cssi/SciSciGPT-SciSciNet huggingface dataset:
Deep learning of free boundary and Stefan problems

Abstract Free boundary problems appear naturally in numerous areas of mathematics, science and engineering. These problems present a great computational challenge because they necessitate numerical methods that can yield an accurate approximation of free boundaries and complex dynamic interfaces. In this work, we propose a multi-network model based on physics-informed neural networks to tackle a general class of forward and inverse free boundary problems called Stefan problems. Specifically, we approximate the unknown solution as well as any moving boundaries by two deep neural networks. Besides, we formulate a new type of inverse Stefan problems that aim to reconstruct the solution and free boundaries directly from sparse and noisy measurements. We demonstrate the effectiveness of our approach in a series of benchmarks spanning different types of Stefan problems, and illustrate how the proposed framework can accurately recover solutions of partial differential equations with moving boundaries and dynamic interfaces. All code and data accompanying this manuscript are publicly available at https://github.com/PredictiveIntelligenceLab/DeepStefan .
Phase 1 study of combinatorial sorafenib, G-CSF, and plerixafor treatment in relapsed/refractory, FLT3-ITD-mutated acute myelogenous leukemia patients.

Stroma-leukemia interactions mediated by CXCR4, CD44, VLA4, and their respective ligands contribute to therapy resistance in FLT3-ITD-mutated acute myelogenous leukemia (AML). We conducted a phase 1 study with the combination of sorafenib (a FLT3-ITD inhibitor), plerixafor (a SDF-1/CXCR4 inhibitor), and G-CSF (that cleaves SDF-1, CD44, and VLA4). Twenty-eight patients with relapsed/refractory FLT3-ITD-mutated AML were enrolled from December 2010 to December 2013 at three dose levels of sorafenib (400, 600, and 800 mg twice daily) and G-CSF and plerixafor were administered every other day for seven doses starting on day one. Sorafenib 800 mg twice daily was selected for the expansion phase. While no dose-limiting toxicities (DLT) were encountered in the four-week DLT window, hand-foot syndrome and rash were seen beyond the DLT window, which required dose reductions in most patients. The response rate was 36% (complete response (CR) = 4, complete remission with incomplete platelet recovery (CRp) = 4, complete remission with incomplete hematologic recovery (CRi) = 1, and partial response (PR) = 1) for the intention to treat population. Treatment resulted in 58.4 and 47 mean fold mobilization of blasts and CD34 /38- stem/progenitor cells, respectively, to the circulation. Expression of the adhesion molecules CXCR4, CD44, and VLA4 on circulating leukemia cells correlated negatively with the mobilization of CD34+/38-, CD34+/38-/123+ "progenitor" cells (all P ≤ .002). Mass cytometry analysis of sequential samples from two patients demonstrated resistance emerging early on from sub-clones with persistent Akt and/or ERK signaling. In conclusion, the strategy of combined inhibition of FLT3 kinase and stromal adhesive interactions has promising activity in relapsed/refractory, FLT3-ITD-mutated AML, which warrants further evaluation in the front-line setting.
Modeling of Magnetic Properties of Magnetorheological Elastomers Using JA Hysteresis Model

Magnetorheological elastomers (MREs) are composite materials that consist of magnetically permeable particles in a nonmagnetic polymeric matrix. Under the influence of an external magnetic field, a reversible deformation change occurs in the mechanical properties of these materials. Due to their coupled magnetomechanical response, these materials have been found suitable for a range of applications including tunable vibration absorbers, sensors, and actuators. Notably, improvement of such devices are prerequisites to efficient energy conversion systems, hence the need to understand further the MRE technology. The Jiles–Atherton (JA) theory takes into consideration the magneto-coupling experienced by effective domains in a magnetic material. Algorithm based on the theory yields five model parameters; saturation magnetization ( ${M} _{\mathbf {s}}$ ), domain density ( ${a}$ ), domain coupling ( $\alpha $ ), loss coefficient ( ${k}$ ), and reversibility ( ${c}$ ). Using JA theory, model parameters were calculated and linked to the physical attributes of Fe powder and isotropic MRE. The results show that the calculated ${M} _{\mathbf {s}}$ for the MRE is reasonably related to that of the Fe powder by a factor of the particle’s volume fraction used in the MRE. The calculated ${k}$ , ${a}$ , and $\alpha $ provided support for the reduced pinning factor, domain density, and increased domain coupling in the MRE due to the changes in the domain structure between the two materials. From the calculated JA parameters, finite-element modeling (FEM) of the MRE hysteresis loop was performed. The analysis showed that the modeled magnetic properties including coercivity, remanence, and coordinates of the hysteresis loop tip vary with geometric position.
Effects of Hurricane Irma on the Endangered Lower Keys Marsh Rabbit

