cssi/SciSciGPT-SciSciNet huggingface dataset:
High-Throughput Analysis of Total RNA Expression Profiles by Capillary Gel Electrophoresis

We studied the expression profiles of total RNA in three types of human tissues. Reverse transcription was performed on total RNA samples extracted from kidney, normal breast, and breast tumor. Then, fluorophor-labeled cDNAs were synthesized by using random hexamers as primers for analysis by capillary gel electrophoresis. By overlaying the electropherograms and by performing multivariate analysis, we found that the RNA patterns were significantly different among the tissue samples. The protocol utilizes only submicroliter volumes of PCR products and is compatible with multiple capillary DNA sequencing instruments. These CE-based RNA patterns provide an alternative to RNA microarrays for expression profiling for understanding the molecular basis of disease.
Conditioned assessment of subjective probabilities : Identifying the benefits of decomposition

Conditioned assessment of subjective probability decomposes an assessment task by using a related event to define a series of conditional probabilities. These component assessments are subsequently aggregated mathematically. Two experiments compared conditioned and unconditioned (direct) assessments of 32 general knowledge questions by graduate business students. Reliability was estimated through repeat administration of the questionnaire and accuracy was measured with a quadratic scoring rule. Conditioned assessments were more reliable and more accurate than direct assessments, confirming previous research on other decomposition approaches. Conditioned assessment appears to be effective because the mathematical combination of conditional probabilities reduces random response errors and reduces the tendency to produce overly extreme probability judgments. Implications for further research and application are considered.
First principles investigation of metal sulfides as membranes in hydrogen purification

Degradation of metal membranes by sulfur in high temperature hydrogen purification is an important challenge in practical use of these membranes. If metal sulfides could be identified with high hydrogen permeabilities, they could potentially sidestep the difficulties faced by metal membranes. We have used first principles calculations to predict the permeability of hydrogen through eight metal sulfides in their defect-free, crystalline form. Although the solubility of H in some of these materials is considerable, H diffusion is extremely slow in every case. Our calculations indicate that films of any of the sulfides we considered will have extremely low permeabilities for hydrogen.
NORMAL AND DISABLED READERS' USE OF ORTHOGRAPHIC STRUCTURE IN PROCESSING PRINT

Two experiments examined whether normal and disabled readers differed in the ability to use orthographic structure information to process printed material. Experiment 1 required subjects to search for a target letter in a six-letter stimulus array held in memory. Experiment 2 required subjects to make word-nonword decisions. Stimulus arrays for both experiments were words and nonwords varying in orthographic regularity and positional frequency. The results of Experiment 1 showed that both disabled and normal readers were able to perform the memory search task more accurately for letter strings high in either type of orthographic structure. In Experiment 2, disabled and younger normal readers produced decision times reflecting greater sensitivity than older normal readers to orthographic regularity. The finding that disabled readers use orthographic structure information to the same extent, and, under some circumstances, to a greater extent than normal readers supports the interactive-compensatory model of...
Population genetic structure of a rare high‐elevation black fly, Metacnephia coloradensis, occupying Colorado lake outlet streams

SUMMARY 1. Using a portion of the mitochondrial cytochrome oxidase I gene, we evaluated the population genetic structure of a geographically rare black fly (Metacnephia coloradensis) that is a habitat specialist in outlet streams of large, productive, alpine lakes in Colorado, U.S.A. Given its rarity and life history traits that restrict dispersal, we hypothesised that genetic structure would show a signature of allopatric fragmentation associated with climatic warming since Pleistocene glaciations. 2. We tested for genetic isolation by distance (IBD) and applied nested clade analysis (NCA) to ask whether current genetic structure is primarily a consequence of historic fragmentation or if there is evidence of ongoing gene flow. 3. Only four populations were located despite a thorough search of potential sites, and they demonstrated a significant degree of genetic structure (FST ¼ 0.17). However, there was some evidence of IBD in a plot of genetic versus geographic distance, and NCA further supported IBD and restricted ongoing gene flow in clades at all nested levels. Compared with a more widespread alpine black fly (Prosimulium neomacropyga) in the same region, M. coloradensis demonstrated significantly less population genetic structure. 4. Although these results counterintuitively implicate limited ongoing gene flow driving current population structure, significant IBD may be a signature of historic gene flow, especially if migration–drift equilibrium has not yet been reached since a late-Pleistocene fragmentation event. Extraordinarily dense local populations probably allowed M. coloradensis to maintain large effective population sizes and minimise genetic drift rates. 5. Despite large local populations, M. coloradensis is vulnerable to continued rapid environmental change because of its limited geographic distribution and high habitat specificity.
Absolute refractometry of dry gas to ±3 parts in 10 9

We present a method of measuring the refractive index of dry gases absolutely at 632.8 nm wavelength using a Fabry–Perot cavity with an expanded uncertainty of <3×10−9 (coverage factor k=2). The main contribution to this uncertainty is how well vacuum-to-atmosphere compression effects (physical length variation) in the cavities can be corrected. This paper describes the technique and reports reference values for the refractive indices of nitrogen and argon gases at 100 kPa and 20 °C with an expanded uncertainty of <9×10−9 (coverage factor k=2), with the additional and larger part of this uncertainty coming from the pressure and temperature measurement.
A seismoacoustic study of the 2011 January 3 Circleville earthquake

