cssi/SciSciGPT-SciSciNet huggingface dataset:
Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation

The Rosetta software suite for macromolecular modeling is a powerful computational toolbox for protein design, structure prediction, and protein structure analysis. The development of novel Rosetta-based scientific tools requires two orthogonal skill sets: deep domain-specific expertise in protein biochemistry and technical expertise in development, deployment, and analysis of molecular simulations. Furthermore, the computational demands of molecular simulation necessitate large scale cluster-based or distributed solutions for nearly all scientifically relevant tasks. To reduce the technical barriers to entry for new development, we integrated Rosetta with modern, widely adopted computational infrastructure. This allows simplified deployment in large-scale cluster and cloud computing environments, and effective reuse of common libraries for simulation execution and data analysis. To achieve this, we integrated Rosetta with the Conda package manager; this simplifies installation into existing computational environments and packaging as docker images for cloud deployment. Then, we developed programming interfaces to integrate Rosetta with the PyData stack for analysis and distributed computing, including the popular tools Jupyter, Pandas, and Dask. We demonstrate the utility of these components by generating a library of a thousand de novo disulfide-rich miniproteins in a hybrid simulation that included cluster-based design and interactive notebook-based analyses. Our new tools enable users, who would otherwise not have access to the necessary computational infrastructure, to perform state-of-the-art molecular simulation and design with Rosetta.
Correlates of tobacco product cessation among youth and adults in the USA: findings from the PATH Study Waves 1-3 (2013-2016).

Objective To report on demographic and tobacco product use correlates of tobacco product initiation (cigarettes, electronic nicotine delivery systems (ENDS), cigars, hookah and smokeless tobacco) among the US population. Design Data were from the first three waves (2013–2016) of the Population Assessment of Tobacco and Health Study, a nationally representative, longitudinal cohort study of US youth (aged 12–17 years) and adults (aged 18+ years). Never users of at least one type of tobacco product at Wave 1 (W1, 2013/14) or Wave 2 (W2, 2014/15) were included (n=12 987 youth; n=25 116 adults). Generalised estimating equations were used to evaluate the association between demographic and tobacco product use characteristics at baseline, and tobacco product initiation at follow-up (ever, past 30 day (P30D), frequent (use on 20 or more of thepast 30 days)) over two 1-year periods (W1–W2 and W2–Wave 3). Results Youth aged 15–17 years were more likely than youth aged 12–14 years and adults aged 18–24 years were more likely than older adults to initiate P30D tobacco use across products; non-heterosexuals were more likely than heterosexuals to initiate P30D cigarette and ENDS use. Older adults were more likely than young adults, and males were more likely than females, to be frequent users of ENDS on initiation. Ever use of another tobacco product predicted P30D initiation of each tobacco product. Discussion Other tobacco product use and age predict P30D tobacco initiation across products whereas associations with other demographic characteristics vary by product. Continued contemporary evaluation of initiation rates within the changing tobacco product marketplace is important.
Comparison of different tidal volume mechanical ventilation strategy on infants with severe congenital heart disease after curative

Objective To analyse the difference of effects of different tidal volume mechanical ventilation strategies in infants with severe congenital heart disease after curative.Methods Sixty-eight cases were chosen from CICU of Anhui Provincial Children's Hospital during Oct 2010 to Jan 2012.Thirty-two cases in A group were used in ventilation strategy by lower tidal volumes (6 ～ 10 ml/kg),36 cases in B group were used in ventilation strategy by larger tidal volumes (10 ～ 15 ml/kg).The time of mechanical ventilation,duration of ICU stay and postoperative complications were compared between the two groups.Results The time of mechanical ventilation of B group was shorter than that of A group [(8.6 ± 2.5) d vs (11.7 ± 3.2) d],duration of ICU stay of B group was shorter than that of A group [(11.4 ± 4.8) d vs (15.6 ± 5.7) d],there were statistical differences between two groups(P ＜ 0.0l).The incidence rate of ventilator associated pneumonia and pneumothorax were 6.3％ and 3.1％ in A group,which were 5.6％ and 5.6％ in B group,there were no statistical differences between two groups (P ＞ 0.05).Conclusion The effects of mechanical ventilation with larger tidal volumes is better than that with lower tidal volumes in infants with congenital heart disease postoperative therapy. Key words: Tidal volumes; Mechanical ventilation; Congenital heart disease; Infants
Synthesis of Discounted-Reward Optimal Policies for Markov Decision Processes Under Linear Temporal Logic Specifications.

We present a method to find an optimal policy with respect to a reward function for a discounted Markov decision process under general linear temporal logic (LTL) specifications. Previous work has either focused on maximizing a cumulative reward objective under finite-duration tasks, specified by syntactically co-safe LTL, or maximizing an average reward for persistent (e.g., surveillance) tasks. This paper extends and generalizes these results by introducing a pair of occupancy measures to express the LTL satisfaction objective and the expected discounted reward objective, respectively. These occupancy measures are then connected to a single policy via a novel reduction resulting in a mixed integer linear program whose solution provides an optimal policy. Our formulation can also be extended to include additional constraints with respect to secondary reward functions. We illustrate the effectiveness of our approach in the context of robotic motion planning for complex missions under uncertainty and performance objectives.
Room temperature deposition of superconducting niobium nitride films by ion beam assisted sputtering

We use room temperature ion beam assisted sputtering to deposit niobium nitride thin films. Electrical and structural characterizations were performed by electric transport and magnetization measurements at variable temperatures, X-ray diffraction, and atomic force microscopy. Compared to reactive sputtering of niobium nitride, films sputtered in the presence of an ion beam show a remarkable increase in the superconducting critical temperature Tc, while exhibiting lower sensitivity to nitrogen concentration during deposition. Thickness dependence of the superconducting critical temperature is comparable to films prepared by conventional methods at high substrate temperatures and is consistent with behavior driven by quantum size effects or weak localization.
Book Review of Roots of Yoga (Mallinson and Singleton, 2017).

Roots of Yoga. Translated and edited with an introduction by James Mallinson and Mark Singleton. London: Penguin Books, 2017. Paperback. xl + 540 pages
Gaspar, Frank X. The Poems of Renata Ferreira. Tagus, 2020.

The celebrated Portuguese-American poet and novelist Frank X. Gaspar is not known for his experimentalism. He is also not known for being provocative or fomenting controversy. His seven previous books could be neatly organized into two categories: poetry (5) and novels (2). The Poems of Renata Ferreira may change that. It is as subversive a book as it is unclassifiable.
Manipulating the torsional mode in pipe-like structures with mechanical lens for extended propagation distance

Guided wave ultrasonic testing (GWUT) has been commercially used in pipelines since the last two decades. T(0,1), the axisymmetric torsional mode, is one of the preferred wave modes in GWUT because it is nondispersive. In this study, the T(0,1) plane wave within a steel pipe is generated using an array of d35 piezoelectric actuators attached around the pipe circumference. A previously designed mechanical lens built of gradient-index phononic crystal is implemented to extend the propagation distance of torsional wave mode by reducing attenuation. The decrease in attenuation is achieved by manipulating the refractive properties of the propagating elastic waves such that the wave energy is focused at a specific point along the pipe. Time-dependent finite element simulations show that the amplitude of the signal received at the focal point is amplified by approximately 80%. Experiments validate the excitation of T(0,1) mode but not the wave focusing as the adhesive layer creates a band gap by changing the dispersion characteristics. Moreover, findings from the numerical studies involving unit cell and full-sized pipe models and are presented. The two-dimensional Fast Fourier Transform on full-pipe models confirms that the pipe with GRIN lens is more sensitive to overall thickness change within the pipe wall, in agreement with the unit cell simulations. The sensitivity of the GRIN lens depends on the location around the pipe circumference in the case of localized defects. Experiments with T(0,1) focusing need to be explored further considering the adhesive.
Does Mode of Access Make a Difference? Mobile Learning and online student engagement

Even though student use of mobile devices for educational purposes has increased in recent years, the research on the possible impact on student success or engagement has been minimal. This study investigated the impact of mobile device use on student engagement and student success in online courses. The theory of Self-Regulated Learning (SRL) was a foundation for understanding and measuring engagement behaviors of online students. The Online Self-Regulated Learning Questionnaire (OSLQ) was the basis of the survey instrument. Participants were categorized into three groups of mobile device use (low, moderate, high). These three groups were used for comparison in each of the research questions. The research questions ask what impacts mobile learning has on student engagement, as measured with SRL; what impact mobile learning has on the SRL constructs of environment structuring, task management, and time management; and what associations mobile learning might have with student success and persistence. The ANOVA showed that mobile learning had a moderate impact on engagement for students in the high group. Students in each group engaged in environment structuring behaviors more than task strategies or time management behaviors. Students in the moderate and high groups engaged in task strategies more than the low group. Students in the high group engaged in time management behaviors more than the other groups. The Crosstab analysis did not show an association between levels of mobile learning and course grade or persistence. These findings have positive implications for online pedagogy and course design. Keywords : Mobile Learning; online learning; student engagement; Self-Regulated Learning; student success
Field Equations for Thermoelastic Bodies with Uniform Symmetry

In a purely mechanical theory of inhomogeneous bodies formulated recently by Noll [1] and Wang [2] two basic assumptions are used: material uniformity and smoothness. In this paper, I generalize that theory in two respects: First, I replace the assumption of material uniformity by a similar but somewhat weaker assumption of symmetry uniformity. That is, I require the points of a body to have the same mate rial symmetry rather than the same material response. Clearly, material uniformity implies symmetry uniformity, but the converse is not true in general. Second, I consider thermodynam-ical state variables and state functions in this paper, and I derive the thermodynamical field equations for inhomogeneous bodies.
Analytical inversion formula for attenuated fan-beam projections