Sylvilagus palustris hefneri (Lower Keys Marsh Rabbit [LKMR]) is an endangered subspecies of marsh rabbit found only in the Lower Florida Keys. In September 2017, Hurricane Irma was measured as a Category 4 storm when it passed through the center of the LKMR range causing significant damage to human infrastructure and natural habitats. To assess the impact of Hurricane Irma to LKMR and its habitat, we compared pre- and post-hurricane monitoring data. Overall, 82% of LKMR habitat patches were abandoned, the average number of pellets per sampling plot decreased 94%, and average patch pellet density decreased by 84% following Hurricane Irma. Generally, pellets were found in plots with greater open cover, an intermediate amount of herbaceous and woody cover, and areas with more standing water post-Hurricane Irma. We also observed a slight decrease in signs of Procyon lotor (Raccoon) and Didelphis virginiana (Virginia Opossum). The decrease in rabbit pellets detected after Hurricane Irma is likely attributed to both direct mortality from the storm and flooding, as well as indirect mortality from the loss of critical, salt-sensitive herbaceous cover. Because climate-change models suggest increases in future flooding and hurricane frequency, we recommend that wildlife managers continue to closely monitor the recovery of LKMR populations and their habitat to determine if more active management actions (e.g., habitat remediation, translocations, or captive breeding) are necessary.
Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice

Food allergy is a potentially fatal disease affecting 8% of children and has become increasingly common in the past two decades. Despite the prevalence and severe nature of the disease, the mechanisms underlying sensitization remain to be further elucidated. The Collaborative Cross is a genetically diverse panel of inbred mice that were specifically developed to study the influence of genetics on complex diseases. Using this panel of mouse strains, we previously demonstrated CC027/GeniUnc mice, but not C3H/HeJ mice, develop peanut allergy after oral exposure to peanut in the absence of a Th2-skewing adjuvant. Here, we investigated factors associated with sensitization in CC027/GeniUnc mice following oral exposure to peanut, walnut, milk, or egg. CC027/GeniUnc mice mounted antigen-specific IgE responses to peanut, walnut and egg, but not milk, while C3H/HeJ mice were not sensitized to any antigen. Naive CC027/GeniUnc mice had markedly lower total fecal IgA compared to C3H/HeJ, which was accompanied by stark differences in gut microbiome composition. Sensitized CC027/GeniUnc mice had significantly fewer CD3+ T cells but higher numbers of CXCR5+ B cells and T follicular helper cells in the mesenteric lymph nodes compared to C3H/HeJ mice, which is consistent with their relative immunoglobulin production. After oral challenge to the corresponding food, peanut- and walnut-sensitized CC027/GeniUnc mice experienced anaphylaxis, whereas mice exposed to milk and egg did not. Ara h 2 was detected in serum collected post-challenge from peanut-sensitized mice, indicating increased absorption of this allergen, while Bos d 5 and Gal d 2 were not detected in mice exposed to milk and egg, respectively. Machine learning on the change in gut microbiome composition as a result of food protein exposure identified a unique signature in CC027/GeniUnc mice that experienced anaphylaxis, including the depletion of Akkermansia. Overall, these results demonstrate several factors associated with enteral sensitization in CC027/GeniUnc mice, including diminished total fecal IgA, increased allergen absorption and altered gut microbiome composition. Furthermore, peanuts and tree nuts may have inherent properties distinct from milk and eggs that contribute to allergy.
A Brief Analysis of Popular Aesthetics in Thailand: Subjective Culture vs. Objective Culture

This paper deals with changes in popular aesthetics in Thailand. Following Georg Simmel’s dialecticdyad of subjective culture and objective culture, it is argued that popular aesthetics in Thailand...
Sister, Sister! Siblings With Simultaneous Early Femoral Insufficiency Fractures After Total Knee Arthroplasty.

Abstract Early periprosthetic fractures after total knee arthroplasty are rare but devastating complications which require revision surgery and lead to poor patient satisfaction. We present 2 siblings who underwent primary total knee arthroplasty on the same day and then both presented 2 weeks after surgery with atraumatic periprosthetic femur fractures. The first patient underwent revision for a cemented distal femoral replacement with stemmed tibial fixation. The second patient underwent an isolated femoral component revision with a stemmed femoral component and distal augment. Histological evaluation identified significant peri-implant osteoporosis. The variation in complexity associated with early periprosthetic femoral insufficiency fractures is highlighted by these 2 cases. Surgeons may consider using stemmed femoral components in similar patients if poor distal femoral bone stock is encountered intraoperatively.
Differential expression of single-cell RNA-seq data using Tweedie models

Summary The performance of computational methods and software to identify differentially expressed genes in single-cell RNA-sequencing (scRNA-seq) has been shown to be influenced by several factors, including the choice of the normalization method used and the choice of the experimental platform (or library preparation protocol) to profile gene expression in individual cells. Currently, it is up to the practitioner to choose the most appropriate differential expression (DE) method out of over 100 DE tools available to date, each relying on their own assumptions to model scRNA-seq data. Here, we propose to use generalized linear models with the Tweedie distribution that can flexibly capture a large dynamic range of observed scRNA-seq data across experimental platforms induced by heavy tails, sparsity, or different count distributions to model the technological variability in scRNA-seq expression profiles. We also propose a zero-inflated Tweedie model that allows zero probability mass to exceed a traditional Tweedie distribution to model zero-inflated scRNA-seq data with excessive zero counts. Using both synthetic and published plate- and droplet-based scRNA-seq datasets, we performed a systematic benchmark evaluation of more than 10 representative DE methods and demonstrate that our method (Tweedieverse) outperforms the state-of-the-art DE approaches across experimental platforms in terms of statistical power and false discovery rate control. Our open-source software (R package) is available at https://github.com/himelmallick/Tweedieverse.
The Burden of Drowning: Issues in Selected Countries - The United States