SUMMARY Wereportonauniquesetofinfrasoundobservationsfromasingleearthquake,the2011January 3Circlevilleearthquake(Mw 4.7,depthof8km),whichwasrecordedbynineinfrasoundarrays inUtah.Basedonananalysisofthesignalarrivaltimesandbackazimuthsateacharray,wefind thattheinfrasoundarrivalsatsixarrayscanbeassociatedtothesamesourceandthatthesource location is consistent with the earthquake epicentre. Results of propagation modelling indicate that the lack of associated arrivals at the remaining three arrays is due to path effects. Based on these findings we form the working hypothesis that the infrasound is generated by body waves causing the epicentral region to pump the atmosphere, akin to a baffled piston. To test this hypothesis, we have developed a numerical seismoacoustic model to simulate the generation of epicentral infrasound from earthquakes. We model the generation of seismic waves using a 3-D finite difference algorithm that accounts for the earthquake moment tensor, source time function, depth and local geology. The resultant acceleration–time histories on a 2-D grid at the surface then provide the initial conditions for modelling the near-field infrasonic pressure wave using the Rayleigh integral. Finally, we propagate the near-field source pressure through the Ground-to-Space atmospheric model using a time-domain Parabolic Equation technique. By comparing the resultant predictions with the six epicentral infrasound observations from the 2011 January 3, Circleville earthquake, we show that the observations agree well with our predictions. The predicted and observed amplitudes are within a factor of 2 (on average, the synthetic amplitudes are a factor of 1.6 larger than the observed amplitudes). In addition, arrivalsarepredictedatallsixarrayswheresignalsareobserved,andimportantlynotpredicted at the remaining three arrays. Durations are typically predicted to within a factor of 2, and in some cases much better. These results suggest that measured infrasound from the Circleville earthquake is consistent with the generation of infrasound from body waves in the epicentral region.
Meeting the Computational Needs of Intelligent Environments: The Metaglue System

Intelligent Environments (IEs) have specific computational properties that generally distinguish them from other computational systems. They have large numbers of hardware and software components that need to be interconnected. Their infrastructures tend to be highly distributed, reflecting both the distributed nature of the real world and the IEs’ need for large amounts of computational power. They also tend to be highly dynamic and require reconfiguration and resource management on the fly as their components and inhabitants change, and as they adjust their operation to suit the learned preferences of their users. Because IEs generally have multimodal interfaces, they also usually have high degrees of parallelism for resolving multiple, simultaneous events. Finally, debugging IEs present unique challenges to their creators, not only because of their distributed parallelism, but also because of the difficulty of pinning down their “state” in a formal computational sense. This paper describes Metaglue, an extension to the Java programming language for building software agent systems for controlling Intelligent Environments that has been specifically designed to address these needs. Metaglue has been developed as part of the MIT Artificial Intelligence Lab’s Intelligent Room Project, which has spent the past four years designing Intelligent Environments for research in Human-Computer Interaction.
Fuel cost, delay and throughput tradeoffs in runway scheduling

A dynamic programming algorithm for determining the minimum cost arrival schedule at an airport, given aircraft-dependent delay costs, is presented. Aircraft arrival schedules are subject to a variety of operational constraints, such as minimum separation requirements for safety, required arrival time-windows, limited deviation from a nominal or FCFS sequence, and precedence constraints on the arrival order. In addition to determining schedules that satisfy these constraints, the proposed approach makes it possible to evaluate tradeoffs in terminal-area schedules, through the comparison of throughput maximizing and delay minimizing schedules. A comprehensive analysis of the tradeoffs between average delay and fuel costs is also conducted, accounting for both the cost of delay and the increased rate of fuel burn incurred by an accelerating aircraft.
Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation.

Innovative algorithms have been developed during the past decade for simulating Newtonian physics for macromolecules. A major goal is alleviation of the severe requirement that the integration timestep be small enough to resolve the fastest components of the motion and thus guarantee numerical stability. This timestep problem is challenging if strictly faster methods with the same all-atom resolution at small timesteps are sought. Mathematical techniques that have worked well in other multiple-timescale contexts--where the fast motions are rapidly decaying or largely decoupled from others--have not been as successful for biomolecules, where vibrational coupling is strong. This review examines general issues that limit the timestep and describes available methods (constrained, reduced-variable, implicit, symplectic, multiple-timestep, and normal-mode-based schemes). A section compares results of selected integrators for a model dipeptide, assessing physical and numerical performance. Included is our dual timestep method LN, which relies on an approximate linearization of the equations of motion every delta t interval (5 fs or less), the solution of which is obtained by explicit integration at the inner timestep delta tau (e.g., 0.5 fs). LN is computationally competitive, providing 4-5 speedup factors, and results are in good agreement, in comparison to 0.5 fs trajectories. These collective algorithmic efforts help fill the gap between the time range that can be simulated and the timespans of major biological interest (milliseconds and longer). Still, only a hierarchy of models and methods, along with experimentational improvements, will ultimately give theoretical modeling the status of partner with experiment.
Multiple skeletal muscle mitochondrial DNA deletions in patients with unilateral peripheral arterial disease