In single photon emission computed tomography (SPECT), photon attenuation within the body is a major factor contributing to the quantitative inaccuracy in measuring the in vivo distribution of radioactivity. Usually the attenuation of the body is not uniform, but for brain imaging, it can be a good approximation to assume that the attenuation is uniformly distributed. For 2D parallel-beam geometry, an exact convolution backprojection algorithm to reconstruct image from attenuated Radon transform with constant attenuation had been developed by Tretiak and Metz (1980). The algorithm can be modified for attenuated fan-beam projections. Unlike the attenuated parallel-beam projections, the filter for attenuated fan-beam projections is no longer spatially invariant, instead, it is a space-variant filter. The algorithm with this spatially variant filter will take more computation time than the algorithm with convolution, but is an exact algorithm. This algorithm has been implemented and simulated using a mathematical phantom. Compared with parallel-beam reconstructions, fan-beam reconstructions have the same image quality.
Tensions and tradeoffs in a design for science classroom: the forces in balloon lecture

"Design for science" curricula employ engineering-type design challenges as means for students to learn science concepts as well as skills in science and design. Teaching science in the context of engineering design, however, is not straightforward; it creates certain tensions and requires tradeoffs. This paper represents part of a larger study that examines and describes tensions and tradeoffs in a "design for science" classroom, Learning by Design™. We examine tensions in a lecture on forces in which the teacher finds herself challenged to build representational bridges between students' designed artifacts and abstract science concepts. Constrained by time and difficulty of the concepts, the teacher chooses a tradeoff that uses a lecture to provide students a model for the science underlying their designs. Our examination reveals the teacher's struggle with representation, the requirement that she engage in modeling, and the importance of in-depth pedagogical content knowledge to successful design-based science instruction.
Investigating the Function of Rho Family GTPases during Salmonella/Host Cell Interactions

Abstract Salmonella enterica comprise a family of pathogenic gram‐negative bacteria that have evolved sophisticated virulence mechanisms to enter non‐phagocytic cells. The entry event is the result of a carefully orchestrated modulation of Rho family GTPase activity within the host cell, which in turn triggers localized remodeling of the actin cytoskeleton. These cytoskeletal rearrangements drive profuse membrane ruffling and lamellipodial extensions that envelop bacteria and trigger their internalization. This chapter describes a number of methods used to investigate the role of Rho family GTPases during Salmonella/host cell interactions. In particular, we detail a variety of complementary techniques, including affinity pull‐down assays and bacterial‐induced membrane ruffling and internalization assays to show that Salmonella‐induced actin remodeling and entry require the Rho family members Rac and RhoG.
Dialysis Access Procedures

Hemodialysis is the main modality for renal replacement therapy in patients with end-stage renal disease. Successful hemodialysis is contingent upon the creation of proper vascular access. Chronic vascular access was first established in 1960 by Scribner and colleagues, who created a shunt between the radial artery and the cephalic vein using an external Silastic device (Quinton et al. 1960). However, this device was fraught with problems such as bleeding, clotting, and infection. In 1966, Breschia and colleagues described a surgical fistula between the radial artery and the cephalic vein just proximal to the wrist, thereby eliminating the external shunt and enabling a high-flow system for hemodialysis. To this day, it remains the procedure of choice for patients with end-stage renal disease in need of chronic hemodialysis.
Neurodegenerative disease and the neuroimmunobiology of glutamate receptors

Publisher Summary This chapter presents a brief introduction to the family of glutamate receptors, which provide the principal means of fast-excitatory neurotransmission in the brain, and discusses their likely role in the progression of many neurodegenerative diseases. A hallmark of many neurodegenerative diseases is the extraordinary speciﬁcity through which they progress through the nervous system. Even in the severest forms of neurodegeneration, it is not uncommon to find that discrete regions of the brain are destroyed, while adjacent regions are spared. Neurotransmission in the brain involves the balanced activity of excitatory and inhibitory neurotransmitter receptor systems acting through ligand-activated ion channel receptors. Glutamate-activated ligand-gated ion channels (GluRs) are the primary receptors responsible for fast excitatory-neurotransmission in the brain and their activation is central to physiological processes associated with learning and memory. The chapter discusses the role of the immune system in neurologic diseases and the ways in which the speciﬁcity of the immune system can be utilized to explore the way the GluR family contributes to the etiology and regional speciﬁcity of neurodegenerative disease progression.
The Challenge of Rethinking History Education: On Practices, Theories, and Policy

Introduction 1. Seeking a More Potent Approach to Teaching History 2. On the Limits of Collective Memorialization and Persistent Instruction 3. The Case of Thomas Becker-Using Knowledge of History as a Domain to Structure Pedagogical Choices 4. Learning History-What Do Students Know and What Can they Do With That Knowledge? 5. Teaching About Indian Removal-Describing and Unpacking the Investigative Approach 6. Assessing Student Learning 7. Theorizing Investigative History Teaching 8. How Are History Teachers to Learn to Teach Using an Investigative Approach?
Building blocks of development [robot learning]