Drowning is the fifth leading cause of unintentional injury death in the United States of America (USA). In 2010, a total of 4,038 persons drowned – including 256 persons who drowned while boating. This corresponds to a death rate of 1.3/100,000 population. The age-adjusted death rate has remained relatively stable for the 15 years preceding 2010, but has decreased by half since 1979 (2.9–1.3/100,000). Furthermore, more than 7,000 nonfatal drowning incidents occur each year in the USA resulting in emergency department visits. Examples of prevention strategies include barriers like pool fencing, swimming skill and bystander cardiopulmonary resuscitation; however, these have not been adopted widely.
To Write of Repeated Patterns

THEY SAY HE'S 16. They say in the dead of the night they really do say this, "the dead of the night" ?he sneaks to the attic, planned or unplanned nobody yet knows, he lifts his daddy's "squirrel gun" from its case, then sneaks back down with it, carefully opens the door to the room in which they're sleeping, and blasts them out of this life, one shot to the temple each, in quick succession. The neighbors are interviewed, ". . . shocked" "... a wonderful boy" "... he loved his parents." Then the camera brings him into its painfully clear-edged imagery. He's seated behind a desk at headquarters, confused by himself, by everything and everyone. He doesn't look over 12, a limp rag doll of a child, being questioned for parricide. Skyler and I are at Sarah's and Eric's. "Change the channel!" What we'd wanted was mild diversion floating in over our afternoon beers. There's TV snow and lightningbolts; then, a couple of numbers up or down the dial, the news is into its loonier wrap-up phase: "There was three of them, three feet high. They was green." A trucker spotted them trotting down a play ground-slideish gangplank "from a silver ship. It looked like, you know ..." ". . . A shark's fin fitted with lateral wings," the one other observer, a priest, chimes in. A priest? "They peered around, returned to the ship, and took off. That's all. I think they were trying to bring us a message." Tonight, while Skyler's asnooze, I'm up with a book. It says, in the voice of classical lamentation, "A man looks on his own son as his enemy. The heart is aggressive, blood is everywhere, no office functions properly. The rich wake poor, the poor wake rich, the land whirls around like a pot ter's wheel." Verily. The television yeasayeth this with every snoopy cam corder shot of a Presidential rally or a weekend convention of skateboard and dirtbike enthusiasts. Some group of PTA sex education fanatics, cos tumed ? la birds and bees. Some show of support for a local pastor in jail on charges of fondling a 10-year-old girl. The remains of an airliner: yes, a three member suicide squadron smuggled a plastic gun on board in six unrecognizable segments. "Everywhere men are killed wrongfully." This text, however, is from the Egyptian Old Kingdom ?2500 b.c. Some nights ?this isn't the first time I've consulted it after overmuch media brouhaha?its cannily contempo applicability leaves me shaking my
Development of a near anesthetic-free isolated canine hindlimb model: The effects of halothane and atropine sulfate on vascular resistance

A denervated, isolated canine hindlimb (HL) model was developed to minimize residual anesthetic contamination. To test the preparation, we determined the peripheral arterial vascular effects of atropine sulfate and the effect of the basal anesthetic on arterial resistance. In four dogs that were under halothane and oxygen anesthesia, the HL was prepared to allow either vascular isolation of the limb or continuity with the systemic circulation. During isolation the HL was perfused by roller pump at a preset flow rate through an infant oxygenator. Inspired gas fed to the oxygenator contained either 0%, 1.25%, or 2.5% halothane to determine that anesthetic's effect on HL arterial vascular resistance. No halothane (0%) was used in the oxygenator inflow during the atropine measurements. Vascular resistance was calculated from HL arterial pressure at constant flow. Halothane caused a significant stepwise fall in vascular resistance, with a decrease of 68% at 2.5% inspired concentration (p < 0.01). Atropine produced a progressive attenuation of resistance that decreased by 18% after the 2.5 mgkg dose (p< 0.01). The model proved stable over time and demonstrated an apparent direct, dose-dependent vasodilating effect of both atropine and halothane in the canine HL muscle arterial bed.
Nutritional Composition of Complementary Infant Foods: Evidence from 109 Commercially Marketed Products in 22 Low-Income Countries

To sustain healthy growth, infants from about 6 to 23 months of age need to complement breastmilk with solid foods that are more nutrient-dense and prepared more frequently during the day than the ...
Reducing the Ising model to matchings

Canonical paths is one of the most powerful tools available to show that a Markov chain is rapidly mixing, thereby enabling approximate sampling from complex high dimensional distributions. Two success stories for the canonical paths method are chains for drawing matchings in a graph, and a chain for a version of the Ising model called the subgraphs world. In this paper, it is shown that a subgraphs world draw can be obtained by taking a draw from matchings on a graph that is linear in the size of the original graph. This provides a partial answer to why canonical paths works so well for both problems, as well as providing a new source of algorithms for the Ising model. For instance, this new reduction immediately yields a fully polynomial time approximation scheme for the Ising model on a bounded degree graph when the magnitization is bounded away from 0.
Assessing the fidelity of AOGCM‐simulated relationships between large‐scale modes of climate variability and wind speeds

