathodic peaks and their potentials are highly dependent on the identity and position of the halogen as well as the composition of the solvent–electrolyte. Intermediates arising from bulk electrolysis of these halides at silver undergo both radical and carbanion reactions. Electrolysis products depend on the identity and position of the halogen, amount of residual water, and size of the electrolyte cation in the solvent–electrolyte. Theoretical calculations of molecular dipole moments and polarizabilities were performed and compared to experimental observations.
PND at 25 Past, Present, and Future Trends in Summarizing Single-Subject Research

Twenty-five years ago, we proposed the use of the PND (percentage of nonoverlapping data) statistic for quantitative synthesis (or meta-analysis) of single-subject research. This procedure was controversial from its beginning, with criticism divided between those maintaining that no quantitative method should be used to summarize single-subject research and those suggesting that other methods may be preferable. Since that time, more than 40 research summaries have been published using the PND statistic or its variants, and a smaller number have been published using other methods. We argue that the PND method has proven to be very useful over time for this purpose, though other methods have also contributed. These procedures to date have led to more systematic, objective summaries of single-subject research. We discuss implications of present knowledge for future applications of research synthesis.
Gq signaling in cardiac adaptation and maladaptation

Accumulating evidence suggests that cardiac responses to a number of circulating or locally released humoral factors contribute to adaptive responses after hemodynamic stress or myocardial injury. In particular, hormones such as angiotensin II, endothelin 1, norepinephrine and prostaglandin F2 alpha which bind to and activate cardiomyocyte membrane receptors coupled to the Gq class of GTP binding proteins have been implicated in the development and ultimate decompensation of cardiac hypertrophy. Herein we summarize recent developments in cultured cardiomyocyte and transgenic mouse systems which are defining the phenotypes resulting from Gq signaling events in cardiomyocytes, and which are elucidating the critical downstream mediators. Postulated roles for protein kinase C, p38 MAP kinase and jun-N terminal kinase are discussed in relation to Gq-mediated cardiomyocyte hypertrophy and apoptotic signaling. The evidence to date suggests that molecular targeting of Gq or its effectors has the potential to modify cardiac adaptive and maladaptive responses to stress or injury.
New methods to investigate infectious disease transmission and pathogenesis — Staphylococcus aureus disease in drug users

Staphylococcus aureus is the single most important bacterial pathogen in infections among drug users. It is responsible for several diseases, ranging from superficial cutaneous abscesses to life-threatening intravascular infections. Although the nature of these infections is well described in published work, there is limited understanding of their epidemiology and pathogenesis. This limitation is in part due to the difficulty of studying disease transmission among drug users in the community, and the limitations of the investigative tools that have so far been used. We review the current understanding of the pathogenesis of staphylococcal disease in drug users and argue for the integration of molecular epidemiological techniques and social network methodology to increase our understanding of the basis for the persistence, distribution, and transmission dynamics of S aureus among drug users. Finally, we propose a framework for investigating the transmission of pathogens in community-based settings.
Tumor response to induction chemoradiation: influence on survival after esophagectomy.

Objective: Preoperative chemoradiation is becoming standard of care for locally advanced esophageal cancer. The objective of this study was to determine if the degree of pathologic response to preoperative chemoradiation could predict survival and recurrence after resection in patients with adenocarcinoma of the distal esophagus. Methods: Between January 1998 and December 2001, 366 patients underwent esophagectomy for adenocarcinoma of the esophagus; 108 (30%) had induction chemoradiation prior to surgery. The records of these 108 patients were reviewed. Results: Histologic examination of the resected specimens documented complete pathologic response (CR) in 24 patients (22%) and residual tumor (RT) in 84 (78%). Operative mortality was 3.7%. Follow-up was complete in all patients and ranged from 1 to 46 months (median, 11 months). Three-year survival for patients with CR was 64% as compared to 34% for patients with RT (P ¼ 0:17). Median survival for patients with CR has not yet been reached; however, median survival for patients with RT was 19 months. Three-year cancer free survival for patients with CR was 57% compared to 30% for patients with RT (P ¼ 0:03). While median survival free of recurrence for patients with CR has not yet been reached, median survival free of recurrence for patients with RT was 9 months. Conclusion: Complete pathologic response to induction chemoradiation is associated with improved early overall and disease-free survival following esophagectomy for adenocarcinoma of the distal esophagus. Because recurrent cancer still develops in many of these patients, even after complete pathologic response, the search for the optimal treatment continues. q 2003 Published by Elsevier B.V.
Solar forcing of Holocene droughts in a stalagmite record from West Virginia in east‐central North America