This article provides a brief introduction to hierarchical discriminant regression and lobe component analysis, two algorithms usable in components of the mental architecture of an AMD system. The processes that guide the development of the "mind" of an autonomously-learning robot must be given within the developmental program. This is what must drive the learning of the robot's eventual behaviors and skills, which emerges in response to the robot's interactions with the environment. A biologically sophisticated version of a developmental program, where behaviors and skills autonomously emerge in the robot with a human level of complexity, has not yet been written. But there has been progress in creating developmental "building blocks." These are designed to be used in components of the developmental program. These algorithms must be specially designed to handle many of the difficult constraints of AMD. In this article, we introduce two such algorithms, briefly outline their purpose and key features, and describe how to use sample versions available on the El lab's Web site
Mechanical characterization of slope sediments: Constraints on in situ stress and pore pressure near the tip of the megasplay fault in the Nankai accretionary complex

We performed mechanical tests on mudstone samples cored in the hanging wall of a major out of sequence thrust fault in the Nankai accretionary complex prism, SW Japan, (1) to understand the consolidation and shear behaviors of slope sediments that form the fault zone and wall rock of this important structural feature in the upper several kilometers, and (2) to constrain in situ stresses and pore pressure, two fundamental parameters governing deformation processes in subduction zones, which are notoriously difficult to measure. We conducted deformation experiments on a suite of samples taken from depths of 20–150 mbsf, including six uniaxial consolidation tests and one isotropic consolidation test. For three of these tests, we conducted undrained triaxial compression testing following consolidation. Our results suggest that in situ pore pressure is hydrostatic and that during sedimentation and burial, the effective horizontal stress is ∼41% of the effective vertical stress. In combination with analysis of wellbore failures documented during drilling of the borehole, our experimental data allow us to define the complete stress tensor, including the magnitude of in situ minimum and maximum horizontal stresses, in the hanging wall of this major fault zone. The maximum horizontal stress magnitude is comparable to that expected for sedimentation and uniaxial burial, whereas the minimum horizontal stress lies below this value. This suggests (1) that the shallow sedimentary section was subjected to extension subparallel to the trench during or following burial and (2) that stresses associated with plate convergence are not effectively transmitted within these shallow sediments.
Site requirements for the reactions of CH3SH and (CH3)2S2 on ZnO(101¯0)

Temperature programmed desorption (TPD) was used to investigate the adsorption and reaction of CH3SH and (CH3)2S2 on the nonpolar (101¯0) surface of ZnO. Methanethiol was found to dissociate on the (101¯0) surface to produce adsorbed methylthiolates. The primary reaction pathways for the methylthiolates were methyl group transfer between adjacent thiolates to produce (CH3)2S at 510 K, and transfer of methyl groups to surface lattice oxygen to produce adsorbed methoxides which were oxidized to CH2O at 525 K and adsorbed formate. Dimethyldisulfide was found to dissociate via cleavage of the S–S bond to form adsorbed methylthiolates. The reaction pathways for thiolates produced in this manner were similar to those produced from CH3SH except for an additional low-temperature pathway for the production of CH2O. Comparison of the results obtained in this study to our previous study of the reaction of CH3SH and (CH3)2S2 on ZnO(0 0 0 1) and published STM studies of ZnO(101¯0) and ZnO(0 0 0 1) indicates that step edges are the active sites for the reaction of thiols and disulfides on these surfaces.
Compactified Jacobians and q,t-Catalan numbers, II

We continue the study of the rational-slope generalized q,t-Catalan numbers c m,n (q,t). We describe generalizations of the bijective constructions of J. Haglund and N. Loehr and use them to prove a weak symmetry property c m,n (q,1)=c m,n (1,q) for m=kn±1. We give a bijective proof of the full symmetry c m,n (q,t)=c m,n (t,q) for min(m,n)≤3. As a corollary of these combinatorial constructions, we give a simple formula for the Poincare polynomials of compactified Jacobians of plane curve singularities x kn±1=y n . We also give a geometric interpretation of a relation between rational-slope Catalan numbers and the theory of (m,n)-cores discovered by J. Anderson.
Isolation of Hematopoietic Stem Cells from Mouse Embryonic Stem Cells

This unit describes a protocol for the isolation of cells from murine embryonic stem cells with hematopoietic stem cell activity, defined by the ability to reconstitute, long term, multiple lineages of the hematopoietic system of lethally irradiated mice. The protocol subjects hematopoietic progenitors specified in differentiating embryoid bodies to ectopic HoxB4 expression (delivered via retroviral infection), followed by coculture and expansion on OP9 stromal cells in the presence of hematopoietic cytokines for 10 days. The protocol results in the generation of hundreds of millions of cells that can rescue mice from lethal irradiation. Although little is known about the phenotype and frequency of the actual hematopoietic stem cell-like cell within the population of cells generated by this protocol, the protocol establishes a system in which these cells can be further studied and the results ultimately translated to the human system.
Modeling large electorates with Fourier series, with applications to Nash equilibria in proximity and directional models of spatial competition

