cssi/SciSciGPT-SciSciNet huggingface dataset:
IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets

Motivation MicroRNA (miRNA) precursor arms give rise to multiple isoforms simultaneously called "isomiRs." IsomiRs from the same arm typically differ by a few nucleotides at either their 5´ or 3´ termini, or both. In humans, the identities and abundances of isomiRs depend on a person's sex, population of origin, race/ethnicity, and on tissue type, tissue state, and disease type/subtype. Moreover, nearly half of the time the most abundant isomiR differs from the miRNA sequence found in public databases. Accurate mining of isomiRs from deep sequencing data is thus important. Results We developed isoMiRmap, a fast, standalone, user-friendly mining tool that identifies and quantifies all isomiRs by directly processing short RNA-seq datasets. IsoMiRmap is a portable "plug-and-play" tool, requires minimal setup, has modest computing and storage requirements, and can process an RNA-seq dataset with 50 million reads in just a few minutes on an average laptop. IsoMiRmap deterministically and exhaustively reports all isomiRs in a given deep sequencing dataset and quantifies them accurately (no double-counting). IsoMiRmap comprehensively reports all miRNA precursor locations from which an isomiR may be transcribed, tags as 'ambiguous' isomiRs whose sequences exist both inside and outside of the space of known miRNA sequences and reports the public identifiers of common single-nucleotide polymorphisms and documented somatic mutations that may be present in an isomiR. IsoMiRmap also identifies isomiRs with 3´ non-templated post-transcriptional additions. Compared to similar tools, isoMiRmap is the fastest, reports more bona fide isomiRs, and provides the most comprehensive information related to an isomiR's transcriptional origin. Availability The codes for isoMiRmap are freely available at https://cm.jefferson.edu/isoMiRmap/ and https://github.com/TJU-CMC-Org/isoMiRmap/. IsomiR profiles for the datasets of the 1000 Genomes Project, spanning five population groups, and The Cancer Genome Atlas (TCGA), spanning 33 cancer studies, are also available at https://cm.jefferson.edu/isoMiRmap/. Supplementary information Supplementary data are available at Bioinformatics online.
Oxidant-Resistant LRRC8A/C Anion Channels Support Superoxide Production by Nox1

Tumor necrosis factor- (TNF) activates NADPH Oxidase 1 (Nox1) in vascular smooth muscle cells (VSMCs), producing superoxide (O2*-) required for subsequent signaling. LRRC8 family proteins A-E comprise volume-regulated anion channels (VRACs). The required subunit LRRC8A physically associates with Nox1, and VRAC activity is required for Nox activity and the inflammatory response to TNF. LRRC8 channel currents are modulated by oxidants, suggesting that oxidant sensitivity and proximity to Nox1 may play a physiologically relevant role. In VSMCs, LRRC8C knockdown (siRNA) recapitulated the effects of siLRRC8A, inhibiting TNF-induced extracellular and endosomal O2*- production, receptor endocytosis, NF-{kappa}B activation, and proliferation. In contrast, siLRRC8D potentiated NF-{kappa}B activation. Nox1 co-immunoprecipitated with 8C and 8D, and co-localized with 8D at the plasma membrane and in vesicles. We compared VRAC currents mediated by homomeric and heteromeric 8C and 8D channels expressed in HEK293 cells. The oxidant chloramine T (ChlorT, 1 mM) weakly inhibited LRRC8C, but potently inhibited 8D currents. ChlorT exposure also greatly reduced subsequent current block by DCPIB, implicating external sites of oxidation. Substitution of the extracellular loop domains (EL1, EL2) of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition. 8A/C channel activity is thus more effectively maintained in the oxidized microenvironment expected to result from Nox1 activation at the plasma membrane. Increased ratios of 8D:8C expression may potentially depress inflammatory responses to TNF. LRRC8A/C channel downregulation represents a novel strategy to reduce TNF-induced inflammation. Key PointsO_LILRRC8A-containing anion channels associate with Nox1 and regulate superoxide production and TNF signaling. Here we show that .LRRC8C and 8D also co-immunoprecipitate with Nox1 in vascular smooth muscle cells. C_LIO_LILRRC8C knockdown inhibited TNF-induced O2*- production, receptor endocytosis, NF-{kappa}B activation, and proliferation while LRRC8D knockdown enhanced NF-{kappa}B activation. Significant changes in LRRC8 isoform expression in human atherosclerosis and psoriasis suggest compensation for increased inflammation. C_LIO_LIThe oxidant chloramine-T (ChlorT, 1 mM) weakly ([~]25%) inhibited 8C currents but potently ([~]80%) inhibited 8D currents. Substitution of the two extracellular loop (EL) domains of 8D onto 8C conferred significantly stronger ChlorT-dependent inhibition. C_LIO_LIChlorT also impaired current block by DCPIB, which occurs through interaction with EL1, further implicating external sites of oxidation. C_LIO_LI8A/C channels most effectively maintain activity in an oxidized microenvironment, as is expected to result from Nox1 activity at the plasma membrane. C_LI
Using vibration controlled transient elastography and FIB-4 to assess liver cirrhosis in a hepatitis C virus infected population.