[1] Elevated Sr/Ca ratios and δ13C values in Holocene-age stalagmite BCC-002 from east-central North America record six centennial-scale droughts during the last five North Atlantic Ocean ice-rafted debris (IRD) episodes, previously ascribed to solar irradiance minima. Spectral and cross-spectral analyses of the multi-decadal resolution Sr/Ca and δ13C time series yield coherent ∼200 and ∼500 years periodicities. The former is consistent with the de Vries solar irradiance cycle. Cross-spectral analysis of the Sr/Ca and IRD time series yields coherent periodicities of 715- and 455-years, which are harmonics of the 1,450 ± 500 year IRD periodicity. These coherencies corroborate strong visual correlations and provide convincing evidence for solar forcing of east-central North American droughts and strengthen the case for solar modulation of mid-continent climates. Moisture transport across North America may have lessened during droughts because of weakened north-south temperature and pressure gradients caused by cooling of the tropical Pacific and Atlantic Oceans.
There is poor reliability of Böhler's angle and the crucial angle of Gissane in assessing displaced intra-articular calcaneal fractures.

Abstract Background Two-dimensional measurements are used to describe displaced intra-articular calcaneal fractures (DIACF). Our study evaluates the performance of Bohler's angle (BA) and the crucial angle of Gissane (CAG) among orthopedic surgeons. Methods Thirty-four pre- and post-operative lateral foot radiographs from patients with DIACF were shown to four orthopedic surgeons who measured BA and the CAG. The intra- and inter-observer reliability were calculated using the intra-class correlation coefficient (ICC). Additionally, we calculated frequency of consensus given an allowed discrepancy. We then determined the tolerance limit for each measurement. Results The ICC for inter-observer reliability of BA was 0.83 in the first session and 0.77 in the second. The ICC for intra-observer reliability ranged from 0.83 to 0.98. For the CAG, the inter-observer ICC was 0.28 and 0.1 in the two sessions. Intra-observer ICC ranged from 0.16 to 0.67. With an allowed discrepancy of 20°, there was lack of consensus for BA in 37.5% and for the CAG in 59% of measurements on average. The 95% confidence interval for 90% agreement in BA involved a range of 76°. For CAG, the 95% confidence interval of tolerance for 90% agreement was 56°. Conclusions For BA and CAG, there is frequent disagreement among experienced observers, even given a wide tolerance range. We recommend use of caution when applying BA as currently measured in making treatment decisions for DIACF. Level of Clinical Evidence: Diagnostic, level III.
In vivo oxygen tension in human septal cartilage increases with age

Objectives/Hypothesis Tissue-engineered septal cartilage may provide a source of autologous cartilage for repair of nasal defects. Production of clinically useful neocartilage involves multiple steps that include manipulating the culture environment. Partial pressure of oxygen (ppO2) is a property that has been shown to influence cartilage development. Specifically, studies suggest low ppO2 augments in vitro growth of articular cartilage. Although in vivo measurements of articular cartilage ppO2 have demonstrated hypoxic conditions, measurements have not been performed in septal cartilage. The objective of this study was to determine the ppO2 of septal cartilage in vivo.
Test preparation in New Jersey: inquiry‐oriented and didactic responses1

As testing becomes more prevalent as a policy tool in the Anglo‐Saxon world, debates continue as to whether it supports central reforms of instruction or leads to a kind of ‘teaching to the test’ that invalidates results and undermines more challenging instruction. This paper reports on a three‐year study of mathematics testing of nine‐year‐olds in New Jersey. Using a mix of surveys and direct observations with interviews, we conclude that New Jersey's testing policies contributed to both results. Where teachers feel more pressure, they respond with short‐term test preparation and focus on more didactic instructional strategies. When they know more about state and national standards and have the opportunity to learn more, they are inclined to use more inquiry‐oriented approaches and integrate test preparation with regular instruction.
Protocol Validation by Duologue-Matrix Analysis

A protocol is a set of rules which governs the interaction between processes. It is difficult to design protocols without errors because there are usually more interactions possible than anticipated. We are concerned with two-process protocols. A technique is described which identifies design errors in protocols. The technique is based on modeling a protocol as a pair of interacting graphs whereby interaction sequences are represented by path pairs (one path in each graph). The technique is currently limited to protocols that must revert to an initial or quiescent state after a finite number of interaction steps. The work represents a theory that can be automated on a digital computer.
Acute hematogenous osteomyelitis of the rib identified on bedside ultrasound.