Peripheral arterial disease (PAD) is associated with metabolic derangements and accumulation of the common 4977 bp mitochondrial DNA (mtDNA) deletion mutation. The current study was undertaken to test the hypothesis that PAD is associated with multiple mtDNA deletions. Gastrocnemius biopsies were obtained from nine patients with unilateral PAD. DNA extracted from the biopsies was analyzed for mtDNA deletions using a primer- shift PCR strategy. Multiple primers and strict, prospective criteria were used to identify deletions. PAD was associated with multiple mtDNA deletions (average of 8.2 distinct deletions in muscle from the hemodynamically affected limb). mtDNA injury was present in both the worse- and less-affected limbs of the unilateral PAD patients, and the estimated degree of mtDNA injury was strongly correlated in the two limbs on an intra-subject basis. The 4977 bp deletion was frequently identified, but was not always the deletion of highest frequency in individual samples. The estimated relative frequency of the 4977 bp deletion was correlated with the overall mtDNA injury in the biopsies. In summary, PAD is associated with mtDNA injury as reflected by multiple deletion mutations. As the mutations are not limited to the ischemic limb in unilateral patients, they are unlikely to contribute to the pathophysiology of claudication.
A model investigation of the velocity and pressure spectra in vascular murmurs

A physical model consisting of an axisymmetrical jet in a rigid plexiglass pipe was used to study the flow and pressure fluctuations downstream from an aortic stenosis. The fluctuating velocity components, u and v, at several locations in the steady liquid jet were measured using a laser Doppler anemometer system. Simultaneous wall pressure fluctuations were monitored by an array of nine miniature pressure transducers wall mounted in the axial direction. This paper presents the detailed measurements of mean velocity profiles, turbulent intensity distributions and RMS pressure fluctuations. The energy spectra obtained for the pressure fluctuations and the u and v velocity components are compared. Contrary to earlier works, we found that the differences between peak frequencies of the pressure spectra and the characteristic frequencies of the velocity spectra vary with positions downstream from the nozzle. These differences are discussed in light of pseudosound generation by the eddy structures in the stenotic flow field.
No Bayesians in foxholes

In World War II, there was a saying, "there are no atheists in foxholes." The implication was that on the front lines and under pressure, soldiers needed someone to pray to. The implication in my title is that when big, real, tough problems need to be solved, there are no Bayesians. For decades, the pages of various statistical journals have been littered with theological arguments on the virtues of the Bayesian approach versus frequentist approaches. I have no intention of continuing the debate on this level. My approach is pragmatic: which approach works best when dealing with real data in solving complex problems?.
Scientific and Computational Challenges in Coupled Plasma Edge/Plasma-Material Interactions for Fusion Tokamaks ∗

Key wordsFusion plasma/material interaction modelling, plasma simulation/supercomputing. Plasma/material interactions is a critical scientific issue for fusion power, with major potential limitations on plasma core and edge operating parameters. Gaining understanding and predictive capability in this area will require simultaneously addressing complex and diverse physics occurring over a wide range of lengths (angstroms to meters) and times (femtoseconds to days). This requires further development and validation of detailed physics models and computational strategies at each of these scales. The overriding numerical need is for petascale real-time coupling between 3-D material response/evolution/trapping codes, plasma edge/SOL codes, and impurity transport codes. We discuss selected science and modeling/computational challenges in this area and our ideas for achieving these goals; this from the standpoint of our existing simulation codes. c
Factors Influencing the Hooking Mortality of Walleyes Caught by Recreational Anglers on Mille Lacs, Minnesota

Abstract Recent implementation of size-based regulations in recreational fisheries for walleye Sander vitreus have led to more released walleyes and presumably to more losses of released fish. We conducted this study to estimate hooking mortality in Mille Lacs, Minnesota, and to determine factors that influence the survival of released walleyes. Volunteers and Minnesota Department of Natural Resources employees sampled walleyes with common angling methods in 2003 and 2004 on Mille Lacs (n = 1,246). Simple hooking mortality rates ranged from 0% (95% confidence interval = 0–1.8%; n = 204) in May, when lake water temperatures were less than 20°C, to 12.2% (9.2–15.9%; n = 392) in the July–August period, when lake water temperatures were at least 20°C. We used logistic regression within generalized linear or additive models to determine influential variables. Hooking mortality was most associated with water temperature, bleeding, fish length, hook location, and fish floating upon release. Mortality increased a...
Bounding estimators for systems with colored noise

Attention has been directed to the problem of estimating the state of a linear dynamic system which has correlated noise. The cross correlations between the random vectors affecting the system are assumed unknown. A linear estimator is developed which bounds the corresponding error covariance matrix for any allowed cross correlation between the random disturbances in the plant and/or in the measuring device. The computational requirements are of the order of the corresponding Kalman filter assuming white and uncorrelated plant and measurement noise processes.
Impacts of Urbanization and Climate Variability on Floods in Northeastern Illinois