In this paper we introduce harmonic analysis (Fourier series) as a tool for characterizing the existence of Nash equilibria in two-dimensional spatial majority rule voting games with large electorates. We apply our methods both to traditional proximity models and to directional models. In the latter voters exhibit preferences over directions rather than over alternatives, per se. A directional equilibrium can be characterized as a Condorcet direction, in analogy to the Condorcet (majority) winner in the usual voting models, i.e., a direction which is preferred by a majority to (or at least is not beaten by) any other direction. We provide a parallel treatment of the total median condition for equilibrium under proximity voting and equilibrium conditions for directional voting that shows that the former result is in terms of a strict equality (a knife-edge result very unlikely to hold) while the latter is in terms of an inequality which is relatively easy to satisfy. For the Matthews [3] directional model and a variant of the Rabinowitz and Macdonald [7] directional model, we present a sufficiency condition for the existence of a Condorcet directional vector in terms of the odd-numbered components of the Fourier series representing the density distribution of the voter points. We interpret our theoretical results by looking at real-world voter distributions and direction fields among voter points derived from U.S. and Norwegian survey data.
Total energies of diamond (111) surface reconstructions by a linear combination of atomic orbitals method

An ab initio linear combination of atomic orbitals approach to local-density theory, capable of handling complex structural geometries, is presented. It incorporates a self-consistent treatment of interatomic charge transfer, which allows an accurate calculation of total energies. The method is applied to study a variety of possible 1 x 1 and reconstructed 2 x 1 models of the diamond (111) surface. Among the many models suggested, only the Pandey ..pi..-bonded chain model has a lower energy than that of the 1 x 1 surface. A minimum-energy structure is obtained for this model after extensive consideration of relaxations. No dimerization of the surface chain is found to occur.
Substrate specificity of the glutathione dehydrogenase (dehydroascorbate reductase) from wheat flour

The substrate specificity of the glutathione dehydrogenase (dehydroascorbate reductase; EC 1.8.5.1) from wheat flour was determined at low substrate concentrations, which are of interest with respect to the improver action of dehydroascorbic acid (DHAA). L -Threo-DHAA was the best and D -threo-DHAA the worst substrate (20% activity relative to L -threo-DHAA) of the four DHAA stereoisomers. The activity of the enzyme towards both erythro-DHAA lies between the threo stereoisomers, but their ranking is dependent on the molar ratio of the erythro-DHAA to the glutathione, 1,2,3-Trioxocyclopentane was reduced at least as rapidly as the L -threo-DHAA. The enzyme was specific for glutathione as hydrogen donor; L -cysteinyl- L -glycine was not active as hydrogen donor.
Relationship between radioreceptor assay and radioimmunoassay estimates of prolactin in rat pituitary tissue, incubation medium, and serum: effects of dialysis on measurements of the hormone.

The relationships between radioreceptorassay (RRA) and RIA estimates of PRL in rat pituitary tissue, in medium in which rat adenohypophyses were incubated, and in serum were determined. The RRA involved l25I-labeled ovine PRL and hepatic PRL receptors from female rats which bore a PRL-secreting pituitary tumor (MtTWl5). A homologous RIA from rat PRL was used for comparison. Highly significant correlations were obtained between both assays with the three types of samples, with r values of 0.90,0.97, and 0.94, respectively. Regression analyses revealed that the RRA estimates of PRL in pituitary homogenate and incubation medium were slightly but significantly higher than those obtained with the RIA, but the RRA measured about 3.5 times more PRL in serum than did the RIA. The results indicate that the RRA gives estimates of PRL in rat serum that are, relative to RIA measurements, quantitatively similar to those obtained previously by bioassay. However, the RRA is subject to some degree of nonspecific interfer...
Histopathologic follow‐up and human papillomavirus DNA test results in 290 patients with high–grade squamous intraepithelial lesion papanicolaou test results

BACKGROUND: The study documents histopathologic outcomes and high-risk (hr) human papillomavirus (HPV) test results in a large cohort of patients with high-grade squamous intraepithelial lesion (HSIL) liquid-based cytology (LBC) Pap test results. METHODS: A total of 352 patients with HSIL results (338 cervical and 14 vaginal) who had hrHPV testing and 290 patients with biopsy follow-up were studied. hrHPV detection rates were compared at different ages, with or without an endocervical/transformation zone sample (EC/TZS), and for cervical and vaginal HSIL Pap smears. Histopathologic follow-up findings were also compared. hrHPV-negative HSIL slides were re-evaluated in a blinded manner. RESULTS: A total of 325 of 338 (96.2%) cervical HSIL and 12 of 14 (87.5%) vaginal HSIL tested hrHPV-positive. A total of 271 of 281 (96.4%) EC/TZS-positive cervical HSIL and 54 of 57 (94.7%) EC/TZS-negative cervical HSIL tested hrHPV-positive. The percentage of hrHPV-positive HSIL declined slightly with increasing age. 197 of 273 (72.3%) hrHPV-positive cervical HSIL had histopathologic cervical intraepithelial neoplasia (CIN) 2/3+ follow-up, including 8 squamous carcinomas, compared with 4 of 12 (33.3%) hrHPV-negative HSIL with CIN2/3 (no carcinomas). 167 of 241 (69.2%) EC/TZS-positive HSIL had CIN2/3+ follow-up, compared with 34 of 44 (77.3%) EC/TZS-negative HSIL. Equivocal HSIL morphology characterized some HPV-negative HSIL without CIN2/3+ follow-up. CONCLUSIONS: hrHPV was detected in LBC vials from 96.2% of 338 cervical HSIL and 85.7% of 14 vaginal HSIL. CIN2/3+ was significantly more likely with hrHPV-positive cervical HSIL than with hrHPV-negative cervical HSIL. Presence or absence of an EC/TZS did not significantly impact HSIL hrHPV or CIN2/3+ rates. Some hrHPV-negative HSIL cases may represent HSIL cytologic mimics. Cancer (Cancer Cytopathol) 2011;. © 2011 American Cancer Society.
Application of Artificial Immune System in Structural Health Monitoring