The ability of atmosphere-ocean general circulation models (AOGCMs) to reproduce associations between surface/near-surface variables over the United States (US) and large-scale modes of climate variability has implications for evaluating possible biases in future climate projections and is an important model diagnostic. Indices of three such modes (El Nino–Southern Oscillation (ENSO), the Arctic Oscillation (AO), and the Pacific-North American (PNA) pattern) and their relationships to wind speeds over the contiguous US are derived using historical reanalysis products and then used to evaluate the fidelity of AOGCM simulations of both the climate modes and the teleconnections. In the reanalysis data, the response of middle and upper troposphere wind speeds to ENSO phase is found to be essentially symmetric with anomalies of opposite sign occurring during the warm and cold phases. The AO and PNA phases are both associated with higher wind speeds relative to “neutral” conditions. AOGCMs from Phase 5 of the Coupled Model Intercomparison Project (CMIP5) produce AO- and PNA-like spatial patterns which exhibit good accord with those from NCEP-NCAR Reanalysis. The AOGCM-derived climate indices also exhibit general agreement with reanalysis-derived indices in terms of the frequencies associated with highest variance, although the agreement is better for AO and PNA than it is for ENSO. The AOGCMs are in good agreement with the NNR in terms of representation of the influence of the AO and PNA on winds over the contiguous US. However, for ENSO, AOGCMs fail to consistently capture the observed relationship between La Nina and near-surface to middle troposphere winds.
Adaptive Sparse Sampling to Estimate Radiation and Scattering Patterns to a Specified Uncertainty with Model-Based Parameter Estimation: Compute patterns using as few as two to four samples per lobe.

Analyzing antennas and scatterers in electromagnetics usually involves evaluating far-field radiation and scattering patterns. For problems involving objects, a few wavelengths to an extent, the computing time needed to evaluate a far field is usually much less than that needed to find the source distribution on that object. As the object size increases, however, the time required to obtain the far field can become significant, especially for a monostatic scattering pattern where a new source distribution occurs for each incidence angle or for the radiation and receiving patterns of large complex objects. This is especially the case if the far field is to be sampled finely enough in angle to ensure that important features of the pattern are not missed.
Methodology and System for Practical Formal Verification of Reactive Hardware

Making formal verification a practicality in industrial environments is still difficult. The capacity of most verification tools is too small, their integration in a design process is difficult and the methodology that should guide their usage is unclear.
Dendritic voltage-gated ion channels regulate the action potential firing mode of hippocampal CA1 pyramidal neurons.

The role of dendritic voltage-gated ion channels in the generation of action potential bursting was investigated using whole cell patch-clamp recordings from the soma and dendrites of CA1 pyramidal...
Design of the iSCSI protocol

The iSCSI protocol enables accessing SCSI I/O devices over an IP network. TCP is used as a transport for SCSI I/O commands. We describe the design considerations and decisions in defining the iSCSI protocol: why we use TCP how multiple TCP connections can be used to increase performance and reliability, why we require allegiance of a command to a particular TCP connection, the importance of Direct Data Placement, various levels and complexity of error recovery, security and naming issues.
Correlation between changes in groundwater levels and surface deformation from GPS measurements in the San Gabriel Valley, California

[1] Changes in groundwater levels cause water-bearing basins to deform. Here we provide a detailed history of horizontal surface displacements in the San Gabriel Valley, California, which we show are highly correlated with the water level changes measured at a nearby well: correlation coefficient of 0.96 ± 0.01. We use the surface response from a one year period during which water level change in the nearby well was over 16 m, to monitor the deformations over a 14 year period from 1998 to 2011. The water level changes lead surface deformation by 21 days, but the significance of the offset is only weakly supported (p-value = 0.129). The projection method can be used as a real-time monitoring or detection system for deformation caused by a variety of mechanisms such as fluid injection and removal (groundwater development, oil production, carbon sequestration), and by seismic and volcanic activity.
Ultrashort TE Imaging of Cryotherapy

Cryotherapy is a promising, minimally invasive surgical technique that uses extremely cold temperatures to destroy localized tissue. As the extent and the outcome of freezing internal tissues cannot be directly visualized in real time, new approaches to monitor cyrotherapy procedures are required. MR imaging (MRI) provides an excellent tool for monitoring the frozen tissue boundary. To determine therapy end points, the tissue temperature is usually monitored with thermal probes. However, the placement of these probes is invasive and they provide information only at a limited number of discrete locations. Monitoring the temperature across the frozen tissue noninvasively with MRI is therefore important. Relating MR parameters to tissue temperature requires detecting the MR signal from the frozen tissue. This in turn requires the use of ultrashort echo time (UTE) pulse sequences to minimize signal loss resulting from the short T2* of frozen tissue. Using UTE MRI, parameters such as signal intensity (SI), T2* and/or R2*, and signal phase have shown promise for directly mapping the temperature of frozen tissue. MRI-guided temperature mapping has the potential to further improve the outcome of cryotherapy. Keywords: cryotherapy; temperature monitoring; ultrashort TE imaging; interventional MRI; radial acquisition; eddy current correction; T2* mapping; cryosurgery
Altered respiratory rhythm in a preBötzinger complex model due to addition of low-threshold, non-inactivating K+ current and tonic input