Trend analysis of annual flood peaks on 12 small urbanizing watersheds in northeastern Illinois indicated that annual peaks, and thus frequency and impact of flooding, increased over the past several decades. An increase in flood peaks could be attributed to intensive urbanization and increasing incidences of heavy rainfall. Average urbanization of the 12 watersheds increased significantly from 10.6% in 1954 to 61.8% in 1996. In addition, numerous studies have reported increasing frequency and intensity of heavy rainfall in the region. This outcome is consistent with lower design rainfall estimates produced by older studies, such as U.S. Weather Bureau Technical Paper No. 40 (TP-40), compared to more recent sources, such as National Oceanic and Atmospheric Administration Atlas-14. This study used a design storm approach and the Hydrologic Engineering Center for Hydrologic Modeling System (HEC-HMS) model to calculate design flood peaks. Hydrologic model parameters were calibrated using hourly rainfall-runo...
Anisotropic, free carrier voigt effect in n-type germanium

Abstract The free carrier Voigt effect has been measured in orientated, single crystal samples of n -type germanium in the spectral range 6–20 micro at room temperature. The observed anisotropy of the effect measures the effective mass anisotropy associated with the [111] energy ellipsoids and is in good agreement with theoretical calculations.
Seminal Plasma of Spinal Cord Injured Men Inhibits Sperm Motility of Normal Men

AbstractPurpose: Seminal plasma was investigated as a contributor to the poor sperm motility of spinal cord injured men.Materials and Methods: Seminal plasma of spinal cord injured men was mixed with sperm of normal men and vice versa. Sperm motility was analyzed at 5 and 60 minutes after mixing.Results: At 5 (but not 60) minutes seminal plasma from spinal cord injured men inhibited motility of sperm from normal men. Concomitantly, seminal plasma from normal men improved motility of sperm from spinal cord injured men.Conclusions: Seminal plasma of spinal cord injured men contributes to poor sperm motility.
Correction for Jacob et al., Prevalence and Relatedness of Escherichia coli O157:H7 Strains in the Feces and on the Hides and Carcasses of U.S. Meat Goats at Slaughter

Volume 79, no. 13, p. 4154–4158, 2013. Page 4156, column 1, line 4: “ stx 1” should read “ stx 2.” Page 4156, column 1, line 6: “ stx 2” should read “ stx 1.” Page 4156, column 2, line 2: “resembles” should read “does not resemble
Measurement of Plasma and Tissue Relaxin Concentrations in the Pregnant Hamster and Fetus Using a Homologous Radioimmunoassay

A homologous hamster relaxin RIA was developed to evaluate plasma and tissue concentrations of relaxin in the latter half of pregnancy in this species. Relaxin protein and mRNA were localized using antibodies developed to synthetic hamster relaxin and gene-specific molecular probes, respectively. Molecular weight and isoelectric point of the synthetic and native hormones were identical by electrophoretic methods, and synthetic hamster relaxin was active in the mouse interpubic ligament bioassay. Synthetic hormone was used as tracer and standard with rabbit antiserum to the synthetic hormone in the RIA. Relaxin was assayed in blood samples recovered from the retro-orbital plexus on Days 6, 8, 10, 12, 14, 15, and 16 of gestation and on Days 1 and 5 postpartum. Relaxin was first detected on Day 8 of gestation (3.7 ± 0.6 ng/ml), increased to reach a maximum in the evening of Day 15 (826.0 ± 124.0 ng/ml), and decreased by Day 16 (day of parturition). Relaxin concentrations were assayed in aqueous extracts of implantation sites (Days 6, 8, and 10) and chorioallantoic placentae (Days 12, 14, and 15). Concentrations were low on Day 6 (0.02 ± 0.001 μg/g tissue), increased to Day 15 (6.96 ± 0.86 μg/g tissue), and subsequently declined by the evening of Day 15. Relaxin protein and mRNA were localized to primary and secondary giant trophoblast cells in the chorioallantoic placental trophospongium. However, relaxin protein was not localized in ovaries of pregnant animals or oviductal tissues of cycling animals. Significant quantities of relaxin were detected in the serum of fetal hamsters recovered on Day 15.
Workplace incivilities: the role of interest conflicts, social closure and organizational chaos

Workplace incivility — that is, negative relational dimensions of employment with consequences for worker integrity and dignity — affects millions every year. In this article, the ‘organizational m...
Do Local Governments Maximize Anything

In the recent empirical literature on local government expenditure determination, researchers have begun to apply the results of classical consumer theory to the public sector. In assuming that public expenditure can be specified in the form of an integrable demand function that is further restricted to satisfy separability, researchers can reduce the number of parameters (equations) to be estimated and interpret their results in terms of familiar price and income elasticities. It is not clear, however, that utility maximization and separability are valid assumptions in the context of the public sector. Based on an empirical test for a sample of 132 municipalities, we reject the hypothesis that unrestricted estimates are consistent with utility maximization and separability.
Hybridization among foundation tree species influences the structure of associated understory plant communities

Understanding how genetic identity influences community structure is a major focus in evolutionary ecology, yet few studies examine interactions among organisms in the same trophic level within thi...
Characterization of Compensatory Stepping in People With Multiple Sclerosis.

