gebhart/patrepeval huggingface dataset:
Slipped Capital Femoral Epiphysis (1996)

We reviewed 59 hips in 44 children with slipped capital femoral epiphysis (SCFE), all treated by in situ pinning. The average clinical and radiographic follow-up was 11.4 years. Fifty-three hips (90%) were rated as either excellent or good. Osteonecrosis or chondrolysis developed in five patients. Postoperative remodeling was noted, not only by a process of local resorption and apposition of bone, but also by correction of the disturbed anatomic axes, in proportion to the severity of the slip, together with global thickening of the femoral neck. We believe that the good long-term results after in situ pinning are the consequence of this important remodeling process.
Gastric Retentive Drug Delivery Systems (2011)

This chapter contains sections titled: Introduction Physiological considerations for gastric retentive drug delivery systems Early developmental work on the gastric retentive delivery devices Physical approaches to gastric retentive drug delivery systems Conclusions References
Static and dynamic disorder in protein folding: Experiments with single Maltoporin channels (2003)

Static and dynamic disorder in protein folding: Experiments with single Maltoporin channels
Parallelization of programs containing loop-carried dependences with resource constraints (1994)

This dissertation proposes scheduling methods for parallelizing programs containing two types of common loops with loop-carried dependencies (LCD's): parallel prefix computation (PPC) and band linear recurrences (BLR). They are major bottlenecks of parallel computations of many important programs (e.g., some Grand Challenge Problems).
My dissertation is based on the belief that a good computer research should bring innovative conceptual advances that will have practical impacts, and these new ideas must be supported with useful theories, and must be validated by implementation.
As such, I propose a new scheduling method, called Harmonic Scheduling (HS). HS is a technique for design space exploration of parallel schedules for evaluation of BLR's. Using HS, I have found time-optimal parallel schedules for PPC (also known as scan) with resource constraints. I have also derived new classes of parallel schedules for computing BLR's with resource constraints and shown that they achieve the optimal time for first and second-order BLR's.
Using HS, I have derived the Regular Schedules, which are scalable and have regular computation structures. Using regular schedules, I have developed a method for parallel programming loops containing PPC and BLR's intermixed with other code. Using the Regular-Schedule-based programming method, we obtained significant performance improvement for a range of benchmark programs on the Convex C240 vector supercomputer, over the same programs coded using highly-optimized BLAS (Basic Linear Algebra System) routines--which are the best available, hand-coded assembly routines for vector parallel computers.
I have also applied HS to the design of special-purpose parallel architectures for computing infinite-impulse response (IIR) filters in digital signal processing (DSP). HS can be used as a tool for design space exploration in both performance-driven and resource-driven system-level design of these architectures in CAD environments. I found the rate-optimal schedules for IIR filters on a class of VLSI architectures with differing types of functional units. Based on this result, I generated the first scalable design for IIR filters using multi-chip module (MCM) technology. Previous designs are not scalable due to the loop-carried dependence bottlenecks. Using HS, I also explored design space of scalable architectures implementing IIR filters based on MCM's and scalable interconnect, and demonstrated that the design space for IIR filter architectures by applying HS is only bound by hardware limits whereas the design space using previous scheduling methods is very limited due to LCD's in the programs.
Directing polymorph specific calcium carbonate formation with de novo protein templates (2023)

Abstract Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals 1–5 , but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain unknown 6–8 . We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we designed helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and found that both protein monomers and protein-Ca 2+ assemblies directly nucleate nano-calcite with non-natural (110) or (202) faces while vaterite, which forms first absent the proteins, is bypassed. The nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials. One sentence summary De novo designed protein templates promote nucleation of nano-calcite and direct its growth by oriented particle attachment.
Abstract 372: Master Transcriptional Regulators of Cardiac Gene Expression in Heart Failure (2018)

Background: Heart failure (HF) is characterized by complex transcriptional networks that direct the heart from a healthy to diseased state. Although some contributing genes have been identified through molecular biology and GWAS, heritability studies suggest that many genes have resisted discovery through these approaches. Identifying connective regulatory loci, especially master transcriptional regulators that affect the expression of many genes, offers a promising means of discovering novel relevant genes that have not been detected with other methods. Methods and Results: Transcriptional regulators of HF were identified using nine-week-old female mice from 93 lines of the Hybrid Mouse Diversity Panel. Mice received 30 ug/g/day of isoproterenol (ISO) for 3 weeks to induce cardiac dysfunction. Transcriptomes were generated from left ventricles of these mice along with age-matched controls. Expression Quantitative Trait Loci (eQTLs) for 13,156 transcripts were identified using a mixed model in three conditions (control, treated, delta). Suggestive (P&lt;1E-4) eQTLs were sorted into 500kb bins tiled across the genome to identify loci that regulate a significant number of transcripts. Ten hotspot loci that regulate over 5% (658 of 13156) of expressed genes were identified, several of which contain genes with known roles in HF, including Drosha , Akap5 and Dicer1 . Several novel regulators were also identified, including the Serine Proteinase Inhibitor, Serpina3n , which resides in a locus that regulates the change in expression of 9.7% (1276 of 13156) of all genes and is strongly correlated with changes in heart weight after ISO treatment. In subsequent in vitro work, Serpina3n knockdown resulted in reduced cellular hypertrophy, changes to hypertrophy-related gene expression, and modulation of the expression of several genes linked to its locus. Conclusion: GWAS performed on over 20,000 transcripts in control and ISO-treated hearts identified 10 genomic loci that regulate over 5% of the expressed genes in the heart. Serpina3n is a novel master regulator of HF. Further analysis of other master regulatory loci will reveal additional genes and improve our understanding of the transcriptional networks that direct the progression towards heart failure.
Two related but differentially expressed potential membrane proteins encoded by the EcoRI Dhet region of Epstein-Barr virus B95-8 (1985)

Three mRNAs in the EcoRI Dhet region of Epstein-Barr virus B95-8 were mapped. Their 3' ends are coterminal. A latent gene containing three exons is transcribed from the ED-L1 promoter and was predicted to lead to expression of a 42-kilodalton protein. An unspliced late mRNA is produced by transcription from the ED-L1A promoter within the first intron of the above gene and was predicted to lead to expression of a 28-kilodalton protein corresponding to the C-terminal two-thirds of the 42-kilodalton protein. