cssi/SciSciGPT-SciSciNet huggingface dataset:
Sensitivity of protein misfolding cyclic amplification versus immunohistochemistry in ante-mortem detection of chronic wasting disease.

As the only prion disease affecting free-ranging animals, ante-mortem identification of affected cervids has become paramount in understanding chronic wasting disease (CWD) pathogenesis, prevalence and control of horizontal or vertical transmission. To seek maximal sensitivity in ante-mortem detection of CWD infection, this study used paired tonsil biopsy samples collected at various time points from 48 CWD-exposed cervids to compare blinded serial protein misfolding cyclic amplification (sPMCA) with the assay long considered the ‘gold standard’ for CWD detection, immunohistochemistry (IHC). sPMCA-negative controls (34 % of the samples evaluated) included tissues from mock-inoculated animals and unspiked negative controls, all of which tested negative throughout the course of the study. It was found that sPMCA on tonsil biopsies detected CWD infection significantly earlier (2.78 months, 95 % confidence interval 2.40–3.15) than conventional IHC. Interestingly, a correlation was observed between early detection by sPMCA and host PRNP genotype. These findings demonstrate that in vitro-amplification assays provide enhanced sensitivity and advanced detection of CWD infection in the peripheral tissues of cervids, with a potential role for spike or substrate genotype in sPMCA amplification efficiency.
Optical Properties of Silicon Nitride

The optical properties of silicon nitride layers formed by the pyrolysis of a mixture of and are presented. These results are used together with published data for materials to formulate a bonding model for and which quantitatively describes their optical characteristics. The basic units of this structure are Si tetrahedra of the type in which the distribution of atoms for all possible is statistical for any given atom ratio.
Analytical and experimental study of control effort associated with model reference adaptive control

Numerical simulation results presently obtained for the performance of model reference adaptive control (MRAC) are experimentally verified, with a view to accounting for differences between the plant and the reference model after the control function has been brought to bear. MRAC is both experimentally and analytically applied to a single-degree-of-freedom system, as well as analytically to a MIMO system having controlled differences between the reference model and the plant. The control effort is noted to be sensitive to differences between the plant and the reference model.
Dialogical Encounters: Contemporary Perspectives on "Chairwork" in Psychotherapy.

This article looks at the use of“chairwork” (2-chair and “empty”chair) dialogues through the lens of 5psychotherapies: Gestalt,process-experiential therapy, redecisiontherapy, cognitive–behavioral therapy,and schema therapy. Many clinicalexamples are provided, and they areorganized into 4 overlapping groups:(a) internal in focus; (b) external infocus; (c) conflictual, that is, whetherthey involve the replaying of difficult ortraumatic scenes from the past; or (d)corrective, which means that theemphasis is on replacing maladaptivecognitions or schemas with ones thatare healthier. A potential foundationfor Gestalt and cognitive–behavioralintegration is proposed on the basis ofthe idea that gestalts are schemas (I. G.Fodor, 1996) and that chairwork isactually a form of cognitiverestructuring (D. J. A. Edwards, 1989).
Think Tanks and the Media: How the Conservative Movement Gained Entry into the Education Policy Arena.

This research examines how the conservative movement has used both conservative think tanks and the media to gain entry into the field of education policy. The study examines how the conservative movement has attempted to use think tanks as legitimating organizations to enter the education policy arena by (a) measuring the historical growth in the number of conservative think tanks focused on education policy, (b) situating that growth within the larger context of efforts on the part of the conservative movement to bring free market ideas to education, and (c) analyzing and comparing conservative think tank media presence to that of centrist and progressive think tanks and university-based education-policy centers. Findings indicate that conservative think tanks produced the largest number of education media citations, followed by centrist think tanks. Liberal/progressive think tanks and university-based education-policy centers had little to no media presence.
Race-Ethnicity, SES, Gender, and Language Proficiency Trends in Mathematics Achievement: An Update

The purpose of this article is to document changes in U.S. mathematics achievement by reviewing national trend studies, college admissions examinations, and Advanced Placement tests. This article examined this quantitative research literature to determine trends in mathematics achievement of various social groups defined along lines of race, class, gender, ethnicity, and language proficiency. The findings of this review indicate that over the last 15 years all demographic groups have improved in mathematics achievement-specifically, in basic skills. Moreover, the mathematics achievement gap is slowly closing between White students and students of color on assessments of basic skills. Males tended to outperform females on standardized measures; however, gender differences were small and generally not significant. Consistent with past reviews of mathematics achievement, course taking was a powerful variable, often resulting in similar achievement gains across diverse groups. This finding has serious implications for equity-related policy. The article concludes with two other recommendations: the need for fiscal and cultural policy to support standards-based reform. The Curriculum and Evaluation Standards for School Mathematics and the Professional Standards for Teaching Mathematics together provide a vision of mathematical goals that have been adopted by a large majority of state departments of education in the United States (Massell, 1994; NCTM, 1989, 1991). In support of these two documents, the philosophical background of the Assessment Standards for School Mathematics (NCTM, 1995) states the following:
A QUANTUM DOT MICROCAVITY TERAHERTZ LASER