The preBotzinger complex (pBC), a region of the ventrolateral medulla, is critically important in the generation of respiratory rhythm [1]. Slice preparations containing the pBC produce rhythmic, fictive inspiratory activity in the absence of stimuli due to autorhythmic and state-dependent bursting neurons that play an unknown role in pattern formation in vivo. Respiratory rhythm is a dynamic process, modulated by input from sensory feedback, neural inputs, extracellular milieu and background excitability to the pBC pattern generator. We used the NEURON simulation environment to investigate modulators of excitability and their effects on inspiratory burst characteristics. Previous network models of the pBC have focused primarily on intracellular properties and synaptic connections; in this model we have added a background tonic drive component and more complex potassium dynamics to examine neural excitability and provide mechanistic insight into the variability we see in vitro. A network of 100 heterogeneous synaptically connected inspiratory cells based on an earlier inspiratory single-cell model [2] was created with twenty percent of cells assigned a conductance profile that allowed intrinsic bursting. A recently characterized low-threshold, non-inactivating (A-type) potassium current [3] was added. Shown in Figure 1, addition of the A-type current decreased baseline excitability, thereby decreasing frequency but did not change intra-burst behavior. A population of tonic-firing cells was created to produce output trains of Poisson-distributed presynaptic stimuli to inspiratory cells. The addition of background tonic stimulation is shown in Figure 2 where the addition of Poisson inputs has a direct impact on the variability of burst initiation and termination. A second modulator of excitability was added via extracellular potassium dynamics. In vitro, extracellular [K+] is commonly used to modulate neural excitability; to better model the effects of this pertubation, a Frankenhauser-Huxley space, a Na+/K+ pump and glial buffering system were added to the individual cells. Raising the extracellular bath concentration of potassium ions depolarize cells and positively shifts the from Eighteenth Annual Computational Neuroscience Meeting: CNS*2009 Berlin, Germany. 18–23 July 2009
Display Holography An SPIE Critical Review Of Technology

Holography has been enjoying an explosion of public interest over the past two years, especially as the number of three-dimensional laser photographs in peoples' homes has increased dramatically. Underlying this public perception of progress has been an authentic and gradual development of holographic imaging technology, but it is fair to say that holographers are still struggling against the same fundamental constraints as they were more than ten years ago. In business, "timing is everything," and the recent events in holography are largely business phenomena (it has always taken a lot of patience to be a holographer, and no less so in these matters!). In this discussion, we will attempt to draw out a few of the long-term threads of holographic progress that underlie the recent good news.
Electron-diffraction and theoretical investigation of the molecular structure of octafluorobicyclo[2.2.0]hex-1(4)-ene in the gas phase: Another example of a molecule with an unusually long C(sp3)-C(sp3) single bond

The molecular structure of octafluorobicyclo[2.2.0]hex-1(4)-ene has been measured in the gas phase by electron diffraction at room-temperature aided by results from molecular orbital theory. The results are consistent with D 2 h symmetry for the molecule. The bond distances (r g /A) and bond angles ( α /deg) with estimates of 2σ uncertainties are r(C 1 =C 4 ) = 1.376(14), r(C 1 -C 2 ) = 1.530(3), r(C 2 -C 3 ) = 1.627(5), r(C-F) = 1.336(2), and (F-C-F) = 108.6(3). The planes of the -CF 2 groups are tipped away from the bisector of the C-C-C angle toward each other by about 2.8°. The measured length of the C 2 -C 3 bond is even greater than the lengths of the structurally similar bonds in hexafluorocyclobutene and 1,2-dichloro-3,3,4,4-tetrafluoro-cyclobutene and agrees with prediction from quantum-mechanical structure optimizations at the B3LYP, B3PW91, and MP2 levels of theory. This and other features of the structure are discussed in terms of the bond-altering effects of electrostatic repulsions and rehybridization arising from electronegativity differences.
Organ Donors with Malignant Gliomas: An Update

The escalating shortage of organs motivates frequent reconsideration of concepts that guide the decision to accept or decline organs from donors with central nervous system (CNS) malignancy. Currently, a minority of patients who die annually of CNS malignancies are organ donors. Specifically, the organs of less than 0.5% of the 13 000 patients dying from glioma are procured and transplanted every year in the United States. This review seeks to clarify the risk of cancer transmission from transplantation of organs from donors with glioma. After considering historical precedence, we will systematically outline the clinical features of a potential organ donor with glioma that might reflect upon the risk of cancer transmission. We will then present recent knowledge regarding basic glioma biology that speaks to their metastatic potential and suggest rational strategies for the post-transplant management of recipients of organs from donors with glioma.
Edge effects in line intersect sampling with segmented transects