ABSTRACT We assessed the performance characteristics of the Fibrosis-4 (FIB-4) score in a veteran population with chronic hepatitis C virus (HCV) infection and used vibration controlled transient elastography (VCTE) as the gold standard.All VCTE studies were performed by a single operator on United States veterans with HCV infection presenting for care at the Atlanta VA Medical Center (AVAMC) over a 2 year period. VCTE liver stiffness measurements (LSM) were categorized as cirrhotic if LSM was >12.5 kPa and non-cirrhotic if LSM was ≤12.5 kPa. FIB-4 scores ≤3.25 were considered non-cirrhotic and scores >3.25 were considered cirrhotic. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for the FIB-4 score. A second analysis was done which identified and excluded indeterminate FIB-4 scores, defined as any value between 1.45 and 3.25.When FIB-4 was used to screen for liver cirrhosis using VCTE as the gold standard, sensitivity was 42%, specificity was 88%, PPV was 62%, and NPV was 76%. When indeterminate FIB-4 scores were excluded from the analysis, sensitivity was 95%, specificity was 61%, PPV was 62%, and NPV was 94.4%. In a veteran population with chronic HCV infection, we found the sensitivity of the FIB-4 score to be unacceptably low for ruling out liver cirrhosis when using a binary cutoff at 3.25. Using a second staging method like VCTE may be an effective way to screen for liver cirrhosis in persons with chronic HCV, especially when the FIB-4 score is in the indeterminate range.
The Effects of Straddling: Evidence From Audit Partners Auditing Both Public Companies and Nonprofit Organizations

Recent research in other disciplines suggests that range (i.e., a broad base of experience in more than one domain) may lead to higher performance under certain conditions. We apply this idea in the context of auditing, examining how audit partner range impacts audit outcomes and how industry overlap might moderate those effects in the setting of public company and nonprofit organization audits. Specifically, we consider audit partners straddling these two economic sectors, i.e. auditing clients in both sectors, as they are subject to a variety of auditing standards and regulatory regimes. Approximately six (ten) percent of individual partners conducting public company (nonprofit organization) audits are “straddlers.” Analyzing audit outcomes from 2015 to 2018, we find that overall, straddling has a negative impact on audit outcomes as measured by restatements for public company clients, material weakness reporting for nonprofit clients, and audit report lag for all clients. However, for public companies, we find that straddling clients within the same industry improves restatement likelihood and going concern reporting while moderating the negative effect of straddling on audit report lag. In nonprofit audits, the negative effects of straddling are exacerbated in going concern reporting with industry overlap but moderated in internal control reporting and audit report lag. These findings extend our understanding of the role of audit partner experience across economic sectors and auditing standards.
Pparα and fatty acid oxidation coordinate hepatic transcriptional architecture

Fasting requires tight coordination between the metabolism and transcriptional output of hepatocytes to maintain systemic glucose and lipid homeostasis. Deficits in hepatic fatty acid oxidation result in dramatic fasting-induced hepatocyte lipid accumulation and induction of genes for oxidative metabolism that are largely driven by Ppar. While fatty acid oxidation is required for a rise in acetyl-CoA and subsequent lysine acetylation following a fast, changes in histone acetylation (total, H3K9ac, and H3K27ac) do not require fatty acid oxidation. Active enhancers in fasting mice are enriched for Ppar binding motifs. Genetically-defined inhibition of hepatic fatty acid oxidation results in higher levels of chromatin accessibility as well as elevated enhancer priming and acetylation proximal to Ppar sites largely associated with genes in lipid metabolism. Also, greater number of Ppar-associated H3K27ac signal changes occur at active enhancers compared to promoters, suggesting a mechanism for Ppar to tune target expression levels at pre-primed sites. Overall, these data show the requirement for Ppar activation in maintaining transcriptionally permissive hepatic genomic architecture particularly when fatty acid oxidation is limiting. HIGHLIGHTSO_LIFasting-induced transcription and histone acetylation are largely independent of acetyl-CoA concentration. C_LIO_LIDeficits in fatty acid oxidation prompt epigenetic changes and Ppar-sensitive transcription. C_LIO_LIFasting prompts enhancer priming and acetylation proximal to Ppar binding sites independent of Ppar. C_LIO_LIPatterns of Ppar target genes can be distinguished by epigenetic marks at promoters and enhancers. C_LI
Virology in the Classroom: Current Approaches and Challenges to Undergraduate- and Graduate-Level Virology Education.