Abstract Background Osteomyelitis is a challenging and commonly considered diagnosis in the emergency department. Early recognition and treatment with appropriate antibiotic therapy is crucial to prevent complications. Objective This case reviews relevant literature and typical ultrasound features of osteomyelitis. It highlights a previously undescribed and practical application of emergency department bedside ultrasonography, adding to the diagnostic armamentarium for this disease process. Case Report A 48-year-old woman presented with fever and left chest wall pain. She had been seen previously for a right axillary abscess requiring incision and drainage. Examination revealed a focal area of chest tenderness without cutaneous changes. Chest x-ray study and laboratory evaluation were nondiagnostic. Bedside ultrasound diagnosed acute hematogenous osteomyelitis of a rib. Conclusions Bedside ultrasound holds great promise in investigating osteomyelitis when suspicion is high and traditional initial testing is nondiagnostic. Further study is required to quantify this benefit in the emergency department setting and explore utility of negative results.
Mahātmā Gandhi's view on euthanasia and assisted suicide

To many in India and elsewhere, the life and thoughts of Mohandas Karamchand Gandhi are a source of inspiration. The idea of non-violence was pivotal in his thinking. In this context, Gandhi reflected upon the possibility of what is now called 'euthanasia' and 'assisted suicide'. So far, his views on these practices have not been properly studied. In his reflections on euthanasia and assisted suicide, Gandhi shows himself to be a contextually flexible thinker. In spite of being a staunch defender of non-violence, Gandhi was aware that violence may sometimes be unavoidable. Under certain conditions, killing a living being could even be an expression of non-violence. He argued that in a few rare cases it may be better to kill people who are suffering unbearably at the end of life. In this way, he seems to support euthanasia and assisted suicide. Yet, Gandhi also thought that as long as care can be extended to a dying patient, his or her suffering could be relieved. Since in most cases relief was thus possible, euthanasia and assisted suicide were in fact redundant. By stressing the importance of care and nursing as an alternative to euthanasia and assisted suicide, Gandhi unconsciously made himself an early advocate of palliative care in India. This observation could be used to strengthen and promote the further development of palliative care in India.
Epidemiology of Type 2 Diabetes in Children and Adolescents

Historically, diabetes in youth was believed to be almost entirely Type 1 (autoimmune and insulin dependent) diabetes. In contrast, those over 30 years at the time of onset were considered to have ...
EFFECT OF ENZYME INHIBITORS AND ACTIVATORS ON THE MULTIPLICATION OF TYPHUS RICKETTSIAE : III. CORRELATION OF EFFECTS OF PABA AND KCN WITH OXYGEN CONSUMPTION IN EMBRYONATE EGGS

A technique is described for measuring the oxygen uptake of embryonate eggs. Statistical analysis has shown that the method is reliable and accurate. Determinations were made on groups of 15 to 20 eggs, in order to average out individual biological variations. Reduction of the CO2 tension and relative humidity to approximately zero previous to analysis has been found to be desirable. The oxygen consumption of normal and typhus-infected eggs, untreated and treated with agents previously found to inhibit or enhance rickettsial growth has been studied. Rickettsial infection caused a slight but significant increase in the rate of oxygen consumption on the 4th day after inoculation, followed by a rapid drop in the rate as the infection developed. The evidence suggests that low concentrations of rickettsial toxins may stimulate respiration, while higher concentrations depress respiration and lead eventually to embryonic death. PABA, which is rickettsiostatic, markedly increased the oxygen uptake of normal eggs, the effect appearing 4 days after injection and lasting for about 4 days. Thereafter, the rate fell below that of the untreated eggs. In typhus-infected eggs, PABA had similar effects, but the oxygen consumption reached much higher levels. A possible explanation of this fact is suggested. MABA and OABA, which are not rickettsiostatic, did not increase oxygen uptake; in fact they depressed cellular respiration moderately, OABA being more active in this way than MABA. These two compounds may compete with PABA for a position in some respiratory enzyme system. Potassium cyanide, which enhances rickettsial growth, caused, in concentrations not lethal to the embryos, a moderate drop in the oxygen consumption of normal eggs, the effect starting almost immediately after injection and lasting usually for 9 days. In infected eggs, its effect was more striking. It is probable that rickettsial toxins and KCN act synergistically to depress cellular respiration. When PABA and KCN were injected simultaneously, the stimulating effect of PABA on respiration predominated. The resulting level of oxygen consumption, though lower than that resulting from PABA alone, was still high enough to inhibit rickettsial growth. As far as our results go, they support the hypothesis that, within certain limits, rickettsial growth is inversely proportional to the respiratory rate of the host cells, regardless of the factors which determine that rate. It is not yet clear that PABA owes its rickettsiostatic action to its ability to increase cellular respiration, but this assumption seems reasonable as a working hypothesis. The respiratory mechanism in which PABA participates is not as yet known. Although PABA forms part of the folic acid molecule, folic acid itself, in concentrations corresponding to effective doses of PABA, did not increase cellular respiration or show rickettsiostatic action.
Positive family history of prostate cancer not associated with worse outcomes after radical prostatectomy.