Transects consisting of multiple, connected segments with a prescribed configuration are commonly used in ecological applications of line intersect sampling. The transect configuration has implications for the probability with which population elements are selected and for how the selection probabilities can be modified by the boundary of the tract being sampled. As such, the transect configuration also affects the performance of methods designed to eliminate edge-effect bias. We show that the reflection method solves the edge-problem for designs that use symmetric radial transects (e.g., straight-line and X-shaped transects centered at the sample point). This method also applies to designs that use asymmetric radial transects, provided the orientation is selected uniformly at random. Asymmetric radial transects include straight lines emanating from the sample point, and L- and Y-shaped transects. The reflection method does not apply to designs where polygonal transects (e.g., triangular, square, and hexagonal transects) are used, or where the orientations of asymmetric radial transects are fixed. We provide a new method that eliminates edge-effect bias for designs that use asymmetric radial transects with fixed orientation, but a workable solution for polygonal transects remains elusive.
Generalization of a theorem on horizon radiation

Abstract A theorem on the horizon radiation, such as that observed in an accelerating system, or outside a black hole, is generalized to include fermion as well as boson fields and with arbitrary interactions. The relationship between the measurements made by an observer restricted within the horizon and the description of the state vector which extends beyond his horizon is analyzed.
Extreme points of Banach lattices related to conditional expectations

Abstract Let ( X , F , μ ) be a complete probability space, B a sub-σ-algebra, and Φ the probabilistic conditional expectation operator determined by B . Let K be the Banach lattice { f ∈ L 1 ( X , F , μ ) : ‖ Φ ( | f | ) ‖ ∞ ∞ } with the norm ‖ f ‖ = ‖ Φ ( | f | ) ‖ ∞ . We prove the following theorems: (1) The closed unit ball of K contains an extreme point if and only if there is a localizing set E for B such that supp ( Φ ( χ E ) ) = X . (2) Suppose that there is n ∈ N such that f ⩽ n Φ ( f ) for all positive f in L ∞ ( X , F , μ ) . Then K has the uniformly λ-property and every element f in the complex K with ‖ f ‖ ⩽ 1 n is a convex combination of at most 2n extreme points in the closed unit ball of K .
Sparse representation via ℓ 1 -minimization for underdetermined systems in classification of tumors with gene expression data

The development of cancer diagnosis models and cancer discovery from DNA microarray data are of great interest in bioinformatics and medicine. In pattern recognition and machine learning, a classification problem refers to finding an algorithm for assigning a given input data into one of several categories. Many natural signals are sparse or compressible in the sense that they have short representations when expressed in a suitable basis. Motivated by the recent successful algorithm developments for sparse signal recovery, we apply the selective nature of sparse representation to perform the above mentioned classification. In order to find such sparse representation we implement an l 1 -minimization algorithm. This methodology overcomes the lack of robustness with respect to outliers. In contrast to other classification algorithms, no model selection dependency is involved. The minimization algorithm is a convex relaxation-like that has been proven to efficiently recover sparse signals. To study its performance, the proposed method is applied to six tumor gene expression datasets and numerically compared with various support vector machine methods (SVM). The numerical results show that the l 1 -minimization algorithm proposed performs at least comparably and often better than SVMs.
Tissue compensation using dynamic collimation on a linear accelerator

PURPOSE: The availability of computer-controlled collimators on some accelerators has led to techniques for dynamic beam modification, mainly to simulate beam wedge filters. This work addresses the practical aspects of dynamic tissue compensation in one dimension using available treatment-planning software. METHODS AND MATERIALS: Data derived from the treatment-planning program is used with an iterative calculational routine to determine the monitor unit settings needed for the collimator-controlling computer. The method was first tested by simulating a 60 degrees physical wedge. Further studies were carried out on a specially fabricated plastic phantom that modeled the sagittal contour of the upper torso, neck, and lower head regions. RESULTS: Dynamic wedge point doses generated by the planning program agreed within 1% with the values directly measured in a polystyrene phantom. In the patient phantom, dynamic collimation achieved calculated dose uniformity within 0.5% in a reference plane near the phantom midline. A comparison of computer-generated and measured point doses in this case showed agreement within 3%. CONCLUSIONS: Dynamic collimation can provide effective compensation for contours that vary primarily along one direction. A conventional treatment-planning program can be used to plan dynamic collimation and deliver a prescribed dose with reliable accuracy.
SMN deficiency causes tissue-specific perturbations in the repertoire of snRNAs and widespread defects in splicing

The survival of motor neurons (SMN) protein is essential for the biogenesis of small nuclear RNA (snRNA)-ribonucleoproteins (snRNPs), the major components of the pre-mRNA splicing machinery. Though it is ubiquitously expressed, SMN deficiency causes the motor neuron degenerative disease spinal muscular atrophy (SMA). We show here that SMN deficiency, similar to that which occurs in severe SMA, has unexpected cell type-specific effects on the repertoire of snRNAs and mRNAs. It alters the stoichiometry of snRNAs and causes widespread pre-mRNA splicing defects in numerous transcripts of diverse genes, preferentially those containing a large number of introns, in SMN-deficient mouse tissues. These findings reveal a key role for the SMN complex in RNA metabolism and in splicing regulation and indicate that SMA is a general splicing disease that is not restricted to motor neurons.
Excitation Pathways of Rare Earth Ions by Energetic Electrons