The pervasive effects of the current coronavirus disease 2019 pandemic are but one reason for educators to refocus their efforts on virology teaching. Additionally, it is critical to understand how viruses function and to elucidate the relationship between virus and host. An understanding of current virology education may improve pedagogical approaches for educating our students and trainees. Faculty who teach undergraduate microbiology indicate that approximately 10% of the course content features viruses; stand-alone virology courses are infrequently offered to undergraduates. Fortunately, virology taught to undergraduates includes foundational material; several approaches for delivery of lecture- and lab-based content exist. At the graduate education level, there is growing appreciation that an emphasis on logic, reasoning, inference, and statistics must be reintroduced into the curriculum to create a generation of scientists who have a greater capacity for creativity and innovation. Educators also need to remove barriers to student success, at all levels of education. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
A Principled Approach Toward Insurance Law: The Economics of Insurance and the Current Restatement Project

This paper applies the principles of the economics of insurance to the proposals emanating from the American Law Institute’s current project to develop a Restatement of the Law of Liability Insurance. The paper attempts to demonstrate that the proposals of the Reporters of this project — Professor Tom Baker of the University of Pennsylvania and Professor Kyle Logue of the University of Michigan — may benefit some policyholders in the short-run, but are likely to harm policyholders in general in the long run. These effects result from the Reporters’ neglect of the economic forces that define current liability insurance contracts.
SITES | Formation Processes

The notion of site formation originally put forward by F. E. Zeuner and K. W. Butzer over four decades ago, received a big impetus from M. B. Schiffer in the late 1980s. Since that time archaeologists and geoarchaeologists have been increasingly aware of the processes that are involved in the formation of archaeological sites and deposits. Such processes include natural and anthropogenic sedimentation, soil formation (pedogenesis), and other post-depositional effects, which can be of biological/human (e.g., trampling, digging, burrowing), or natural origin (diagenesis and mineralogical transformations). Methods used to study site formation involve detailed field recording and observation, and the use of numerous techniques in the laboratory, such as soil micromorphology, scanning electron microscopy (SEM), X-ray analyses (e.g., microprobe and X-ray diffraction), and Fourier Transform Infrared spectrometry (FTIR). Establishing site formation processes is a requirement to comprehend fully the archaeological record and human history.
Optimal Conjunctive Use of Groundwater and Recycled Wastewater

Inasmuch as water demand is multifaceted, infrastructure planning should be part of a general specification of efficient quantities and qualities of water deliveries over time. Accordingly, we develop a two-sector dynamic optimization model to solve for the optimal trajectories of groundwater extraction and water recycling. For the case of spatially increasing costs, recycled water serves as an intermediate resource in transition to the desalination steady state. For constant unit recycling cost, recycled wastewater eventually supplies non-potable users as a sector-specific backstop, while desalination supplements household groundwater in the steady state. In both cases, recycling water increases welfare by shifting demand away from the aquifer, thus delaying implementation of costly desalination. Implementation of the model provides guidance on the appropriate timing and size of backstop and recycling infrastructure as well as water deliveries from the various sources to the water-demand sectors.
Measurement of HbA1c from stored whole blood samples in the Atherosclerosis Risk in Communities study

Background: The aims of the present study were to demonstrate the reliability of HbA1c measurements during two time periods and to compare these measurements with HbA1c distribution in the general US population. Methods: HbA1c was measured in 14 069 whole blood samples in the Atherosclerosis Risk in Communities (ARIC) study using different HPLC instruments across two time periods, namely 2003–2004 and 2007–2008. At the time of measurement, samples had been in storage at −70°C for up to 18 years. To assess differences in values, HbA1c measurements were repeated in 383 samples at both periods. Indirect comparisons were made by comparing our measurements against those from a nationally representative study. Results: The coefficients of variation for quality control samples were 1.8% (n = 89) in 2003–2004 and 1.4% (n = 259) in 2007–2008. The correlation between measurements at the two time points was high (r = 0.99), but with a slight bias: 0.29% points higher in 2007–2008 vs 2003–2004 (n = 383; P < 0.0001). The comparison yielded the following Deming regression equation: y(2007–2008) = 0.073 + 1.034x(2003–2004). After alignment using this equation, the distribution of HbA1c in the ARIC study was similar to that in the national study using fresh samples. Conclusions: Measurements of HbA1c from samples stored for up to 18 years are highly reliable when using state-of-the-art HPLC instruments, but with some bias introduced over time. The HbA1c data now available in the ARIC study should be invaluable for investigations into the clinical utility of HbA1c as a diagnostic test for diabetes.
Flow-through microfluidic photoionization detectors for rapid and highly sensitive vapor detection

A photoionization detector (PID) is well known for its high sensitivity, large dynamic range, and non-destructive vapor detection capability. However, due to its tardy response, which results from the relatively large ionization chamber and dead volume, the application of the PID in gas chromatography (GC) has been limited. Here, we developed a rapid, flow-through, and highly sensitive microfluidic PID that was microfabricated directly on a conductive silicon wafer. The microfluidic PID has a significantly reduced ionization chamber volume of only 1.3 μL, nearly 10 times smaller than that of state-of-the-art PIDs and over 100 times smaller than that of commercial PIDs. Moreover, it has virtually zero dead volume due to its flow-through design. Consequently, the response time of the microfluidic PID can be considerably shortened, ultimately limited by its residence time (7.8 ms for 10 mL min−1 and 78 ms for 1 mL min−1). Experimentally, the response of the microfluidic PID was measured to be the same as that of the standard flame ionization detector with peak full-widths-at-half-maximum of 0.25 s and 0.085 s for flow rates of 2.3 mL min−1 and 10 mL min−1, respectively. Our studies further show that the microfluidic PID was able to detect analytes down to the picogram level (at 3σ of noise) and had a linear dynamic range of six orders of magnitude. Finally, because of the very short distance between the electrodes, low voltage (<10 VDC, over 10 times lower than that in a regular PID) can be used for microfluidic PID operation. This work will open a door to broad applications of PIDs in gas analyzers, in particular, micro-GC and multi-dimensional GC.
Reports of ‘growth’ in survivors of non‐small cell lung cancer and healthy controls: what is the value‐added by the cancer experience?