A large number of methods have been proposed in the area of structural health monitoring (SHM). However, many of them rely on the prior knowledge of structural-parameter-values or the assumption that the structural-parameter-values do not change without damage. This dependence on specific parameter values limits these methods’ applicability. This paper proposes an artificial immune system- (AIS-) based approach for the civil structural health monitoring, which does not require specific parameter values to work. A linear three-floor structure model and a number of single-damage scenarios were used to evaluate the proposed method’s performance. The high success rate showed this approach’s great potential for the SHM tasks. This approach has merits of less dependence on the structural-parameter-values and low demand on the training conditions.
THE ANAEROBIC DISSIMILATION OF D-GLUCOSE-1-C14, D-ARABINOSE-1-C14, AND L-ARABINOSE-1-C14 BY AEROBACTER AEROGENES

D-Glucose-1-C14, D-arabinose-1-C14, and L-arabinose-1-C14 were dissimilated anaerobically by Aerobacter aerogenes. The major products (2,3-butanediol, ethanol, acetic acid, lactic acid, formic acid...
The role of Caudal transcription factors during segmentation of the nervous system and paraxial mesoderm

The segmental nature of the embryo is most evident within the paraxial mesoderm during the formation of somites and within the nervous system during the formation of hindbrain rhombomeres. Classic and modern embryological experiments show that the posterior neural plate gives rise to the hindbrain and spinal cord portions of the central nervous system. Then, the hindbrain is subdivided into neuromeres that are required for proper structural patterning of the adult brain stem while the spinal cord remains unsegmented, although able to receive signaling cues from the adjacent mesoderm to organize its neuronal populations into an iterative pattern. What sets up the difference between segmented and unsegmented regions? Here, we use genetic and molecular approaches in zebrafish to address the mechanisms involved in the determination of the hindbrain and spinal cord regions from a common posterior neural plate territory. In all species studied so far, including zebrafish, members of the Caudal (Cdx) family of homeobox transcription factors are required for proper development of the most posterior regions of the embryo. We examined hindbrain and spinal cord neuronal populations in zebrafish embryos lacking cdx1a and cdx4 activities. Single cdx1a or cdx4 depleted embryos show mild shifts in the distribution of these neuronal populations. In contrast, double cdx1a/cdx4-deficient embryos display the presence of hindbrain neuronal populations throughout the trunk and tail of the animal and the absence of spinal cordspecific neuronal markers. In addition, hox expression analysis in double mutants reveals the presence of extra neuromeres that are arranged in a mirror image duplication pattern to the native hindbrain segments. Our data suggest that members of the Cdx family of homeobox transcription factors are required to suppress segmentation of the posterior portion of the neural plate and thus allow the development of the spinal cord. We further suggest that a common mechanism involving cdx genes may play a role in the segmentation of both the nervous system and the paraxial mesoderm.
Arctic and Antarctic climatology of a GLAS general circulation model

A Jan.-Feb. climatology model was constructed from the GLAS general circulation model by averaging eight 30-day means of periods from Jan. 15-Feb. 14. The position and intensity of the Aleutian and Icelandic lows in the winter, the central Arctic pressure distribution during winter and summer, and the summertime North Atlantic and North Pacific high pressure regimes were satisfactorily simulated; sensible and evaporative heat fluxes and radiation budget parameters were reasonable, although a rigorous comparison is difficult due to data deficiencies. The model is less successful in simulating the Southern Hemisphere climatology; the 500 mb circumpolar flow is adequate, but the stationary low pressure centers at the surface around the Antarctic continent are not well reproduced.
On the Non-Approximability of Points-to Analysis

Determining points-to sets is an important static-analysis problem. Most of the classic static analyses (used e.g., by compilers or in programming environments) rely on knowing which variables might be used or defined by each expression in a program. In the presence of pointers, the use/def set of an expression like *p = *q can only be determined given (safe) points-to sets for p and q. Previous work has shown that both precise flow-sensitive and precise flow-insensitive pointer analysis is NP-Hard, even when restricted to single-procedure programs with no dynamic memory allocation. In this paper, we show that it is not even possible to compute good approximations to the precise solutions (i.e., to compute points-to sets whose sizes are within a constant factor of the sizes of the precise points-to sets) unless P=NP.
The STICH trial: misguided conclusions.