We discuss a THz laser device based on a semiconductor quantum dot (QD) gain medium, where the lasing occurs through discrete conduction states. An ensemble of QDs is selectively placed in a high quality cavity, called a microdisk, which is resonant with a terahertz intersublevel QD transition. We simulate the rate equations governing lasing and discuss a variety of processes affecting lasing including nonradiative recombination and the ground state decay rate.
Irradiation-enhanced interdiffusion in the diffusion zone of U-Mo dispersion fuel in Al

Uranium-molybdenum (U-Mo) alloy fuel particles dispersed in an aluminum (Al) matrix, designated as U-Mo/Al dispersion fuel, is in the development stage in the worldwide RERTR (Reduced Enrichment for Research and Test Reactors) program. The main issue in developing U-Mo/Al dispersion fuel is the diffusion reaction occurring at the interface between the fuel particles and matrix. To accurately analyze fuel performance, a model to predict the diffusion kinetics is necessary. For this purpose, the authors developed a diffusion layer growth rate correlation for out-of-pile annealing tests and a similar correlation for in-reactor tests. The correlation for in-reactor tests is considerably different from that of out-of-pile tests because it contains factors that amplify diffusion kinetics by fission damage in the diffusion reaction zone. This irradiation enhancement was formulated by a combination of the fission rate in the fuel and fission fragment damage distribution in the diffusion reaction zone. Using a computer code, fission damage factors were obtained as a function of diffusion reaction layer thickness and composition. The model correlation was established and fitted to the in-reactor data. As a result of this data fitting, the interaction layer growth rate is found to be proportional to the square root of the fission fragment damage rate and to have a temperature dependence characterized by the effective activation energy of 46 to 76 kJ/mole, which is smaller by a factor of 4 to 7 than that of out-of-pile tests.
Analysis of Robotic Performance Times to Improve Operative Efficiency

Abstract Study Objective To estimate the efficiency of procedural steps in robotic sacrocolpopexy and concomitant hysterectomy. Design Retrospective study (Canadian Task Force classification II-2). Setting University hospital. Patients One hundred forty-seven patients who underwent robotic-assisted procedures from November 2007 through December 2010. Interventions Robotic-assisted sacrocolpopexy. Sixty patients (40.8%) underwent concomitant hysterectomy; 37 (25.2%), mid-urethral sling placement; and 7 (4.8%), concomitant colporrhaphy. Measurements and Main Results Comparison of the first 20 procedures with the subsequent 127 demonstrated that there was considerable improvement in time of cuff closure (p = .04); sacral dissection (p = .004); anterior (p = .006), posterior, (p = .003), and sacral (p = .003) mesh attachment; peritoneal closure (p Conclusion Robotic efficiency improves over a short learning period, with greatest differences in intracorporeal suturing and overall times. Identifying these steps may aid surgeons and learners in improving overall efficiency and establishing benchmarks for performance.
Transparent, Optical, Pressure‐Sensitive Artificial Skin for Large‐Area Stretchable Electronics

Optical pressure sensors are highly responsive and are unaffected by surrounding parameters such as electronic noise, humidity, temperature, etc. A new type of optical pressure sensor is described that demonstrates the stretchability and transparency of a polydimethylsiloxane waveguide, while also serving as a substrate. The pressure sensors are both robust and easy to fabricate over a large area.
Cytokine mRNA expression in tolerant heart allografts after immunosuppression with cyclosporine, sirolimus or brequinar

Abstract We sought to examine the impact of the preferential activation of Th2 cells on the induction and maintenance of a tolerant state in heart allograft rat recipients treated with a short course of cyclosporine (CsA), sirolimus (SRL) or brequinar (BQR). A quantitative polymerase chain reaction (PCR) method was used to measure the levels of cytokine mRNAs, namely interferon (IFN)-γ and interleukin (IL)-2 in T helper 1 (Th1) cells and IL-4, IL-5 and IL-10 in Th2 cells. Our main findings were that on day 5 postgrafting allografts from untreated recipients had increased levels of IFN-γ(216 ± 119 fg), IL-2 (449 ± 75 fg), IL-4 (6.2 ± 1.3 fg), IL-5 (34.8 ± 9.3 fg) and IL-10 (1554 ± 184 fg) mRNAs compared with normal hearts. CsA reduced the levels of IFN-γ, IL-2, IL-5 and IL-10, but not IL-4, mRNAs. SRL did not affect the expression of cytokine mRNAs. BQR decreased the levels of IFN-γ, IL-2 and IL-10, but not IL-5 or IL-4 mRNAs. Compared with grafts from untreated recipients, those from CsA- or BQR-treated tolerant hosts (day 100) displayed undetectable IL-2 mRNA levels, and reduced levels of IFN-γ, IL-4 and IL-10 mRNAs. In fact, the patterns of cytokine mRNA expression in grafts from CsA- and BQR-treated tolerant hosts were similar to those of normal hearts. Grafts from SRL-treated tolerant hosts merely showed slightly increased Th2 cell activity. In conclusion the selective activation of Th2 cells is not absolutely required for induction or maintenance of tolerance.
A Roller Device to Scan for Surface-Breaking Cracks and to Determine Crack Depth by a Self-Calibrating Ultrasonic Technique