Background Reports of ‘growth’ following cancer diagnosis and treatment are common and are considered evidence for the transformative potential of the cancer experience. However, reports of growth are also common in the general population. This study sought to identify the unique, ‘value-added’ with regard to the nature and magnitude of growth represented by the cancer experience. Methods Lung cancer (LC) survivors (n = 190; mean 15 months post-diagnosis) completed the Posttraumatic Growth Inventory (PTGI), reporting changes occurring ‘as a result of having cancer’. Community-based, healthy controls (HC) (n = 152) completed the PTGI, reporting changes occurring ‘in the past year’. Results Reports of growth were common in both the LC and HC groups. However, the LC group reported greater total PTGI scores (effect size (ES) = 0.39 SD) and greater growth for 3 of 5 subscales (ESs 0.34–0.48 SD). The LC group was more likely to report any degree of change for 11 of 21 PTGI items (mean odds ratio (OR) across 21 items = 1.92) and were more likely to report ‘moderate’ to ‘very great’ change for eight of 21 items (mean OR = 1.75). The LC group was more likely to report growth in the areas of social relationships and appreciation for life. Conclusions In sum, the growth evidenced by LC survivors after diagnosis quantitatively and qualitatively differs from growth reported by the general population over a similar period. Estimates of the value-added by the cancer experience suggest a magnitude representing at least the lower range of clinical significance. Copyright © 2013 John Wiley & Sons, Ltd.
Feasibility of in situ implementation of vibrations to mobilize NAPL ganglia

Abstract A growing number of incidents of nonaqueous phase liquid (NAPL) spills in the recent past have warranted development of innovative and cost‐effective remediation technologies. Of particular concern is the entrapment of LNAPL (NAPL lighter than water) in the form of ganglia or blobs near the water table by virtue of strong capillary forces. The residual ganglia are the leftover component after pumping of free product and typically occupy 20 to 60% of the pore space. Mobilization of these ganglia would require unrealistically high hydraulic gradients and is often beyond the scope of pump‐and‐treat processes. This paper deals with the feasibility of in situ implementation of localized vibrations for controlled mobilization and collection of LNAPL ganglia. Specifically, the paper covers three components. First, the principles involved in soil‐water‐NAPL interactions under the influence of vibrations are discussed. The effects of vibrations on a soil‐NAPL‐water medium are postulated in terms of pore s...
Surface L-type Ca2+ channel expression levels are increased in aged hippocampus.

Age-related increase in L-type Ca2+ channel (LTCC) expression in hippocampal pyramidal neurons has been hypothesized to underlie the increased Ca2+ influx and subsequent reduced intrinsic neuronal excitability of these neurons that lead to age-related cognitive deficits. Here, using specific antibodies against Cav1.2 and Cav1.3 subunits of LTCCs, we systematically re-examined the expression of these proteins in the hippocampus from young (3 to 4 month old) and aged (30 to 32 month old) F344xBN rats. Western blot analysis of the total expression levels revealed significant reductions in both Cav1.2 and Cav1.3 subunits from all three major hippocampal regions of aged rats. Despite the decreases in total expression levels, surface biotinylation experiments revealed significantly higher proportion of expression on the plasma membrane of Cav1.2 in the CA1 and CA3 regions and of Cav1.3 in the CA3 region from aged rats. Furthermore, the surface biotinylation results were supported by immunohistochemical analysis that revealed significant increases in Cav1.2 immunoreactivity in the CA1 and CA3 regions of aged hippocampal pyramidal neurons. In addition, we found a significant increase in the level of phosphorylated Cav1.2 on the plasma membrane in the dentate gyrus of aged rats. Taken together, our present findings strongly suggest that age-related cognitive deficits cannot be attributed to a global change in L-type channel expression nor to the level of phosphorylation of Cav1.2 on the plasma membrane of hippocampal neurons. Rather, increased expression and density of LTCCs on the plasma membrane may underlie the age-related increase in L-type Ca2+ channel activity in CA1 pyramidal neurons.
Human resource development as adult education: Fostering the educative workplace

Human resource development needs to move away from its reliance on the market model as a way of framing its practice and embrace the democratic ideal represented in the tradition of adult education.
Tapered Couplers for Group-Velocity insensitive coupling to Photonic Crystal Waveguide Modes

We present a systematic method for designing couplers for high efficiency coupling of electromagnetic energy from a ridge waveguide into a Photonic Crystal Waveguide (PCW) irrespective of the group velocity of the PCW modes.
3D Reconstruction of Fluorescence Microscopy Image Intensities Using Multiple Depth-Variant Point-Spread Functions