gestive heart failure (CHF) after ischemic dilated cardiomyopathy following myocardial infarction because the authors conclude that adding surgical ventricular reconstruction to reduce ventricular volume to coronary artery bypass grafting (CABG) does not improve symptoms or exercise tolerance and fails to lower death rate or cardiac rehospitalization. The original study examined the role of surgical ventricular reconstruction or ‘‘surgical ventricular restoration’’ (SVR) in the dilated ventricles of patients with CHF with regional scar after anterior myocardial infarction (Figure 1). The adverse effects of dilatation are codified by White and associates 2 (Figure 2,A), who showed that increased ventricular volume rather than altered ejection fraction became the principal surrogate for mortality. Dor 3 showed that the SVR procedure excludes the underlying culprit scar that causes stretch of compensating remote muscle, identified similar regional noncontraction from either aneurysm or akinetic segments that received thrombolysis or angioplasty, and demonstrated that rebuilding left ventricular (LV) size and shape toward normal improves cardiac efficiency by restoring remote muscle function. The keynote finding of similarly absent function in aneurysm without reperfusion (in which the thinned scar collapses during venting) and akinesia after reperfusion (in which the thick myocardium with inner shell scar is covered by normal anterior myocardium that does not collapse during venting) introduced a ‘‘new SVR target’’ and initiates ‘‘a learning curve’’ for procedure application. SVR after CABG is based on an international database registry of more than 5000 patients. 3-5 This database (Figure 3) demonstrates favorable survival compared with CHF natural history studies 6 and a CABG patient cohort whose abnormal ejection fraction and class III/IV New York Heart Association classification matched the RESTORE (Reconstructive Endoventricular Surgery, returning Torsion Original Radius Elliptical Shape) group registry cohort 4,7 in National Heart, Lung, and Blood Institute STICH grant application and the worldwide SVR registry. A prospective randomized trial was designed for ‘‘evidence based medicine’’ confirmation. The 490 STICH trial patients requiring SVR did not show survival or rehospitalization differences compared with the greater than 5000 patient registry SVR database, thereby raising this question: Is SVR an improper concept or did the STICH trial have improper execution? The solution to this question will determine whether STICH results provide credible data that guide the treatment of patients with CHF. We conclude that it did not, and this editorial supports this deduction with trial evidence, reports casualties of the STICH findings, poses new questions requiring answers, and outlines future STICH report meaningful data analysis that may properly respond to grant questions.
Ex vivo static tensile loading inhibits MMP-1 expression in rat tail tendon cells through a cytoskeletally based mechanotransduction mechanism

To determine the effect of various degrees of ex vivo static tensile loading on the expression of collagenase (MMP-1) in tendon cells, rat tail tendons were statically loaded in tension at 0.16, 0.77, 1.38 or 2.6 MPa for 24 h. Northern blot analysis was used to assay for mRNA expression of MMP-1 in freshly harvested, 24 h load deprived, and 24 h statically loaded tendons. Western blot analysis was used to assay for pro-MMP-1 and MMP-1 protein expression in fresh and 24 h load deprived tendons. Freshly harvested rat tail tendons demonstrated no evidence of MMP-1 mRNA expression and no evidence of the pro-MMP-1 or MMP-1 protein. Ex vivo load deprivation for 24 h resulted in a marked increase in the mRNA expression of MMP-1 which coincided with a marked increase of both pro-MMP-1 and MMP-1 protein expression. When tendons were subjected to ex vivo static tensile loading during the 24 h culture period, a significant inhibition of this upregulation of MMP-1 mRNA expression was found with increasing load (p<0.05). A strong (r2=0.78) and significant (p<0.001) inverse correlation existed between the level of static tensile load and the expression of MMP-1. Disruption of the actin cytoskeleton with cytochalasin D abolished the inhibitory effect of ex vivo static tensile loading on MMP-1 expression. The results of this study suggest that up-regulation of MMP-1 expression in tendon cells ex vivo can be inhibited by static tensile loading, presumably through a cytoskeletally based mechanotransduction pathway.
Physical models for predicting the performance of Si/Si, AlGaAs/GaAs, and Si/SiGe solar cells

Abstract Analytical and physical models for homojunction and heterojunction solar cells are developed, and the performances of solar cells made by the Si/Si homojunction and made by the increasingly important and popular AlGaAs/GaAs and Si/SiGe heterojunctions compared. The models developed, which include relevant device physics such as the effective surface recombination velocity at the high-low junction and band discontinuities associated with heterojunctions, correctly explain the solar cell characteristics experimentally observed. Our calculations suggest that the highest efficiencies attainable for AlGaAs/GaAs, Si/Si, and Si/SiGe cells, with optimized doping concentrations but without surface passivation and geometry optimization, are 21.25%, 17.8% and 13.5%, respectively, under 1 AM1.5 sun condition. For concentrator cell applications, the efficiencies improve to about 24.5%, 22.2%, and 22.0% for AlGaAs/GaAs, Si/Si, and Si/SiGe cells, respectively, under 100 AM1.5 suns. While the AlGaAs/GaAs cell possesses the highest efficiency among the three cells, the Si/Si and Si/SiGe cells can achieve a satisfactory conversion efficiency at high sun concentration (22% at 100 suns), making them attractive for concentrator cell applications because their processing is the same as or is compatible with existing silicon technology. Model predictions for two Si/Si and one AlGaAs/GaAs cells compare favorably with data reported in the literature.
Fractures of the Humerus in Dogs and Cats A Retrospective Study of 130 Cases