A roller device using a square or a rectangular configuration of four roller transducers is used to scan a surface for surface-breaking cracks, by monitoring the reflection and transmission of surface waves. A self-calibrating ultrasonic technique is presented to determine the reflection and transmission coefficients or their ratio. For two configurations, namely, when one or both front rollers have crossed the surface trace of the crack, expressions have been obtained for the reflection and transmission coefficients in terms of measured voltages only, independent of parameters defining the coupling of the transducers to the specimen and the attenuation of surface waves propagating over the specimen. For a two dimensional configuration of a crack normal to the surface, the experimental results for the magnitude of the transmission coefficient show good agreement with theoretical results. For that case, the crack depth can be determined from the measured data.
Estimating model parameter values for total system performance assessment

The intrinsic dissolution rates of nine borosilicate waste glasses were extracted from the results of MCC-1 tests conducted for durations long enough that the solution pH reached a nearly constant value but short enough that the buildup of dissolved species did not affect the dissolution rate. The effects of the pH and temperature on the measured rates were deconvoluted to determine the sensitivity of the rate to the glass composition. The intrinsic dissolution rates were similar for all of these glasses and were not correlated with the glass composition. The mean and standard deviation of the intrinsic dissolution rates of these glasses are log k{sub 0}/[g/(m{sup 2}{center_dot}d)] = 8.2 {+-} 0.2.
THE ACTIVATION OF SKIN GRAFTS

Rabbit skin rendered hyperplastic by various agents showed less tendency than normal skin to contract when sliced off, and when used for grafts it united with the bed more rapidly and was vascularized sooner. The stimulated epidermis proliferated practically at once, and abundantly, to cover adjacent raw surfaces. Also the donor area healed much more swiftly than usual and became infected less often. Certain grave limitations and hazards encountered during the experiments with hyperplastic grafts are considered.
HTFFR kinetics studies: A chemiluminescence titration method for the determination of absolutes Sn concentrations

Abstract Absolute gas phase Sn concentrations in the range 1 × 10 13 ⩽ [Sn] ⩽ 1 × 10 14 ml −1 have been determined utilizing a technique based on the rapid (at T ⩾ 900 K) titration reaction Sn + NO 2 → SnO + NO ( k (900–1100 K) ≈ 1 × 10 −10 ml molecule −1 s −1 ) and the chemiluminescent indicator reaction Sn + N 2 O → SnO + N 2 + hv (SnO a 3 Σ-X 1 Σ).
Vortex equilibria in turbulence theory and quantum analogues

Abstract A family of statistical vortex equilibria and related quasi-equilibria in models of classical incompressible flow is analyzed; it is suggested that these equilibria constitute approximate models of the inertial scales in turbulence. Inertial exponents γ are calculated; the equilibrium that has maximum entropy has a spectrum close to the Kolmogorov spectrum. At maximum entropy, the vortex filaments have axes that are self-avoiding random walks. The velocity statistics are non-Gaussian even at equilibrium. The classical vortex system is contrasted with a quantum vortex system; it is shown that classical vortex folding is a manifestation of the Kosterlitz-Thouless transition mechanism. Universality properties of the inertial exponent are discussed, as is the effect of a strong cascade on vortex reconnection. A relation with some recent work on the λ transition in superfluidity is pointed out.
Alterations in the Activity of Pentothal, Phenobarbital, Pentylenetetrazol, and Strychnine by Cholinesterase Inhibitors

Mice pretreated with anticholinesterases showed enhanced stimulation in the presence of pentylenetetrazol and strychnine, a decreased lag period with anesthetic doses of phenobarbital, and a prolongation of anesthesia with pentothal. An attempt was made to correlate these changes in response with the depression of acetylcholine hydrolyzing enzymes.
Changes in concanavalin A capping of human lymphocytes with age

Abstract Cap formation of peripheral blood lymphocytes from human donors of different ages was compared using fluorescein-labeled concanavalin A as the ligand. The mean percentage capping in donors aged 20–40 years (21.6 ± 0.7%) was significantly higher than values found for donors aged 40–60 years (18.4 ± 1.1%) and for donors aged > 60 years (14.5 ± 1.3%). Regression analysis of the entire age range studied (3–95 years) indicated that capping decreases in a linear fashion with age, although in the old age group some individuals showed capping values comparable to those of young donors. Preincubation of lymphocytes with colchicine increased capping in both young and old donors. Cells from both young and old donors with capping values of more than 20% showed a marked increase in capping following colchicine treatment. Capping values after colchicine in these two groups were significantly greater than values after colchicine treatment of old donors' cells with low pretreatment capping values. This finding suggests that abnormalities of microtubules do not totally account for the age-related reduction of concanavalin A capping unless colchicine interacts differently with lymphocyte microtubules in the aged. This study provides further evidence for altered cell membrane function with age.
Variability in Risk Factors for Knee Injury in Construction