We show that the use of multiple depth-variant point-spread functions in 3-D fluorescence intensity reconstruction provides improved optical sectioning over deconvolution methods by correcting depth-induced aberrations in 3-D cell images.
Castaing Instabilities in Longitudinal Spin-Diffusion Experiments

We analyze the anomalous long-lived NMR signals which have been observed in longitudinal spin-diffusion experiments with Fermi fluids. These signals have been attributed to the Castaing instability of the spin current in the Leggett equation. By considering an idealized experimental geometry in which diffusion occurs between two reservoirs of up and down spins connected via a thin tube, we are able to carry out a full stability analysis of the longitudinal spin current. We show that, in the absence of a field gradient, the instability of the spin current sets in when the spin-rotation parameter exceeds the critical value μM = π/2. In the unstable regime, we obtain spontaneous domain-wall structures as solutions to the steady-state Leggett equation, and discuss their formation from small perturbations. We find that the domain wall reduces the spin current through the tube, leading to an extraordinary increase of the lifetime of the magnetization in the reservoirs. We also show that a magnetic field gradient confines the instability, and that a large enough gradient stabilizes the longitudinal spin current.
Cassini Solstice Mission overview and science results

In October 2010, after 6.25 years of successful observations in orbit around Saturn, the Cassini project embarked on a new phase of exploration called the Cassini Solstice Mission. This mission phase not only continues and enhances the goals of the prime mission, but aims to study seasonal-scale phenomena of Saturn's rings, atmosphere, magnetosphere, icy satellites, and Titan. The Saturn year is almost 30 Earth-years long and the eight Earth-years of observations completed so far have spanned the majority of the northern winter/ southern summer through equinox. The northern summer/ southern winter is now approaching and solstice will occur in May 2017; Cassini plans to be in orbit until September of that year. The Solstice Mission features 54 close flybys of Titan, 11 close flybys of Enceladus, 5 close flybys of other icy satellites, and 154 additional orbits of Saturn. The mission will culminate with a spectacular series of orbits that bring Cassini between Saturn's innermost ring and the cloud tops of the planet. This paper provides an overview of the Solstice Mission, systems engineering strategies employed to maintain or improve the science achieved within limited budgets, and highlights exciting science results from the first two years of the Solstice Mission phase to date.
Brief Communication: Evidence of Pathology on the Frontal Bone From Gongwangling

The hominid fossil from Gongwangling (Lantian) is well known and described (Woo, [1965] Scientia Sinca 14:1032-1036; Woo [1966] Curr. Anthropol. 7:83-86; Wu and Dong [1985] in R Wu and JW Olsen (eds.): Palaeoanthropology and Paleolithic Archaeology in the People's Republic of China [New York: Academic Press, pp. 79-89]; Wu and Poirier [1995] Human Evolution in China: A Metric Description of the Fossils and a Review of the Sites [Oxford: Oxford University Press]). However, evidence of pathology on the frontal bone has been previously unreported. Two lesions occur on the right supraorbital region that can be distinguished from marks of erosion prevalent on this specimen. These are discrete and irregularly shaped, with evidence of secondary bone formation surrounding them. The cause of the condition is unclear. Possibilities include trauma or abscess from an unspecified infection.
Three-Dimensional Simulation of Scour-Inducing Flow at Bridge Piers

Presently available formulas for estimating the maximum depth of scour near bridge piers often lead to unreliable results. A fully three-dimensional hydrodynamic model is therefore used in this study to simulate the flow occurring at the base of a cylindrical bridge pier within a scour hole. The results of the numerical simulation are compared with laboratory observations by Melville and Raudkivi (1977). Quantitative and qualitative agreement between the studies is quite good. Discrepancies between the results of the two studies are of an order that may be attributed to choices in numerical model parameters. The simulations may be supplemented by Lagrangian particle-tracking to estimate the depth of the equilibrium scour condition.
Determination of traces of gold by hollow-cathode emission

Abstract The utility of a commercially available demountable hollow-cathode tube for emission spectrometric trace element analysis of solutions is demonstrated. The effects of cathode material, clean-up procedure, filler gas, and tube current were investigated to determine the conditions resulting in a satisfactory compromise between sensitivity and stability. Solutions of gold as myochrysine and as the metal dissolved in aqua regia were analyzed to show application of the commercial tube.
Shoulder muscle forces and tendon excursions during glenohumeral abduction in the scapular plane