Abstract Objectives To determine the clinical outcomes in men with (FH) and without (NFH) a family history of prostate cancer after radical prostatectomy. Methods We performed a retrospective analysis of 557 men with localized prostate cancer treated by radical prostatectomy between 1989 and 2000. We defined a positive FH as having one or more first-degree relatives such as a father or brother with prostate cancer. The clinical and pathologic features, as well as biochemical disease-free survival, defined as an undetectable prostate-specific antigen level (less than 0.2 ng/mL), were compared between the FH and NFH groups. Results Compared with the NFH group, the FH men were younger at surgery (median 62 years versus 64 years, P = 0.01), had a lower median preoperative prostate-specific antigen level (7.2 ng/mL versus 7.8 ng/mL, P = 0.05), and were more likely to have only low-grade disease at the final pathologic evaluation (26.2% versus 17.8%, P = 0.05). At a median follow-up of 7.5 years (mean 7.6 ± 2.9 years), 17% of the FH group had biochemical disease recurrence compared with 30% in the NFH group. The actuarial disease-free survival rate at 5 and 10 years for the two groups was 86% and 80% compared with 73% and 66%, respectively ( P = 0.01). When controlled for pathologic variables in a multivariate analysis, FH was not an independent predictor of disease-free survival. Conclusions The association of improved disease-free survival in the FH patients may have been driven by an earlier age at diagnosis and more favorable pathologic features.
MULTIPLE SCATTERING OF RADIATION IN CLUSTERS OF DIELECTRICS

A fast, accurate, and general technique for solving Maxwell{close_quote}s equations in the presence of a finite cluster of arbitrarily disposed dielectric objects is presented. The electromagnetic field is first decomposed into multipoles with respect to centers close to each of the objects of the cluster and multiple scattering is carried out until convergence is achieved. Radiation scattering cross sections are obtained using this method for clusters formed by homogeneous spheres and coated spheres made of different materials (Al, Si, and SiO{sub 2}), including magnetic ones. Near- and far-field distributions are offered as well. {copyright} {ital 1999} {ital The American Physical Society}
Exact feedback linearization and control of space station using CMG

Based on feedback linearization theory, an approach to attitude control of a space station using control moment gyros (CMGs) is developed. A linearizing transformation is derived to obtain a simple linear representation of the nonlinear pitch axis dynamics. A feedback control law for trajectory tracking is derived. Extension of this approach to linearization of the coupled yaw and roll axis dynamics and control is presented. >
Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff

MOTIVATION In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo β-diversity. RESULTS We present a set of tools to identify and correct for the presence of pseudo β-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo β-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo β-diversity in pairwise community contrasts. AVAILABILITY AND IMPLEMENTATION A Perl script for calculating the DwOdum score from a taxon abundance table and performing pairwise contrasts with OTUshuff can be obtained at http://www.ars.usda.gov/services/software/software.htm?modecode=30-12-10-00. CONTACT daniel.manter@ars.usda.gov SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Accretion and Ejection

The processes by which stars stars accrete their mass are not fully understood. Accretion in early stellar evolution appears to be highly timevariable. Since accretion and mass ejection are closely connected — the energy for winds and jets comes from accretion — this means that mass loss is also highly time-variable. Understanding the origin of this variable accretion is an important outstanding issue in star formation that has not received su cient attention.
Prostate cancer: Caveat Emptor - long-term outcomes in the Göteborg active surveillance cohort.