This study investigated sources of variance in exposure to risk factors for knee pain in a variety of highway construction trades, operations, and tasks. Over 15,000 discrete observations of leg postures and weights handled were made on 120 construction workers in five construction trades, in nine operations over 79 days. The contributions of trade, operation, task, and worker to the variability in work time spent kneeling, squatting, and carrying loads were evaluated with multilevel random effects models. Construction operation and task explained about 20% to 30% of total variation in kneeling, squatting, and carrying loads. There was a large unexplained component of variance thought to represent day-to-day variability of exposure within task. Reliable assessments of knee exposures require multiple days to accommodate the high variability of exposures among operations and tasks and over time. These sources of variability should be carefully considered in efforts to estimate exposures to knee loading for ...
Genomics of AML: Clinical Applications of Next-Generation Sequencing

In the past decade, a series of technological advances have revolutionized our ability to interrogate cancer genomes, culminating in whole-genome sequencing, which provides genome-wide coverage at a single base-pair resolution. As sequencing technologies improve and costs decrease, it is likely that whole-genome sequencing of cancer cells will become commonplace in the diagnostic workup of patients with acute myelogenous leukemia (AML) and other cancers. The unprecedented molecular characterization provided by whole-genome sequencing offers the potential for an individualized approach to treatment in AML, bringing us one step closer to personalized medicine. In this chapter, we discuss how next-generation sequencing is being used to study cancer genomes. Recent publications of whole-genome sequencing in AML are reviewed and current limitations of whole-genome sequencing are examined, as well as current and potential future clinical applications of whole-genome sequencing.
Optimizing outcomes of robotic mitral valve repair for all prolapse anatomy: the Suri-Burkhart technique.

Early mitral valve (MV) repair is the evidence-based care standard for those with severe degenerative MV regurgitation and has been shown to improve long-term patient outcomes in comparison to non-surgical management (1). Despite evidence favoring the performance of MV repair prior to symptom onset or the appearance of left ventricular (LV) dysfunction, some physicians are hesitant to refer asymptomatic patients for MV repair involving traditional median sternotomy (2). Alternatively, cardiac surgical procedures including MV repair performed through small incisions utilizing videoscopic assistance are now common-place, and have been shown to be capable of sparing patients the physiological challenge of recuperating from a sternum-dividing operation (3,4). The spectrum of benefits potentiated by use of minimally invasive incisions is well documented in the literature (5). Several large health care delivery systems have embraced minimally invasive surgical approaches aiming to replicate the “gold standard” results of a trans-sternal (open) MV repair aiming to improve patient acceptance and facilitate earlier referral. This thereby minimizes the delayed but substantial costs associated with the evolution of chronic debilitating heart failure or the poor outcomes of rescue surgery once symptoms or LV dysfunction develop (3,6). Recent efforts to uphold the safety and efficacy of standard open operations while decreasing costs have launched robotic MV repair to the forefront of available treatment options for asymptomatic mitral regurgitation (MR).
Simplified realization of two-qubit quantum phase gate with four-level systems in cavity QED

We propose a method for realizing two-qubit quantum phase gate with 4-level systems in cavity QED. In this proposal, the two logical states of a qubit are represented by the two lowest levels of each system, and two intermediate levels of each system are utilized to facilitate coherent control and manipulation of quantum states of the qubits. The present method does not involve cavity-photon population during the operation. In addition, we show that the gate can be achieved using only two-step operations.
Screening Cellular Feature Measurements for Image-Based Assay Development

The typical “design” approach to image-based assay development involves choosing measurements that are likely to correlate with the phenotype of interest, based on the researcher’s intuition and knowledge of image analysis. An alternate “screening” approach is to measure a large number of cellular features and systematically test each feature to identify those that are best able to distinguish positive and negative controls while taking precautions to avoid overfitting the available data. The cell measurement software the authors previously developed, CellProfiler, makes both approaches straightforward, easing the process of assay development. Here, they demonstrate the use of the screening approach to image assay development to select the best measures for scoring publicly available image sets of 2 cytoplasm-to-nucleus translocation assays and 2 Transfluor assays. The authors present the resulting assay quality measures as a baseline for future algorithm comparisons, and all software, methods, and images they present are freely available.
THE ADRENAL CORTEX AND CARBOHYDRATE METABOLISM

DIRECT PARTICIPATION of the adrenal cortex in the hormonal control of carbohydrate metabolism has been the subject of vigorous debate for a number of years. The interest in this problem has centered not only on the interpretation of the alterations in carbohydrate metabolism that occur in adrenalectomiz;ed animals, but also on their relation to the function of the adrenal cortex. This problem would appear to be capable of a simple solution were it not for the fact that other changes follow adrenalectomy that at first sight appear to be of greater significance than the disturbances in carbohydrate metabolism that have been reported. There is now no doubt that many adrenalectomized animals suffer such widespread disturbances intheir water and electrolyte balance that their ultimate death can hardly fail to be associated with them.
Improving the Diagnosis of Acute Hepatitis C Virus Infection with Expanded Viral Load Criteria