Muscle force values and tendon excursions across the glenohumeral joint during unconstrained glenohumeral abduction in the scapular plane were evaluated with a dynamic shoulder testing apparatus. This evaluation was achieved by simulated rotator cuff and middle deltoid activity applied in four plausible muscle force ratios: (1) equal force to each tendon, (2) 2:3 ratio of force applied to the middle deltoid/supraspinatus tendons, (3) 3:2 ratio of force applied to the middle deltoid/supraspinatus tendons, and (4) zero force applied to the supraspinatus tendon to simulate supraspinatus paralysis. The glenohumeral joint was then moved to 5 degrees, 15 degrees, 30 degrees, 45 degrees, 60 degrees, and maximum glenohumeral abduction while muscle forces, tendon excursions, and glenohumeral joint kinematics were monitored. Full glenohumeral abduction was achieved in all four test conditions. When the muscle force combination favored the middle deltoid, the smallest supraspinatus force was required from 30 degrees to maximum glenohumeral abduction; however, when the supraspinatus was favored, the largest supraspinatus force was necessary to achieve maximum glenohumeral abduction. With simulated supraspinatus paralysis the middle deltoid required the greatest increase in force from 15 degrees through 45 degrees of glenohumeral abduction. These results indicate that muscle efficiency during glenohumeral abduction is highly dependent on the ratio of applied force between the middle deltoid and supraspinatus. A larger contribution of force from the supraspinatus was required near the beginning of motion, whereas the middle deltoid was more important near the end of glenohumeral abduction in the scapular plane. Tendon excursion for the middle deltoid (6.4 +/- 0.2 cm) and supraspinatus (3.8 +/- 0.2 cm) were proportionately larger than those for the subscapularis and infraspinatus. Humeral head translations on the glenoid were less than 2 mm in all four conditions evaluated; therefore the glenohumeral joint behaves kinematically as a "ball-and-socket" articulation during glenohumeral abduction. Simulated supraspinatus paralysis does not change normal joint kinematics and does not prevent full glenohumeral abduction.
Invited commentary: ''Objective evaluation of the effect of noise on the performance of a complex laparoscopic task''

FOR MANY SURGEONS, performing an operation is relaxing. The surgeon is focused on a task that has a well-defined beginning and ending. More often than not, the surgeon has successfully completed similar tasks and confidence breeds comfort. Complex operations comprise a series of small tasks, and it is the correct sequencing of these tasks that requires concentration and judgment in the operating room. For skilled surgeons, placing and tying a suture, even laparoscopically, is neither complex nor taxing. It is merely one more step along the path to a successful operation. Hence it is not surprising that Moorthy et al1 find that noise and music do not worsen performance of an isolated surgical task in a laboratory setting. As the authors point out in their discussion, little is known about the impact of audio distraction on the performance of motor tasks. There is increased public focus on surgeons’ competence, accountability, and what really goes on in the operating room when patients are anesthetized and most vulnerable. This study breaks new ground in shining the spotlight on environmental factors that might affect a surgical team’s performance. While the authors should be commended for identifying an important area for research, this study leaves many important questions unanswered. What impact does noise have on communication between members of the surgical team? What is the impact of failed communication? Does noise interfere with the judgment or higher cognitive functions required to properly sequence the multiple steps of an operation? As surgeons know, there is much more to a successful operation than just cutting and sewing. We should all stay tuned because certainly more will be heard on this topic.
Three reasons to avoid the use clause

Ada's use clause is regarded by some as the nemesis of the language, and by others as the only reasonable mechanism of importing visibility from other program units. Many organizations have struggled with the problem of whether to allow their programmers to use the use clause. Often their decisions are based on erroneous, slanted, emotional, or political rationale. This paper shows by means of example why th e use clause should be avoided completely. It focuses solely on the technical aspects of systems which rely on the use clause.
On the exact distribution of the Fisher-Behren’-Welch statistic

For testing the significance of the difference between the unknown means of two normal populations having different unknown variances, we have the known Fisher-Behren’s-Welch test statistic. Several expressions for the distribution of this test statistic are available, and this paper is yet another attempt in the same direction. However, the expression given here appears to be, perhaps, more elegant and straight-forward than the ones available at present.
Randomly Broken Nuclei and Disordered Systems

Similarities between models of fragmenting nuclei and disordered systems in condensed matter suggest corresponding methods. Several theoretical models of fragmentation investigated in this fashion show marked differences, indicating possible new methods for distinguishing models using yield data. Applying nuclear methods to disordered systems also yields interesting results.
Children’s and adults’ judgments of the controllability of cognitive activities

Two experiments investigated 1st-, 3rd-, and 5th-grade children’s and adults’ judgments related to the controllability of cognitive activities, including object recognition, inferential reasoning, counting, and pretending. In Experiment 1, fifth-grade children and adults rated transitive inference and interpretation of ambiguous pictures as more effortful than object recognition or deduction by elimination, and first-grade children rated transitive inference as more effortful than deduction by elimination. In Experiment 2, third- and fifth-grade children rated it more difficult to arrive at alternative outcomes for object recognition than for pretending, and adults distinguished object recognition and deduction from pretending and interpreting ambiguous pictures. From first-grade to adulthood there were increases in the number of distinctions made among cognitive activities in terms of level of controllability.
William Rowan Hamilton's paper of 1837 on the arithmetization of analysis