Abstract Objective To characterize postural responses to forward and backward external perturbations in people with multiple sclerosis (PwMS), and to relate performance to commonly used clinical outcomes. Design Cross-sectional study. Postural responses were tested during large stepping and smaller feet-in-place perturbations in forward and backward directions. Setting University research laboratory. Participants PwMS (n=54) and age-matched controls (n=21) (N=75). Interventions Not applicable. Main Outcome Measures Center of mass displacement and step latency after external perturbations. Results PwMS exhibited larger center of mass displacements and step latencies than control participants in response to stepping perturbations ( P =.003 and P =.028, respectively). Stepping deficits were more pronounced during backward stepping and were significantly correlated to increased severity on clinical measures (European Database for Multiple Sclerosis disability score and Timed 25-Foot Walk). Conclusions Compensatory stepping is impaired in PwMS and correlates with clinical disability. Measurement of backward compensatory stepping may be more effective at identifying postural dysfunction in PwMS than forward compensatory steps. Prolonged step latencies, large anticipatory postural adjustments, and multiple compensatory steps are especially altered in PwMS, suggesting possible targets for neurorehabilitation.
ROLE OF CELL PROLIFERATION IN HEPATIC CARCINOGENESIS.

SummaryPrimary hepatic carcinoma, without accompanying cirrhosis or fibrosis of the liver, was induced in rats with diethyl-nitrosamine. Hyperplastic nodules and nodular cytoplasmic alterations were found in the same livers. Autoradiographs after administration of tritiated thymidine showed no increase in DNA synthesis in morphologically normal areas or in foci of cytoplasmic alterations, but a striking increase in both hyperplastic nodules and carcinoma. It is concluded that primary hepatic carcinoma in the non-cirrhotic liver may arise through stages of increased nodular regeneration.
TU-H-CAMPUS-TeP1-02: Seated Treatment: Setup Uncertainty Comparable to Supine

Purpose: For some head and neck patients, positioning in the supine position is not well tolerated. For these patients, treatment in a seated position would be preferred. We have evaluated inter- and intra- fraction uncertainty of patient set-up in a novel treatment chair which is compatible with modern linac designs. Methods: Five head-and-neck cancer patients were positioned in the chair, fitted with immobilization devices, and imaged with orthogonal X-rays. The couch (with chair attached) was rotated to simulate delivery (without actual treatment), another set of images were acquired, providing a measure of intra-fraction displacement. The patient then got off of and back onto the chair and the process was repeated, thus providing a measure of inter-fraction set-up uncertainty. Six sub-regions in the head-and-neck were rigidly registered to evaluate local intra- and interfraction displacement. Image guidance was simulated by first registering one sub-region; the residual displacement of other sub-regions was then measured. Additionally, a patient questionnaire was administered to evaluate tolerance of the seated position. Results: The chair design is such that all advantages of couch motions may be utilized. Average inter- and intrafraction displacements of all sub-regions in the seated position were less than 2 and 3 mm, respectively. When image guidance was simulated, interfraction displacements were reduced by an average of 4 mm, providing comparable setup to the supine position. The enrolled patients, who had no indication for a seated treatment position, reported no preference for the seated or the supine position. Conclusion: The novel chair design provides acceptable inter- and intra-fraction displacement, with reproducibility similar to that observed for patients in the supine position. Such a chair will be utilized for patients who cannot tolerate the supine position and use with CBCT images for planning, in a fixed-beam linac system, and for other treatment sites is under investigation. Funding: Varian Medical Systems
Tissue culture and Agrobacterium-mediated transformation of watercress

Adventitious shoot regeneration could be obtained from more than 80% of the calluses initiated from stem explants of watercress (Rorippa nasturtium-aquaticum) by using an induction medium and a shoot regeneration medium. The induction medium contained 1.15 μM 2,4-dichlorophenoxyacetic acid and 5 μM thidiazuron; the shoot regeneration medium was composed of 0.5 μM thidiazuron and 2.25 μM 6-benzylaminopurine. This regeneration procedure was incorporated into an Agrobacterium-mediated transformation procedure for gene transfer into watercress. Factors affecting transformation included preculture, selection agents, use of tobacco nurse cells, and the length of coculture. A transgenic line of watercress transformed with a wild-type Bacillus thuringiensis insecticidal gene, cry1Ia3, was not toxic to larvae of the diamondback moth (Plutella xylostella), presumably due to premature polyadenylation of the transcript encoded by this gene in the plant.
Interfacial Polarization Effects Associated with Surfaces and Interfaces