Background. The diagnosis of acute hepatitis C virus (HCV) infection is imprecise because antibody testing does not differentiate between acute and chronic infection. Although virologic features, such as viral load fluctuations and low levels of viremia, have been noted to be characteristic of acute HCV infection, these parameters have not been used for diagnosis. Methods. We validated the use of these novel parameters (ie, viral load fluctuations >1 log and HCV RNA levels <100,000 IU/mL) in a cohort of acute HCV seroconverters. We then applied standard diagnostic criteria for acute HCV infection in a cohort of high-risk injection drug users entering prison with suspected acute HCV infection (n = 37). We subsequently assessed whether these novel virologic parameters, measured serially over a 10-week period, could enhance the diagnosis of acute infection. Results. Low-level viremia and viral load fluctuations were highly prevalent in our cohort of acute seroconverters (81% and 86%, respectively), whereas low-level viremia occurred in only 13% of control patients with chronic infection. With use of standard criteria, 37 inmates received a diagnosis of acute HCV infection. Among the 35 patients with HCV RNA detectable at baseline, we found low-level viremia to be highly prevalent (n = 27; 77%); among patients with a minimum of 2 HCV RNA samples, we demonstrated viral fluctuations in more than one-third (n = 9; 36%). Conclusions. The diagnosis of acute infection in HCV-seropositive patients is strengthened by the use of virologic parameters that are uncommon in chronic disease. Viral load fluctuations and low levels of HCV RNA should be incorporated into standard diagnostic criteria.
Third-party intervention and escalation in Kosovo: Does moral hazard explain it?

ABSTRACT This piece provides a critique of the moral-hazard theory of third-party interventions. While the author agrees with the proponents of the theory that threats of intervention may have radicalizing effects on a minority's behaviour by reducing its risks in carrying out violence, he argues that this is an incomplete causal argument, if what we are trying to explain is escalated violence and not just minority radicalization. This criticism is based on two claims in particular. First, if the minority and the state observe the same third-party threat, they should both adjust their bargaining calculations. This means that such threats should affect the terms of settlement, and not the likelihood of violence. Second, he argues that cases where the minority radicalization results from explicit or implicit encouragement by third parties should not count as evidence supporting the moral-hazard theory. An internally consistent moral-hazard account requires an explanation of why third parties were unable to ...
El Partido de los Trabajadores y el uso político del poder judicial

This paper draws on the experience of the Brazilian Workers’ Party (PT), during periods of opposition and incumbency, to develop a theoretical approach to the use of Courts by political actors. I argue that the use of Courts by political parties is an outcome of their relations with executive incumbents, the institutional architecture of the judiciary, and a strategic evaluation of the different judicial mechanisms that are available to them.
Explicitly modeling the effects of aging on response time.

Research into the effects of aging on response time has focused on Brinley plots. Brinley plots are constructed by plotting mean response times for older subjects against those for young subjects for a set of experimental conditions. The typical result is a straight line with a slope greater than 1 and a negative intercept. This linear function has been interpreted as showing that aging leads to a general slowing of cognitive processes. In this article, we show that the slope of the Brinley plot is actually a measure of the relative standard deviations of older versus young subjects’ response times; it is not a measure of general slowing. We examine current models of the effects of aging on mean response time and show how they might be reinterpreted. We also show how a more comprehensive model, Ratcliff’s diffusion model (1978), can account for Brinley plot regularities and, at the same time, provide an account of accuracy rates, the shapes of response time distributions, and the relative speeds of error and correct response times, aspects of the data about which models designed to account for Brinley plots are mute. We conclude by endorsing a research approach that applies explicit models to response time data in aging in order to use the parameters of the model to interpret the effects of aging.
Transistor scaling with constant subthreshold leakage

A model for scaling transistors with constant subthreshold leakage is presented. In contrast with other scaling theories, the scaling formulation presented does not necessarily lead to transistors with long channel characteristics. Instead, the transistor is scaled only to enhance circuit performance while meeting circuit specifications-in this case, subthreshold leakage current. The model is critically dependent upon the drain induced barrier lowering effect which has been evaluated as a function of channel length, gate thickness, and channel doping. The effect is found to vary as L^{-m} where m = 1.2-1.4 .
Segmental Ostial Ablation to Isolate the Pulmonary Veins During Atrial Fibrillation: Feasibility and Mechanistic Insights

Background— The purpose of this study was to determine the feasibility and mechanistic implications of segmental pulmonary vein (PV) ostial ablation during atrial fibrillation (AF). Methods and Results— Forty consecutive patients underwent PV isolation for AF. Among 125 PVs targeted for isolation, ablation was performed during AF in 70 veins and during sinus rhythm in 55 veins. A decapolar Lasso catheter was positioned near the ostium. During AF, ostial ablation was performed near the Lasso catheter electrodes that recorded a tachycardia with a cycle length shorter than in the adjacent left atrium. During sinus rhythm, ostial ablation was guided by PV potentials. Complete PV isolation was achieved in 70 PVs (100%) ablated during AF and in 53 PVs (96%) ablated during sinus rhythm (P=0.4). The mean durations of radiofrequency energy needed for isolation were 7.4±4.4 and 5.2±3.9 minutes during AF and sinus rhythm, respectively (P<0.01). Before ablation, an immediate recurrence of AF (IRAF), occurred after ca...
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry

Motivation: Statistical evaluation of the confidence of peptide and protein identifications made by tandem mass spectrometry is a critical component for appropriately interpreting the experimental data and conducting downstream analysis. Although many approaches have been developed to assign confidence measure from different perspectives, a unified statistical framework that integrates the uncertainty of peptides and proteins is still missing. Results: We developed a hierarchical statistical model (HSM) that jointly models the uncertainty of the identified peptides and proteins and can be applied to any scoring system. With data sets of a standard mixture and the yeast proteome, we demonstrate that the HSM offers a reliable or at least conservative false discovery rate (FDR) estimate for peptide and protein identifications. The probability measure of HSM also offers a powerful discriminating score for peptide identification. Availability: The algorithm is available upon request from the authors. Contact: chashen@iupui.edu Supplementary information: Supplementary data are available at Bioinformatics online.
The signal response of IkappaB alpha is regulated by transferable N- and C-terminal domains.

IkBa retains the transcription factor NF-kB in the cytoplasm, thus inhibiting its function. Various stimuli inactivate IkBa by triggering phosphorylation of the N-terminal residues Ser32 and Ser36. Phosphorylation of both serines is demonstrated directly by phosphopeptide mapping utilizing calpain protease, which cuts approximately 60 residues from the N terminus, and by analysis of mutants lacking one or both serine residues. Phosphorylation is followed by rapid proteolysis, and the liberated NF-kB translocates to the nucleus, where it activates transcription of its target genes. Transfer of the N-terminal domain of IkBa to the ankyrin domain of the related oncoprotein Bcl-3 or to the unrelated protein glutathione S-transferase confers signal-induced phosphorylation on the resulting chimeric proteins. If the C-terminal domain of IkBa is transferred as well, the resulting chimeras exhibit both signal-induced phosphorylation and rapid proteolysis. Thus, the signal response of IkBa is controlled by transferable N-terminal and C-terminal domains.
Tectonic history of the metamorphic basement rocks of the Sierra del Carmen, Coahuila, Mexico

The Ouachita interior zone, arching through central Texas into the Big Bend region of the Rio Grande, has been defined chiefly on the basis of well samples and its associated gravity high. The only known exposure of rocks of the interior zone lies at the base of the Sierra del Carmen normal fault escarpment under approximately 1100 m of Lower Cretaceous carbonates in northern Coahuila, Mexico. These lower greenschist facies metamorphic rocks are thinly interlayered graphitic muscovite schist, graphitic marble, and minor quartzite with abundant quartz veins. The dominant structures shown by the metamorphic rocks are isoclinal folds (F2) that have a well-defined axial planar foliation (S2). Earlier (F1) folds refolded by F2 are locally preserved. At the microscopic scale, S2 is a crenulation cleavage of the S1 foliation that has been enhanced by pressure solution. Feldspar porphyroblasts overgrow a folded graphitic S1 foliation. Throughout the area a second crenulation cleavage (S3) is present on the S2 foliation surface as an intersection lineation (L3). Subsequent Laramide regionalto outcrop-scale folds and associated thrusts overprint these ductile structures. Lower Cretaceous carbonates form a large, east-verging overturned to recumbent anticline-syncline fold pair with a northwest-trending fold axis. The S2 metamorphic foliations define an antiform that is nearly coincident in trend to that of the fold in the overlying carbonates, indicating that the metamorphic rocks were also folded by this regional structure. A Basin and Range normal fault is interpreted to have reactivated the Laramide thrust fault responsible for the contractional deformation. One to two normal faults cut the carbonates and metamorphic rocks and truncate the anticline-syncline fold pair. The maximum offset along the normal fault is 1600 m. Rb/Sr data from the muscovite schist gives a six-point, mineralÐwhole-rock isochron age of 277 ± 10 Ma, indicating that polyphase deformation and metamorphism occurred during the late Paleozoic Ouachita orogeny. An initial Sr ratio of 0.721 suggests an ancient source for these metasediments. Common Pb ratios of the metamorphic whole rock and galena from the Puerto Rico Mine are isotopically distinct from those of the North American craton, suggesting that they were derived from a nonÐNorth American source and thus may be equivalent to unmetamorphosed Ouachita flysch sediments. This indicates that the metamorphic rocks of the Ouachita interior zone were derived from an ancient allochthonous source that was deformed and metamorphosed during the late Paleozoic Ouachita orogeny.
Related Methods for Three-Dimensional Imaging

The ability of confocal laser-scanning microscopy to collect stacks of optical sections has made three-dimensional (volumetric) imaging a standard analytical tool in experimental cell and developmental biology. Parallel developments in deconvolution techniques, especially as computational power increased and costs decreased, offered tools to make three-dimensional (3D) imaging from widefield as well as confocal microscopes possible. Despite the high spatial resolution provided by these 3D methods, they all suffer from a common limitation: light scattering in the specimen limits them to operating in the outer few hundred micrometers of the specimen.
Synthesis and identification of the N-glucuronides of norgallopamil and norverapamil, unusual metabolites of gallopamil and verapamil.