Using cathodoluminescence measurements, we studied the excitation of rare earth ions in LiNbO 3 and compare it with previously studied Eu ions in GaN. We find that in both hosts and all dopants the most efficient excitation pathways involves a defect traps that capture the energy from the electron-hole pairs created in the host by E-beam irradiation. Even then the excitation efficiency in LiNbO 3 is very low. Moreover, only a small fraction ( -4 ) of the RE ions that are optically active can be excited through this pathway. We explain this behavior by a negligible direct excitation and a strong dependence of the excitation efficiency on the distance between the defect trap and the rare earth ion. The density of the defect traps is small such that many rare earth ions are far away from traps.
Petrogenetic linkages among fO2, isotopic enrichments-depletions and crystallization history in Martian basalts. Evidence from the distribution of phosphorus in olivine megacrysts

An important geochemical characteristic of the shergottites is the large range in initial Sr isotopic ratios and initial e^(Nd) values. The depleted olivine-phyric shergottites are commonly reduced (∼IW+1) and exhibit limited variation in fO_2 during crystallization, whereas the enriched olivine-phyric shergottites are more oxidized and exhibit a substantial variation in fO_2 during crystallization (∼IW+1 (1 log unit above the iron-wustite buffer) to FMQ+0.7 (0.7 log units above the fayalite-magnetite-quartz buffer). Using a reduced, depleted shergottite Y980459 (Y98) and an oxidized, enriched shergottite (NWA1183), we reconstructed the crystallization history of the olivine megacrysts using phosphorus zoning and placed trace element variation and indices of oxygen fugacity into the context of that crystallization history. The olivine megacrysts in Y98 and NWA1183 exhibited various episodes of growth defined by the P zoning. Common to both samples were continuous and discontinuous oscillatory chemical zoning in the outer portions of the olivine megacrysts. However, the morphologies of the cores suggest a xenocrystic origin for the core of Y98 and a phenocrystic origin for the core of NWA1183. Phosphorus in the olivine ranges from less than 0.02 to up to 0.70 wt.% P_2O_5. The P in the olivine megacrysts manifests subtle, but real differences, in the P content of different shergottite melts, incompatible element behavior of P during olivine crystallization, and solute trapping during periods of rapid olivine growth. Although P should behave incompatibly in basaltic systems, there is little relationship between the isotopic characteristics and P content in the enriched-depleted array of shergottites. In the olivine, Al is generally correlated with P enrichment and reflects a coupled substitution of P–Al. On the other hand, V is not correlated with P in Y98, but correlated with P in the oscillatory zoned regions of the olivine in NWA1183. The changes in correlation to P may reflect differences in V valance state during olivine crystallization. Within the crystallization histories defined by the P zoning in olivine, the calculated fO_2 remains fairly constant at ∼IW+1 for Y98, but changes dramatically for NWA1183 from olivine core to rim (∼IW+1.8 to FMQ+.07). Numerous lines of evidence suggest that the changes in fO_2 during olivine crystallization may reflect auto-oxidation that may be at least partially due to degassing of the NWA1183 magma prior to eruption. These observations suggest a limited variation in the fO_2 of the Martian mantle (IW to IW+1), that enriched and depleted sources for the shergottites reside in the mantle, and that magmas produced in these sources have different capabilities for changing their redox state during crystallization.
Response to preoperative chemoradiation in stage II and III rectal cancer.

PURPOSE: The purpose of this study was to determine whether a complete pathologic response after neoadjuvant therapy in rectal cancer patients improves disease control and survival. METHODS: The study reviewed Stage II and III rectal cancer patients treated with preoperative chemoradiation and resected for cure. Complete pathologic response was defined as no cancer in the resected specimen. The main outcome measures were cancer-specific and disease-free survival in patients achieving a complete pathologic response and a noncomplete pathologic response. Kaplan-Meier curves were evaluated using log-rank analysis. RESULTS: Eighty-nine rectal cancer patients received neoadjuvant chemoradiation followed by radical resection for cure. Twenty-one patients (24 percent) achieved a complete pathologic response. Median follow-up for the complete pathologic response group was 23.5 months and 31 months for the noncomplete pathologic response group. There were more Stage III patients in the noncomplete pathologic response group than the complete pathologic response group (P = 0.005). Complete pathologic response patients were less likely to receive postoperative adjuvant chemotherapy than noncomplete pathologic response patients (P = 0.004). Cancer-specific and disease-free survival were not statistically different between the two groups. However, a trend was noted toward improved survival and decreased recurrence in association with a complete pathologic response. CONCLUSION: Stage III patients were less likely to be in the complete pathologic response group than Stage II patients. Complete pathologic response patients were less likely to receive postoperative adjuvant chemotherapy than noncomplete pathologic response patients. Complete pathologic response after neoadjuvant chemoradiation for rectal cancer patients demonstrated a trend toward improved survival and decreased recurrence compared with noncomplete pathologic response patients.
Pulmonary Tuberculosis in University of Buffalo Medical Students