The dispersion of the capacitance and conductance of a specimen with frequency, arising from the presence of interfaces between regions of differing dielectric properties, can be used to study the geometry and electrical properties of the more conducting regions. The measurement and interpretation of these interfacial polarization effects are discussed, with particular emphasis on their application to studies of surface effects in single crystals. The results of experimental studies of the variation in electrical properties of relatively thick (approximately 10μ) surface layers in sapphire produced by the adsorption and desorption of gases, incomplete equilibration of composition in various oxygen partial pressures, and the presence of impurities and preliminary results of interfacial polarization studies in sodium chloride crystals are presented.
Genetic and Signaling Abnormalities in Waldenstrom’s Macroglobulinemia

The genomic alterations that drive the signaling of Waldenstrom’s macroglobulinemia distinguish it from related malignancies such as marginal zone lymphoma, chronic lymphocytic leukemia, and IgM secreting multiple myeloma. The most frequent of these somatic changes are heterozygous activating MYD88 mutations observed in over 90 % of WM patients and 50–80 % of patients with IgM monoclonal gammopathy of undetermined significance. In addition to MYD88, activating mutations are also found in the carboxyl terminal tail region of CXCR4 in up to 43 % of WM patients. These mutations are often sub-clonal and almost always occur in the context of MYD88 mutations. Together, these mutations impact overall survival, serum IgM, presence of nodal involvement and bone marrow infiltration at diagnosis. Mutant MYD88 drives critical BTK and HCK signaling and is highly predictive of response to the BTK inhibitor ibrutinib. Additional characteristics of these and other recurrent genomic alterations such as ARID1A and CD79B mutations as well as chromosome 6q deletions are discussed.
Re-evaluation of re-hospitalization and rehabilitation in renal research.

Introduction The use of administrative data to capture 30-day readmission rates in end-stage renal disease is challenging since Medicare combines claims from acute care, inpatient rehabilitation (IRF), and long-term care hospital stays into a single "Inpatient" file. For data prior to 2012, the United States Renal Data System does not contain the variables necessary to easily identify different facility types, making it likely that prior studies have inaccurately estimated 30-day readmission rates. Methods For this report, we developed two methods (a "simple method" and a "rehabilitation-adjusted method") to identify acute care, IRF, and long-term care hospital stays from United States Renal Data System claims data, and compared them to methods used in previously published reports. Findings We found that prior methods overestimated 30-day readmission rates by up to 12.3% and overestimated average 30-day readmission costs by up to 11%. In contrast, the simple and rehabilitation-adjusted methods overestimated 30-day readmission rates by 0.1% and average 30-day readmission costs by 1.8%. The rehabilitation-adjusted method also accurately identified 96.8% of IRF stays. Discussion Prior research has likely provided inaccurate estimates of 30-day readmissions in patients undergoing dialysis. In the absence of data on specific facility types particularly when using data prior to 2012, future researchers could employ our method to more accurately characterize 30-day readmission rates and associated outcomes in patients with end-stage renal disease.
Local tumour progression after percutaneous ablation of colorectal liver metastases according to RAS mutation status.

Background Percutaneous ablation is a common treatment for colorectal liver metastasis (CLM). However, the effect of rat sarcoma viral oncogene homologue (RAS) mutation on outcome after ablation of CLMs is unclear. Methods Patients who underwent image-guided percutaneous ablation of CLMs from 2004 to 2015 and had known RAS mutation status were analysed. Patients were evaluated for local tumour progression as observed on imaging of CLMs treated with ablation. Multivariable Cox regression analysis was performed to determine factors associated with local tumour progression-free survival. Results The study included 92 patients who underwent ablation of 137 CLMs. Thirty-six patients (39 per cent) had mutant RAS. Rates of local tumour progression were 14 per cent (8 of 56) for patients with wild-type RAS and 39 per cent (14 of 36) for patients with mutant RAS (P = 0·007). The actuarial 3-year local tumour progression-free survival rate after percutaneous ablation was worse in patients with mutant RAS than in those with wild-type RAS (35 versus 71 per cent respectively; P = 0·001). In multivariable analysis, negative predictors of local tumour progression-free survival were a minimum ablation margin of less than 5 mm (hazard ratio (HR) 2·48, 95 per cent c.i. 1·31 to 4·72; P = 0·006) and mutant RAS (HR 3·01, 1·60 to 5·77; P = 0·001). Conclusion Mutant RAS is associated with an earlier and higher rate of local tumour progression in patients undergoing ablation of CLMs.
Connections of Faith: Religion as Community

Much of religion is communal. Churchgoing produces social connections; religiously involved people know more people (Putnam, Bowling alone: the collapse and revival of American community. Simon & Schuster, New York, 2000a; Putnam (ed), Democracies in flux: the evolution of social capital in contemporary society. Oxford University Press, New York, 2000b). The fellowship of like-minded believers also provides a sense of community and group solidarity. Putnam (Bowling alone: the collapse and revival of American community. Simon & Schuster, New York, 2000a; Putnam (ed), Democracies in flux: the evolution of social capital in contemporary society. Oxford University Press, New York, 2000b) observed, “connectedness, not merely faith is responsible for the beneficence of church people” (p. 67). Nearly half of all associational membership in America is church related, half of all personal philanthropy is religious, and half of all volunteering takes place in a religious context.
Crime is not the only problem: Examining why violence & adverse health outcomes co-vary across large U.S. counties