Case histories of 130 dogs and cats with humeral fractures were reviewed. The different types of fractures were classified. Most animals with proximal, shaft, and supracondylar fractures had excellent results. The poor prognosis associated with distal articular fractures was due most often to failure of the fixation device in the supracondylar area; best results were achieved with a plate on the caudal and medial surface of the distal humerus.
Silicon-on-sapphire epitaxial bipolar transistors

Abstract All-epitaxial bipolar transistors have been fabricated in silicon-on-sapphire films which exhibit a common-emitter low frequency current gain hfe of 10 at room temperature. The value of hfe increases approximately as the square of the absolute temperature, which suggests recombination by charged coulomb centers in the base region. Monotonic increase in hfe with collector current up to 100 mA (emitter dimensions are 0.8 × 1.2 mil) is probably due to trap-filling in the base region. No conductivity modulation, which would result in beta fall-off, is seen up to 500 mA of collector current. This is a consequence of the narrow (0.6 μ), heavily-doped (∼ 1017 cm−3) base region. High-frequency measurements indicate an fT of 350 MHz at 15 mA and extrapolation of a plot of 1 f T vs. 1 I e yields a base transit time of 350 psec. Minority carrier lifetime in the base region is measured to be 0.6–0.9 nsec. The silicon is deposted on single crystal sapphire oriented in the [1102] plane which results in the growth of [100]-oriented silicon. Arsenic and boron are used as the dopants in the n+, n, p, n+ structure. The total film thickness is approx 6 μ and the transistor structure contains a mesa-emitter and mesa-collector.
A quality comparison of breads baked by conventional versus nonconventional ovens: A review

Undesirable qualities of breads baked in nonconventional ovens have been observed by most researchers. The altered heat and mass transfer patterns and much shorter baking times associated with microwave radiation resulted in a crustless product with tougher, coarser, but less firm texture. Insufficient starch gelatinization, microwave-induced gluten changes, and rapidly generated gas and steam caused by the heating mode could be reasons for quality changes in the microwave-baked breads. Although breads baked in an electrical resistance oven did not brown, their interior characteristics and shelf-life were superior to those of products baked in a conventional oven. Bread with a superior keeping quality was obtained using an air impingement convection oven. The determination and explanation of the physical and biochemical changes that occur in products during baking in conventional versus nonconventional ovens are fruitful areas for future research.
Changes in the digestible lysine and sulfur amino acid needs of broiler chicks during the first three weeks posthatching

Four experiments were conducted to study the changes in the digestible lysine (DLYS) and sulfur amino acid (DSAA) requirements of broilers during the first 21 d posthatching. Cobb 500 by-product male broilers were fed corn-corn gluten meal-soybean meal diets formulated to be isocaloric and isonitrogenous. Five graded levels of either Lys or SAA were used, varying from 0.78 to 1.28% DLYS (experiments 1 and 2) and from 0.61 to 1.08% DSAA (experiments 3 and 4). Body weight gain (BWG) and gain:feed ratio (GF) were calculated at 4, 7, and 21 d. The DLYS requirements based on BWG varied from 0.98 at 4 d of age to 1.01% at 21 d in experiment 1 and from 0.95 at 4 d of age to 0.99% at 21 d, in experiment 2. Based on GF, the DLYS requirement varied from 1.08 to 1.10% in experiment 1, and from 0.98 to 0.94% in experiment 2 at 4 and 21 d, respectively. The estimated DSAA requirements for BWG varied from 0.83 to 0.88% or from 0.71 to 0.75% for 4 and 21 d in experiments 3 and 4, respectively. For GF, the DSAA decreased slightly from 0.88% at 4 d to 0.83% at 21 d in experiment 3, but did not change in experiment 4 (0.81%). Minimal changes in the DLYS or DSAA estimated requirements occurred during the first 21 d of age, which suggests that the recommended DLYS and DSAA levels determined at 21 d of age appear to be adequate to meet chick needs for the first week of age.
Gibbs-Duhem integration: a new method for direct evaluation of phase coexistence by molecular simulation

A method that combines the best elements of thermodynamic integration and the Gibbs ensemble technique is proposed for the direct evaluation of phase equilibria by molecular simulation. Given the conditions of coexistence at a single state point, simultaneous but independent NPT simulations of each phase are performed in succession along the saturation line. In each simulation, the pressure is adjusted to satisfy chemical potential equality according to the Gibbs-Duhem equation. Each coexistence point is determined by just one simulation, and particle insertions are never performed or attempted. Vapourliquid coexistence for the Lennard-Jones model is evaluated, and extensions are discussed.