The work [10] of William Row an Hamilton (1805-1865) during the 183O's on Algebra as the Science of Pure Time * was an attempt to give a system of axioms or principles for analysis2 so that it can be "a Science properly so called; strict, pure, and independent; deduced by valid reasonings from its own intuitive principles; and thus not less an object of priori contemplation than Geometry ..." [10, p. 295]. Hamilton believed that our intuitive notion of order in time is more deep-seated than that of order in space and, as geometry is founded on the latter, so can analysis be founded on the former. In his Essay HAMILTON attempts to use these principles to construct and explain positive and contra-positive (negative) numbers, fractional quantities (rational numbers), and the set of all real numbers, all towards showing that analysis, like geometry, can be a Science. Hamilton's Essay on the foundations of analysis neither had an influence on the definitive work on this topic done in Germany during the last half of the century, which completed the arithmetization of analysis, nor was seen by the leading English mathematicians as more than either a philosophical argument that time can and ought to provide a source for an axiomatization of analysis, or an attack on the view of algebra held by such men as Peacock, DeMorgan, and Gregory. Why this is so is of interest, particularly when one recalls that Hamilton was a highly respected mathematician in both the British Isles and the Continent. Jacobi, in 1842, referred to him as "le Lagrange de votre pays;" he was elected corresponding member of the Royal Academies or Societies of Berlin and France; and, in addition to many other forms of recognition from British institutions or persons, he was asked to become a fellow of the Royal Society. (Hamilton declined, giving as reason his inability to pay conveniently the annual dues.)
The interactive patterns of occupations and workers in predicting excessive occupational stress

A rural hospital was selected for this research. Respondents (n = 330) completed questionnaires which collected biographical/occupational characteristics and perceptions regarding five dimensions of occupational stress. A two-way ANOVA procedure indicated that substantial interactive effects existed between a number of respondent characteristics and their departmental affiliation with regard to predicting elevated stress perceptions in four of the five categories.
A rejoinder: On power, identities and culture in the network society

(1998). A rejoinder: On power, identities and culture in the network society. New Political Economy: Vol. 3, No. 3, pp. 473-483.
A mathematical model for the asymmetric dynamic response in microbial systems

Abstract It has been widely observed that the nature of the dynamic response of microbial systems varies depending on whether the concentration of growth-limiting substrate in the extracellular environment dictates an increase or a decrease in the specific growth rate. A general model is formulated to describe these asymmetric responses; it includes dynamic rate expressions for cell mass synthesis and the synthesis of enzymes subject to genetic-level control. The active rate expressions are determined by the relationship of a specific synthesis rate to its ‘target’ value. The model is simple, but has a considerable predictive capability.
Link, Search, Interact The Co-Evolution of NGOs and Interactive Technology

International institutions are being transformed by the twinned appearance of new non-governmental organizations (NGOs) and new technologies. How do these processes co-evolve? If we were limited to...
Management of life-threatening blunt head trauma in childhood-A case report.

INTRODUCTION Traumatic head/brain injury (TBI) is a leading cause of death and life-long disability in children. The key to successful management of extradural haematoma is early recognition and evacuation.
MO‐EE‐A1‐06: Performance of MPC‐Based Adaptive Radiotherapy Optimization

Purpose: An adaptive re‐planning framework was used to account for tissue deformation during RT treatment courses. The framework is based on a multivariate control concept called model predictive control (MPC). A variety of control rules and optimization schemes were investigated using a prioritization‐based optimization method. Performance of the MPC control was evaluated with conventional evaluation metrics such as DVH, coverage, and homogeneity as well as model‐based plan evaluation metrics. Method and Materials: The Head/Neck IMRT treatment process was simulated using mid‐course CT scans, tracking treatment doses to tissues at the voxel level. Off‐line adaptation was performed with the changing patient model, updating the state of the process along with the dose‐to‐date information. Constrained optimizations were performed for re‐planning as well as for pre‐treatment planning. Multivariate control schemes including maximum constraint violation were utilized for re‐planning. Results: With the adaptation of the treatment plan to the patient‐specific anatomical changes, the predicted outputs could be efficiently controlled improving the robustness to those changes. Although the results show that the general trend in the predicted outputs follow the tissue volume changes, the clinical decision to re‐plan should be made by assessing the total predicted treatment output expectations. For cases investigated, a limited number (3∼4) of re‐plans were sufficient to control high priority outputs while the use of a tighter tolerance increased the number of re‐plans. Re‐plans were triggered mostly by the target coverage criteria. The studied course simulations indicate that significant changes are shown early in treatment. Therefore, frequent updates of the patient models may be necessary and critical to plan adaptation. Conclusion: The proposed multivariate control framework provided an intuitive method of articulating clinicians' decisions and priorities for re‐planning. In addition, the use of prioritization in re‐optimization may allow more efficient re‐planning which requires fewer planning resources. Supported in part by CA‐P01‐CA59827
Elder care as "frustrating" and "boring": understanding the persistence of negative attitudes toward older patients among physicians-in-training.