SUMMARY During a four year period 679 medical students were given intra-cutaneous tuberculin tests once annually and all, regardless of tuberculin reaction, were required to report three times each school year for a chest roentgenogram. There was an over-all incidence of 1.8 per cent significant pulmonary tuberculosis and in this group of 12 students there were two who demonstrated moderately advanced disease, nine in the minimal group and one with tuberculous pleural effusion. Five students developed their disease during the first year, three during the second year, none during the third year and four during the fourth year. One of the students with moderately advanced disease was a Freshman and his disease antedated admission to medical school since it was discovered on the first survey after admission. The percentage of tuberculin reactors in the entering Freshman classes averaged 22.6 per cent. Twenty-seven per cent of the students who entered as negative reactors became positive by the time they graduated. The average increase in percentage of reactors from the Freshman to Sophomore years was 5.9 per cent, from Sophomore to Junior 8.2 per cent, and Junior to Senior 7.2 per cent.
Arnold Arluke, Brute Force: Animal Police and the Challenge of Cruelty

Animals have been an important part of human society since time immemorial. Whether it is in association with hunting, exploiting them for their potential labor, or valuing them for the roles they play in providing comfort to humans, animals have been and are deeply embedded within human society. The treatment of animals by humans has even served as a marker for the “civilizing” trends of modern society. For instance, the American Society for the Prevention of Cruelty to Animals (ASPCA), founded in 1866 in New York City, preceded the institutionalization of the first child welfare agency, the New York Society for the Prevention of Cruelty to Children. The ASPCA led crusades against cruelty to animals and lobbied for legislation to protect a broad range of animals, years before the initiation of efforts to protect children. Similarly, some of the first environmental laws in the US were directed at regulating game animals and wildlife. What animals could be hunted and the “purpose” of hunting, whether for sport or for market profiteering, were subject to legal control. From a sociological perspective, these and other initiatives regarding animals speak volumes about the values and ideologies evident within human society. For several years, sociologists conducting human-animal studies have offered fresh insights into what the treatment of animals means for human society and social order. Whether it’s understanding animals for their potential to assist in the construction of the self, the relationship between animals and social problems such as inequality or violence, the occupational lives and careers of animal workers, or the significance of animals to social movements and social conflict, this work has explored themes central to mainstream sociology. Arluke’s book, Brute Force: Animal Police and the Challenge of Cruelty, provides further evidence of the value of sociological inquiry into human-animal relationships. Arluke offers a richly textured, and at times deeply disturbing, ethnography of the occupational practices, roles, and ideologies of humane law enforcement officers as they encounter, investigate, and prosecute incidents of animal cruelty. Like all skilled ethnographers, Arluke gained access to the subjective worldviews of his subjects by becoming an active participant in their daily
Anisotropic dielectric response and surface aging of mercuric iodide crystal studied by variable angle spectroscopic ellipsometry

Abstract Variable angle spectroscopic ellipsometry (VASE) was employed to study the anisotropic optical properties and surface aging phenomena of mercuric iodide (HgI 2 ) — a material for room-temperature radiation detectors. In the optical property study, two surface orientations of this tetragonal crystal were selected, i.e. an a-plane and a c-plane sample. Room temperature multiple-angle SE measurements from both samples with three different optical configurations along with polarized transmission measurements were analyzed simultaneously by the VASE analysis through multiple-sample, multiple-model methods. Anisotropic dielectric functions of single crystal HgI 2 , e ⊥ (ω) and e ‖ (ω), for optical electric field vectors oriented perpendicular and parallel to the c axis, respectively, were obtained over the range of 1.24–5.1 eV. In the surface aging characterization, three different initial HgI 2 surface conditions were selected, i.e. an as-grown surface, a cleaved surface, and a surface chemically etched by 10% KI solution. A model of the HgI 2 crystal including top surface roughness and subsurface defects was established and characterized, as a function of time, by the VASE analysis. In this model, the surface defects associated with the surface aging were modeled by the Bruggeman effective-medium approximation (EMA) as a HgI 2 /void mixed overlayer. The relative 2-dimensional (2D) surface-defect-densities were then monitored as the surface aging proceeded.
Complete primary structure of ribulosebisphosphate carboxylase/ oxygenase from Rhodospirillum rubrum☆☆☆

Abstract Of the 14 cyanogen bromide fragments derived from Rhodospirillum rubrum ribulosebisphosphate carboxylase/oxygenase, four are too large to permit complete sequencing by direct means [ F. C. Hartman, C. D. Stringer, J. Omnaas, M. I. Donnelly, and B. Fraij (1982) Arch. Biochem. Biophys. 219 , 422–437]. These have now been digested with proteases, and the resultant peptides have been purified and sequenced, thereby providing the complete sequences of the original fragments. With the determination of these sequences, the total primary structure of the enzyme is provided. The polypeptide chain consists of 466 residues, 144 (31%) of which are identical to those at corresponding positions of the large subunit of spinach ribulosebisphosphate carboxylase/oxygenase. Despite the low overall homology, striking homology between the two species of enzyme is observed in those regions previously implicated at the catalytic and activator sites.