Prior reports demonstrate a near-zero risk of prostate-cancer death among patients with very low-risk tumours managed on active surveillance (AS). However, outcomes from an AS cohort in Sweden suggest that observing men with low-risk and intermediate-risk tumours carries a small — but significant — risk of treatment failure and death from prostate cancer.
Relationship of disease-associated gene expression to cardiac phenotype is buffered by genetic diversity and chromatin regulation

Expression of a cohort of disease-associated genes, some of which are active in fetal myocardium, is considered a hallmark of transcriptional change in cardiac hypertrophy models. How this transcriptome remodeling is affected by the common genetic variation present in populations is unknown. We examined the role of genetics, as well as contributions of chromatin proteins, to regulate cardiac gene expression and heart failure susceptibility. We examined gene expression in 84 genetically distinct inbred strains of control and isoproterenol-treated mice, which exhibited varying degrees of disease. Unexpectedly, fetal gene expression was not correlated with hypertrophic phenotypes. Unbiased modeling identified 74 predictors of heart mass after isoproterenol-induced stress, but these predictors did not enrich for any cardiac pathways. However, expanded analysis of fetal genes and chromatin remodelers as groups correlated significantly with individual systemic phenotypes. Yet, cardiac transcription factors and genes shown by gain-/loss-of-function studies to contribute to hypertrophic signaling did not correlate with cardiac mass or function in disease. Because the relationship between gene expression and phenotype was strain specific, we examined genetic contribution to expression. Strikingly, strains with similar transcriptomes in the basal heart did not cluster together in the isoproterenol state, providing comprehensive evidence that there are different genetic contributors to physiological and pathological gene expression. Furthermore, the divergence in transcriptome similarity versus genetic similarity between strains is organ specific and genome-wide, suggesting chromatin is a critical buffer between genetics and gene expression.
The Early Life of Knut Wicksell

Situated at the northernmost vantage point of Europe, Scandinavia has always offered a unique perspective, on both markets and the role of government, and on how these two institutions ought to interact. Other schools of thought, such as the Austrian or the Chicago School, might emphasize individualism. The Chicago School often concludes that the public sector can do nothing which could not be done by the private sector either equally well or better. The Communists of the late 19th and early 20th centuries swung the pendulum hard in the other direction. The Stockholm School charted a middle course between the two extremes of socialism and fully privatized economies. In doing so, the Stockholm School recognized what could cause either extreme to fail, and articulated the need for government to correct failings in the private economy.
Investigating short-range magnetic correlations in real space with the magnetic pair distribution function (mPDF)

A recurring theme in the study of complex materials is the importance of nanoscale structural correlations and fluctuations that deviate from the average structure [1]. Local structure of this type...
Biomolecular detection at ssDNA-conjugated nanoparticles by nano-impact electrochemistry.

We describe the use of ssDNA functionalized silver nanoparticle (AgNP) probes for quantitative investigation of biorecognition and real time detection of biomolecular targets using nano-impact electrochemistry. The method is based on measurements of the individual collision events between ssDNA aptamer-functionalized AgNPs and a carbon fiber miroelectrode (CFME). Specific binding events of target analyte induced collision frequency changes enabling ultrasensitive detection of the aptamer target in a single step. These changes are assigned to the surface coverage of the NP by the ssDNA aptamers and subsequent conformational changes of the aptamer probe which affect the electron transfer between the NP and the electrode surface. The method enables sensitive and selective detection of ochratoxin A (OTA), chosen here as a model target, with a limit of detection of 0.05nM and a relative standard deviation of 4.9%. The study provides a means of characterizing bioconjugation of AgNPs with aptamers and assessing biomolecular recognition events with high sensitivity and without the use of exogenous reagents or enzyme amplification steps. This methodology can be broadly applicable to other bioconjugated systems, biosensing and related bioanalytical applications.
Imaging for infected cardiac implantable electronic devices: A new trick for your pet

Cardiac implantable electronic devices (CIEDs), having been shown capable of improving the quality as well as duration of life, are playing an increasingly important role in the management of patients with disorders of heart rhythm and/or function. Over the last decade there has been a remarkable
Improvement journey of strip test sticky issue