Abstract Objectives This study explores the attitudes of physicians-in-training toward older patients. Specifically, we examine why, despite increasing exposure to geriatrics in medical school curricula, medical students and residents continue to have negative attitudes toward caring for older patients. Methods This study used ethnography, a technique used by anthropologists that includes participant-observation, semi-structured interviews, and facilitated group discussions. Research was conducted at two tertiary-care academic hospitals in urban Northern California, and focused on eliciting the opinions, beliefs, and practices of physicians-in-training toward geriatrics. Results We found that the majority of physicians-in-training in this study expressed a mix of positive and negative views about caring for older patients. We argue that physicians-in-trainings' attitudes toward older patients are shaped by a number of heterogeneous and frequently conflicting factors, including both the formal and so-called “hidden” curricula in medical education, institutional demands on physicians to encourage speed and efficiency of care, and portrayals of the process of aging as simultaneously as a “problem” of inevitable biological decay and an opportunity for medical intervention. Discussion Efforts to educate medical students and residents about appropriate geriatric care tend to reproduce the paradoxes and uncertainties surrounding aging in biomedicine. These ambiguities contribute to the tendency of physicians-in-training to develop moralizing attitudes about older patients and other patient groups labeled “frustrating” or “boring”.
Fabrication of optically transparent carbon electrodes by the pyrolysis of photoresist films: approach to single-molecule spectroelectrochemistry.

This paper describes the preparation, physical and chemical characterization, and performance of carbon-based optically transparent electrodes (C-OTEs) fabricated by the pyrolysis of thin films of photoresist. The electrodes are prepared by spin coating dilute solutions of the positive photoresist AZ 4330 onto quartz substrates. Pyrolysis of these samples at 1000 °C in a reducing atmosphere yields optically transparent carbon films that have thicknesses ranging between 10 and 80 nm. Sheet resistance measurements, X-ray photoelectron spectroscopy, Raman spectroscopy, and atomic force microscopy were used to determine the physical and chemical properties of the films, and cyclic voltammetry and chronoabsorptometry were employed to delineate the electrochemical and conventional spectroelectrochemical performance of the C-OTEs. These findings showed that the transparency of this material improves as film thickness decreases, but at the expense of an increase in film resistance. At a wavelength of 500 nm, for ...
Psychological predictors of recovery from low back pain: a prospective study.

Recovery from low back pain (LBP) is an important outcome for patients and clinicians. Psychological factors are known to impact the course of LBP but have not been extensively investigated for predicting recovery. The purposes of this study were to: 1) describe LBP recovery rates at 6 months following 4 weeks of physical therapy; 2) identify psychological factors predictive of 6 month recovery status; and 3) identify psychological factors that co-occur with 6 month recovery status.
Electronic properties of (ZnSe)m(Cd1-xZnxSe)n superlattices.

We present theoretical calculations on the electronic structures of (ZnSe${)}_{\mathit{m}}$(${\mathrm{Cd}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Zn}}_{\mathit{x}}$Se${)}_{\mathit{n}}$ superlattices. First-principle pseudopotential calculations are performed to obtain the valence-band offset for CdSe grown on ZnSe. We then use an empirical nonlocal pseudopotential method, including the spin-orbit interaction to calculate the band structures and effective masses of (ZnSe${)}_{\mathit{m}}$(${\mathrm{Cd}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Zn}}_{\mathit{x}}$Se${)}_{\mathit{n}}$ superlattices grown on ZnSe. The empirical pseudopotentials are taken to be linear combinations of Gaussian functions with a few adjustable parameters. The parameters of ZnSe and CdSe are fitted to available experimental data. The effects of strain due to lattice mismatch have been properly taken into account. We have also studied the band gap as a function of composition and layer thicknesses of constituent materials in superlattices. The results are in agreement with recent experimental data.
Elements and degrees of SI: A case study of Nikkei Brazilian immigrants in Japan

This article provides an overview of the recent immigrant phenomenon in Japan and explains the complexity of the social integration (SI) of Nikkei Brazilians. Through the research, factors that explain the degree of social integration (SI) of Nikkei Brazilians are identified. Basic data include triangulated results from a survey of 80 people and interviews with 8 individuals. This mixed method case study presents a formula for assessing the degree of SI (SI score), empirically tests and questions several key hypotheses derived from previous literature, and explores the possibility of developing a new non-conventional theory to explain this phenomenon.
Classroom climate and instruction: New goals demand new approaches

Uniformly, science teachers express the same goals for their students, goals that emphasize attitude, communication, creativity, and application of knowledge. Yet, the traditional role of the teacher ignores these goals and focuses on attainment of knowledge, rarely going on to applications. This paper suggests, rather specifically, how to provide instruction that leads to the expressed goals. These specific behaviors come from a three-part model where expressed goals define the role of the student and the student's roles are, in turn, stimulated by the teacher.
Pattern detection and the two-dimensional Fourier transform: Flickering checkerboards and chromatic mechanisms

Abstract Fourier effects are obtained from simple detection thresholds for checkerboard and striped gratings, without using complex waveforms, masking or pattern adaptation. Spatial contrast predicts that the checkerboard thresholds should be lower than the bar-grating thresholds, but this never occurs. The opposite result, predicted by magnitude detection in the two-dimensional Fourier domain, occurs in a variety of flicker experiments, with red or green homochromatic fields, and under selective chromatic adaptation. It persists at spatial frequencies as low as 1.4 c/deg. and cannot be attributed to stray light, image blur, or orientational selectivity. Even with opponent-color patterns of unvarying luminance, the bar-check sensitivity ratio is still π/2 (as predicted by the Fourier magnitudes) over a broad frequency range. This Fourier mechanism seems to affect both achromatic and opponent-color pathways equally; therefore, we cannot infer that its location is post-retinal.