N-Glucuronides of norgallopamil and norverapamil were found as biliary metabolites after administering the corresponding tertiary amines, gallopamil and verapamil, to rats. The structures of these unusual metabolites were established by comparison with spectral data of synthesized authentic standards and by enzymic hydrolysis of the conjugates. The N-glucuronide standards were synthesized by coupling the secondary amines to either glucuronic acid or to methyl tetra-O-acetyl-beta-D-glucopyranuronate. On i.p. dosing of rats with gallopamil or verapamil, 13 and 2% of the dose, respectively, appeared in the bile as the N-glucuronide of the secondary amine metabolite over an 8-hr period. Administration of norgallopamil resulted in approximately 25% of the dose being excreted as N-glucuronide conjugate in the bile. Substantially more of the S- than R-enantiomer of both gallopamil and verapamil was converted to the corresponding secondary amine N-glucuronide. The observed high S/R ratios suggest enantio-selectivity in this pathway could contribute to the observed stereoselectivity in other routes of metabolism of the parent tertiary amines.
Imparadising, transhumanizing, intrining: Dante’s celestial vision

In Canto XXVIII of the Paradiso, Beatrice reveals to Dante the nine spheres of the celestial hierarchies, each controlled by one of the ranks of angels. In the opening of this canto, Dante coins the word ‘imparadises,’ which coordinates with two earlier coinages in the Paradiso: ‘transhumanize’ and ‘intrine.’ This essay explores the meaning and context of these three words, along with discussions of Robert Duncan’s and Osip Mandelstam’s involvements with Dante’s poem, all of which leads to a more personal investigation of the origin of a poem of my own, ‘When Twilight into Noonday Knowledge Gyres,’ in which I try to recreate some of the effects of Dante’s poem.
Polyglandular Autoimmune Syndromes

Dysfunction of multiple endocrine glands may develop as the result of hypopituitarism, various infiltrative disorders, or an organ-specific autoimmune mechanism. When dysfunction of two or more endocrine glands occurs in association with circulating organ-specific antibodies directed against the involved glands, the term polyglandular autoimmune syndrome is applied. Characteristics of polyglandular autoimmunity include specific patterns of disease association and frequently a family history of similar involvement. The principal endocrine components of these syndromes are adrenal insufficiency, autoimmune thyroid disease, insulin-dependent diabetes mellitus, and premature gonadal failure. In addition, primary hypoparathyroidism is a key feature of one form of polyglandular autoimmunity that occurs in children. Several nonendocrine organ-specific autoimmune disorders are also associated with polyglandular autoimmunity, of which pernicious anemia is the most frequent. The underlying abnormality responsible for polyglandular autoimmunity is most likely a defect in T suppressor cell function, but there is evidence that aberrant expression of HLA DR antigens also plays an important role in the pathogenesis of these disorders.
Validation of the five-factor model of PTSD symptom structure among delinquent youth.

This study compared the Diagnostic and Statistical Manual of Mental Disorders (4th ed., text rev.; DSM–IV–TR; American Psychiatric Association, 2000) diagnostic 3-factor structure of posttraumatic stress disorder (PTSD) symptoms with leading 4-factor models and the newly proposed 5-factor dysphoric arousal model in a sample of 1,363 juvenile-justice-involved adolescents (990 boys, 373 girls). Structural equation modeling suggested that the 5-factor dysphoric arousal model fit significantly better than each of the other models. The model fit better for girls than for boys, and girls evidenced stronger factor loadings for items on all but the Anxious Arousal factor. The factors of the 5-factor model were then tested as mediators of the association between interpersonal and noninterpersonal trauma and mental health problems. Interpersonal trauma was associated with PTSD symptoms for boys and girls, whereas noninterpersonal trauma exposure was only associated with PTSD symptoms for boys, despite equal levels of exposure across genders, suggesting that girls may be more sensitive to the effects of interpersonal, but not noninterpersonal, trauma. Patterns in mediation were moderated by gender, as girls’ data showed stronger paths leading to depression/anxiety, somatic complaints, and suicidal ideation through PTSD symptoms, whereas for boys, paths were stronger leading to anger/irritability symptoms. Mediation results suggested differential patterns of influence for dysphoric versus anxious arousal and also indicate the importance of numbing for delinquent youth. These results add to the evidence base supporting the 5-factor dysphoric arousal model in establishing developmentally sensitive criteria for the diagnosis of PTSD among traumatized youth.
Verbal Disagreements and Philosophical Scepticism

ABSTRACTMany philosophers have suggested that disagreement is good grounds for scepticism. One response says that disagreement-motivated scepticism can be mitigated to some extent by the thesis that philosophical disputes are often verbal, not genuine. I consider the implications of this anti-sceptical strategy, arguing that it trades one kind of scepticism for others. I conclude with suggestions for further investigation of the epistemic significance of the nature of philosophical disagreement.
Liver Glycogen Synthetase