Quite number of material was affected with sticky issue in an excursion which contributed to 0.10% yield drop. This excursion was caused by the presence of a strong bond between the UV tape and the device which made the device inseparable for tape and reel process. The study involves analysis of the root cause of the bonding layer as well as the measures taken to deal with the affected material and improvement actions done to qualify a new UV tape which does not have sticky issue. An alternate process was qualified to clear the affected material after thorough quality analysis was made. The yield and DPPM comparison of the UV tapes are taken into consideration to gauge the performance of the new UV tape while saving realized through qualification of the alternate process for sticky devices were discussed.
The Empire that Would Not Die: The Paradox of Eastern Roman Survival, 640-740: Haldon, John. Cambridge, MA: Harvard University Press 418 pp., $45.00, ISBN 9780674088771 Publication Date: April 2016

John Haldon is professor of Byzantine History and Hellenic Studies at Princeton University. This book is about the period in Byzantine history from ca. 640–740 CE, which, according to the author, i...
QRS loop folding phenomenon in vectorcardiogram of healthy individuals

Recently, we developed a novel approach to study the rapid and sudden changes in the direction of ventricular activation called folding phenomenon. In order to better understand this phenomenon, we were interested in studying the variation of the orientation of QRS t for i=1… N where QRS t represents the QRS vector at the ith sample point. In this study, we described the orientation of the QRS vector and the rotation of its frame of reference in details in 81 healthy participants from the Intercity Digital Electrocardiogram Alliance (IDEAL) study using unit quaternions and Euler angles. We observed that the variance of the elevation of rotation axis u was significantly higher in men compared to women (1340±421 vs. 1063±381, P=0.003, respectively). Additionally, there was a significant negative correlation between the variance of the azimuth of u and height (CC=-0.26, P=0.019) while the elevation of u and height were significantly positively correlated (CC=0.24, P=0.034). Moreover, the elevation of u had a positive significant correlation with weight and body surface area (CC=0.22, P=0.045 and CC=0.26, P=0.020 respectively).
Prohibited Contaminants in Dietary Supplements

Context:With the increasing use of unregulated dietary supplements, athletes are at continued risk from adverse medical events and inadvertent doping.Evidence Acquisition:A review of Clinical Key, ...
NPV Analysis: Should ABR Buy and Restart the St. Croix Refinery?

Atlantic Basin Refining, Inc. (ABR) went through a tumultuous legal battle for the right to purchase and reopen an oil refining complex in St. Croix (US Virgin Islands), once the largest refinery in the world, which had fallen on hard times and closed in 2012. Having been offered a settlement that could make reopening of the refinery a possibility, ABR has to consider whether it should still pursue purchasing and reopening it. ABR is faced with uncertainty, such as how much the restart will cost, how long it will take, and what oil prices will be in the future.
US Rural Poverty and International Trade

There appears to be limited research on the effects of recent international trade treaties on US poverty rates. Previous literature has discussed reasons why rural poverty and urban poverty have somewhat different sets of causes. Using 1985-2015 annual data, rural poverty and urban poverty rates are regressed on the unemployment rate and dummy variables reflecting the time periods for NAFTA and the Chinese entry into the WTO. In particular, the two dummies are statistically insignificant for both poverty rates.
A novel human induced pluripotent stem cell blood-brain barrier model: Applicability to study antibody-triggered receptor-mediated transcytosis

We have developed a renewable, scalable and transgene free human blood-brain barrier model, composed of brain endothelial cells (BECs), generated from human amniotic fluid derived induced pluripotent stem cells (AF-iPSC), which can also give rise to syngeneic neural cells of the neurovascular unit. These AF-iPSC-derived BECs (i-BEC) exhibited high transendothelial electrical resistance (up to 1500 Ω cm2) inducible by astrocyte-derived molecular cues and retinoic acid treatment, polarized expression of functional efflux transporters and receptor mediated transcytosis triggered by antibodies against specific receptors. In vitro human BBB models enable pre-clinical screening of central nervous system (CNS)-targeting drugs and are of particular importance for assessing species-specific/selective transport mechanisms. This i-BEC human BBB model discriminates species-selective antibody- mediated transcytosis mechanisms, is predictive of in vivo CNS exposure of rodent cross-reactive antibodies and can be implemented into pre-clinical CNS drug discovery and development processes.
Supervoxel-based segmentation of 3D imagery with optical flow integration for spatiotemporal processing