Abstract Beginning with the moral statisticians, social science researchers have shown interest in explaining why outcomes like crime and disease varied together across aggregate social communities. Underlying this interest was a notion that deleterious social phenomena exhibit persistent and regularized variation across geospatial units because they are influenced by a common set of underlying causes. But because of specialization trends in the social sciences, our grasp of the degree to which crime and other undesirable social phenomena vary together across macro-social units, or our ability to explain that covariance, has not sufficiently progressed. This study sought to reinvigorate interest in documenting and explaining the overlap of crime and adverse health outcomes. It examined the extent of covariance between both criminal (homicide) and non-criminal (infant mortality and sexually transmitted diseases) deleterious social outcomes across 524 large U.S. counties. Drawing from social disorganization, immigrant revitalization, racial isolation, and social support perspectives, the study posited hypotheses arguing that lethal violence and two adverse health events are similarly impacted by theory-specified explanatory factors. Findings reveal support for each theoretical perspective and identify important “common causes” that are reasons why homicide, infant mortality and sexually transmitted diseases co-vary across aggregate social communities.
Patient and nonradiographic tumor characteristics predicting lipid-poor angiomyolipoma in small renal masses: Introducing the BEARS index.

PURPOSE To create a simple model using clinical variables for predicting lipid-poor angiomyolipoma (AML) in patients with small renal masses presumed to be renal cell carcinoma (RCC) from preoperative imaging. MATERIALS AND METHODS A series of patients undergoing partial nephrectomy (PN) for renal masses ≤4 cm was identified using a prospectively maintained database. Patients were excluded if standard preoperative imaging was not consistent with RCC. Chi square and Mann-Whitney U analyses were used to evaluate differences in characteristics between patients with AML and other types of pathology. A logistic regression model was constructed for multivariable analysis of predictors of lipid-poor AML. RESULTS A total of 730 patients were identified that underwent PN for renal masses ≤4 cm between 2007-2015, including 35 with lipid-poor AML and 620 with RCC. In multivariable analysis, the following features predicted AML: female sex (odds ratio, 6.89; 95% confidence interval, 2.35-20.92; p<0.001), age <56 years (2.84; 1.21-6.66; p=0.02), and tumor size <2 cm (5.87; 2.70-12.77; p<0.001). Sex, age, and tumor size were used to construct the BEnign Angiomyolipoma Renal Susceptibility (BEARS) index with the following point values for each particular risk factor: female sex (2 points), age <56 years (1 point), and tumor size <2 cm (2 points). Within the study population, the BEARS index distinguished AML from malignant lesions with an area under the curve of 0.84. CONCLUSIONS Young female patients with small tumors are at risk for having lipid-poor AML despite preoperative imaging consistent with RCC. Identification of these patients may reduce the incidence of unnecessary PN for benign renal lesions.
Predicting Trust Relations Within a Social Network: A Case Study on Emergency Response

Trust is a fundamental construct underpinning modern society and the social exchanges it contains. The rise of Web 2.0 technologies and the increased use of online social networks, promotes the study of trust among users. Drawing on social and psychological theory, we detect pairwise and global trust relations between users in the context of emergent real-world crisis scenarios. In such situations and scale, seeking explicit pairwise trust assessments between users is impractical. Instead, in an unsupervised manner we integrate the implicit factors of social influence exerted by each user over the network, the underlying network structural topology and the affective valence expressed by the users in the textual content they communicate. A key finding is the importance of modeling influence and affective valence in such exchanges and their role in detecting stable trust relationships. We extensively evaluate these ideas and demonstrate significant gains over competitive baselines across multiple datasets drawn from both crisis and non-crisis scenarios, including those with normative ground truth.
Application of a Schizosaccharomyces pombe Edc1-fused Dcp1–Dcp2 decapping enzyme for transcription start site mapping

Changes in the 5' leader of an mRNA can have profound effects on its translational efficiency with little effect on abundance. Sequencing-based methods to accurately map the 5' leader by identifying the first transcribed nucleotide rely on enzymatic removal of the 5' eukaryotic cap structure by tobacco acid pyrophosphatase (TAP). However, commercial TAP production has been problematic and has now been discontinued. RppH, a bacterial enzyme that can also cleave the 5' cap, and Cap-Clip, a plant-derived enzyme, have been marketed as TAP replacements. We have engineered a Schizosaccharomyces pombe Edc1-fused Dcp1-Dcp2 decapping enzyme that functions as a superior TAP replacement. It can be purified from E. coli overexpression in high yields using standard biochemical methods. This constitutively active enzyme is four orders of magnitude more catalytically efficient than RppH at 5' cap removal, compares favorably to Cap-Clip, and the 5' monophosphorylated RNA product is suitable for standard RNA cloning methods. This engineered enzyme is a better replacement for TAP treatment than the current marketed use of RppH and can be produced cost-effectively in a general laboratory setting, unlike Cap-Clip.
Germline pathologic mutations and cancer family history in prostate cancer patients.