Homogeneous glycogen synthetase b has been obtained from both trout liver and rat liver. A molecular weight in the range of 260,000 was obtained for the enzyme from both sources. The trout enzyme appears to have less affinity for homologous glycogen than the rat enzyme as evidenced by the lesser fraction of the former which sediments with the glycogen pellet and by the dissociation of the glycogen-enzyme complex from the former but not the latter on DEAE-cellulose columns. A subunit molecular weight of 85,000 was determined for the rat enzyme, suggesting that it exists as a trimer. Further aggregation to a component of twice the original size occurs on storage in the cold. Determinations of alkali-labile phosphate and reactive sulfhydryl groups gave values of 12.4 and about 6, respectively. Activity decreased linearly to zero with the titration of the first 3 sulfhydryl groups (or the first 2 when glycogen was present), indicating that at least one of the most reactive groups is essential for activity. Incubation of the purified synthetase at 0° led to inactivation which was reversed on rewarming. Glycogen protected against this cold inactivation. Homogeneous rat liver synthetase b serves as a substrate for synthetase phosphatase which is currently being purified.
Medical considerations and perioperative care for rheumatoid surgery.

SUMMARY Surgery on patients with RA should be undertaken after careful consideration of a number of issues. These include an overall assessment of the status of the patient’s arthritis, general health and preparedness for the procedure and the rehabilitation which follows. Special attention must be given to organs that may be affected by the systemic involvement which occurs with rheumatoid disease. Sites requiring specific review include the cervical spine, lungs, airway, bone, and bone marrow. Intraoperatively and postoperatively rheumatoid patients may require supplementary corticosteroids and an adjustment of the dose of their antirheumatic medications. Various systemic rheumatic diseases can have predominantly hand signs and symptoms at their onset. It is valuable to be familiar with the clinical features of gout with tophaceous inflammation, psoriatic arthritis, Raynaud’s disease, and amyloidosis.
Determination of oxytetracycline in bovine kidney and medicated milk replacer by liquid chromatography.

Improvements and optimization of AOAC INTERNATIONAL Official Method 995.09 for the detection of oxytetracycline in bovine kidney at the new U.S. tolerance of 12 ppm are reported. Recoveries from kidney fortified at 4 concentrations over the range of 3-40 ppm averaged 84-98%. Results from the kidney of a calf fed medicated milk replacer containing oxytetracycline are also reported. Additionally, adaptation of this method to the detection of oxytetracycline in medicated milk replacer is discussed.
Controlled Study of Guanfacine XR in ADHD

A multicenter, double-blind, placebo-controlled, fixed-dosage escalation study of an extended release formulation of guanfacine is reported from the Massachusetts General Hospital, Boston, and other centers in the US and UK.
Agricultural Trade: USA and USSR

The “natural fit” in US-USSR agricultural relations realised in 1972 has grown, albeit unevenly, over the course of the decade: exports have become critical to the profitability of the American agricultural sector; imports have become critical to the attainment of Soviet consumption goals. In the future, however, this “natural fit” would seem to be more functional within an East-West multilateral trading context than within a US-USSR bilateral trading context.
Caveolin-1: a novel prognostic biomarker of radioresistance in cancer

AbstractPurpose: Caveolin-1 is a membrane protein highly expressed in many tumors and plays an important role in tumor progression and metastasis. This review describes the structure of the Caveolin-1 protein and its pre-clinical and clinical significance, demonstrating that Caveolin-1 is a novel biomarker for radioresistance which has the promising potential to improve the clinical outcome of cancer patients undergoing radiation treatment.Summary: Targeted radiation therapy has shown immense benefits for cancer treatment. However, one of the major challenges for effective clinical outcome of radiation therapy for cancer patients is the development of radioresistance during radiation treatment. As a consequence, radiation therapy becomes a less effective modality for successful clinical outcome. Furthermore, a radioresistant tumor has the ability to repair its genome, and therefore becomes more aggressive and metastasizes. The plausible mechanisms for tumor radioresistance include the rapid DNA repair, so...
In Situ Shape Estimation of Triangular Moored Hydrophone Arrays Using Ambient Signals

In this paper, a method is presented for correcting relative errors in the locations of individual sensors in a three-element bottom-moored array, using ambient signal arrivals recorded by the array. It has the benefit that knowledge of absolute source positions is not required to determine the relative shape of the array. The procedure is demonstrated using episodic ambient signal arrivals recorded by the southern array of the Wake Island hydrophone station, which is a component of the Comprehensive Nuclear-Test Ban Treaty Organization's (CTBTO) International Monitoring System (IMS). The original coordinates of sensors 2 and 3 were adjusted by 75 and 115 m, respectively, removing approximately 4 $^{\circ}$ of error in estimating the arrival angles of signals. The estimated coordinates compared favorably with the results of a position revision by the CTBTO a year after the triad installation.
A modelling approach to the dynamics of gait initiation

Gait initiation is an integral and complex part of human locomotion. In this paper, we present a novel compliant-leg model-based approach to understanding the key phases of initiation, the nature of the effective forces involved in initiation, and the importance of the anticipatory postural adjustments (APAs). The results demonstrate that in the presence of APAs, we observe a change in the characteristic of forcing required for initiation, and the energetic cost of gait initiation is also reduced by approximately 58%. APAs also result in biologically relevant leg landing angles and trajectories of motion. Furthermore, we find that a sublinear functional relationship with the velocity error from steady state predicts the required force, consistent with an open loop control law basis for gait initiation.