The past 20 years has seen a progressive evolution of computer vision algorithms for unsupervised 2D image segmentation. While earlier efforts relied on Markov random fields and efficient optimization (graph cuts, etc.), the next wave of methods beginning in the early part of this century were, in the main, stovepiped. Of these 2D segmentation efforts, one of the most popular and, indeed, one that comes close to being a state of the art method is the ultrametric contour map (UCM). The pipelined methodology consists of (i) computing local, oriented responses, (ii) graph creation, (iii) eigenvector computation (globalization), (iv) integration of local and global information, (v) contour extraction, and (vi) superpixel hierarchy construction. UCM performs well on a range of 2D tasks. Consequently, it is somewhat surprising that no 3D version of UCM exists at the present time. To address that lack, we present a novel 3D supervoxel segmentation method, dubbed 3D UCM, which closely follows its 2D counterpart while adding 3D relevant features. The methodology, driven by supervoxel extraction, combines local and global gradient-based features together to first produce a low-level supervoxel graph. Subsequently, an agglomerative approach is used to group supervoxel structures into a segmentation hierarchy with explicitly imposed containment of lower-level supervoxels in higher-level supervoxels. Comparisons are conducted against state of the art 3D segmentation algorithms. The considered applications are 3D spatial and 2D spatiotemporal segmentation scenarios. For the latter comparisons, we present results of 3D UCM with and without optical flow video pre-processing. As expected, when motion correction beyond a certain range is required, we demonstrate that 3D UCM in conjunction with optical flow is a very useful addition to the pantheon of video segmentation methods.
Development of QSPR Model Relating Solvent Structure to Crystal Morphology

Abstract This contribution outlines the development of a quantitative structure-property relationship (QSPR) that relates solvent structure to the morphology of ibuprofen crystals grown within that solvent. Morphology can be quantified by aspect ratio, and ibuprofen aspect ratio data was obtained for crystals grown in 16 different organic solvents. A combination of 2D and 3D molecular descriptors are calculated to provide a quantitative representation of the geometry optimized solvent molecules. Empirical force fields were used to estimate the three-dimensional structure of the solvent molecules and three different force fields are implemented while their effect on the developed models is analyzed. The descriptor data matrix, containing a multitude of descriptor types, is reduced in size, using Bayesian Information Criterion (BIC) methods and also Principal Component Analysis (PCA), for regression into linear models through Principal Component Regression. The predictive capabilities of these models were also analyzed through means of internal and external validation methods.
The effects of coupled output chokes on loop dynamics in multiple output converters

An investigation of the dynamic effects of coupled output chokes on multiple output buck converters reveals the potential presence of two zeros in the plant equation. These zeros can have a significant effect on the loop dynamics of the converter depending upon the relative turns ratios of the transformer and the coupled choke.
Project BOOST implementation: lessons learned.

Objectives Enhancing care coordination and reducing hospital readmissions have been a focus of multiple quality improvement (QI) initiatives. Project BOOST (Better Outcomes by Optimizing Safe Transitions) aims to enhance the discharge transition from hospital to home. Previous research indicates that QI initiatives originating externally often face difficulties gaining momentum or effecting lasting change in a hospital. We performed a qualitative evaluation of Project BOOST implementation by examining the successes and failures experienced by six pilot sites. We also evaluated the unique physician mentoring component of this program. Finally, we examined the impact of intensification of the physician mentoring model on adoption of BOOST interventions in two later Illinois cohorts (27 hospitals). Methods Qualitative analysis of six pilot hospitals used a process of methodological triangulation and analysis of the BOOST enrollment applications, the listserv, and content from telephone interviews. Evaluation of BOOST implementation at Illinois hospitals occurred via mid-year and year-end surveys. Results The identified common barriers included inadequate understanding of the current discharge process, insufficient administrative support, lack of protected time or dedicated resources, and lack of frontline staff buy-in. Facilitators of implementation included the mentor, a small beginning, teamwork, and proactive engagement of the patient. Notably, hospitals viewed their mentors as essential facilitators of change. Sites consistently commented that the individualized mentoring was extremely helpful and provided significant accountability and stimulated creativity. In the Illinois cohorts, the improved mentoring model showed more complete implementation of BOOST interventions. Conclusions The implementation of Project BOOST was well received by hospitals, although sites faced substantial barriers consistent with other QI research reports. The unique mentorship element of Project BOOST proved extremely valuable in helping sites overcome their distinctive challenges and identify facilitators for success. The findings from this qualitative study should contribute to future BOOST implementation success and others' efforts to optimize hospital discharge transitions.