378Background: Prostate cancer (PCa) patients (pts) with metastases and/or strong family history (FH) of cancer (Ca) are at higher risk of a germline mutation. The identification of alterations in ...
Comparison of Techniques for Preimplantation Treatment of Osteochondral Allograft Bone.

Articular defects are a major problem with few effective treatment options. Osteochondral allograft (OCA) transplantation can be an effective treatment; however, lack of OCA bone integration can cause failure. This controlled laboratory study was designed to compare clinically applicable methods for marrow element removal and enhanced delivery of bone marrow aspirate concentrate (BMC) to OCA bone. We hypothesized that compressed carbon dioxide (CO2) treatment of OCA bone would result in significantly better marrow element removal, significantly more retention and distribution of viable osteoprogenitor cells, and significantly higher osteoinductive protein elution from OCAs compared with other preimplantation treatments. Fresh humeral heads (n = 24) were harvested and stored for 14 days, then randomly assigned to treatment based on marrow element removal and bone treatment: (standard of care [SOC]) (n = 4) - SOC high-pulse saline lavage, no BMC; (BMC) (n = 5) - saline lavage then canine BMC; (Drill + BMC) (n = 5) - 1.1 mm drill-hole immediately subchondral then saline lavage then BMC injection through drill hole; (Carb + BMC) (n = 5) - saline lavage then CO2 then BMC; or (Saline-Carb + BMC) (n = 5) - saline lavage and CO2 together then BMC. Treated OCAs were cultured for 14 days. On day 3, media were collected, centrifuged to isolate cells, and replaced. Cells were cultured for 11 days for colony forming unit (CFU) determination. OCA media were collected on days 7 and 14 of culture for analysis. On day 14, each graft was assessed for viable cell retention and distribution, and bone marrow element removal. BMC had significantly higher (p = 0.001) viable cell distribution compared with the SOC, Drill + BMC, Carb + BMC, and Saline-Carb + BMC groups. BMC and Drill + BMC had significantly higher (p < 0.05) CFUs than SOC, Carb + BMC, and Saline-Carb + BMC. Drill + BMC and Carb + BMC had the highest media concentrations of the osteoinductive biomarkers. The Carb + BMC and Saline-Carb + BMC groups were associated with significantly superior marrow element removal (p < 0.02) compared with the SOC, Drill + BMC, and BMC groups. Saline irrigation plus saturation with autogenous BMC appears to be the most advantageous preimplantation treatment for OCA transplantation.
High school autonomous vehicle competition

The High School Autonomous Vehicle Competition is a new national competition Sponsored by Ford, MathWorks, and NXP. The competition introduces high school students to applications of engineering, science and mathematics. It introduces college-level topics such as feedback control, microcontrollers, vision systems, programming, and autonomous vehicles. Held at Rose-Hulman Institute of Technology, the competition has over fifty teams participating in the 2018 competition from eighteen high schools across the United States.
Sexuelle Gewalt während des Luftkriegs: Eine neue Perspektive auf weibliches Leiden in Gert Ledigs Die Vergeltung

Most discourse surrounding mass rape committed against German women at the end of World War II identify the occupying soldiers as the main perpetrators of this violence. In Gert Ledig’s 1956 novel Payback, however, we find an atypical victim-perpetrator constellation wherein the abuser is a German man who rapes a German woman during an airraid attack. Ledig’s Payback exposes female suffering using a unique narrative style that understands the woman’s body as, in Colette Lawson’s words, a “mediating force”. The young woman falls prey to the unsympathetic narrator’s voyeuristic lens, which exposes every intimate detail of her body’s reactions to surrounding dangers. The distanced and sober depictions of the woman’s sufferings distinguish Payback from other postwar rape memoirs, which are written from a sympathetic perspective towards the female victim. Even though Payback is a fictional piece, many airwar survivors praised Ledig for his realistic depictions of the destruction during the raids. By including a story of rape in Payback, Ledig is likely to be the only author who understands German women’s wartime suffering in World War II as twofold: they feared the Allied bomber pilots, but they also feared sexual violence spurred by the moral decay of the war’s destruction. It is my goal to provide a much-needed gendered discussion on airwar literature, which has treated women’s roles as a side phenomenon.
Research and management priorities for Hawaiian forest birds

ABSTRACT Hawai‘i's forest birds face a number of conservation challenges that, if unaddressed, will likely lead to the extinction of multiple species in the coming decades. Threats include habitat loss, invasive plants, non-native predators, and introduced diseases. Climate change is predicted to increase the geographic extent and intensity of these threats, adding urgency to implementation of tractable conservation strategies. We present a set of actionable research and management approaches, identified by conservation practitioners in Hawai'i, that will be critical for the conservation of Hawaiian forest birds in the coming years. We also summarize recent progress on these conservation priorities. The threats facing Hawai‘i's forest birds are not unique to Hawai‘i, and successful conservation strategies developed in Hawai‘i can serve as a model for other imperiled communities around the world, especially on islands.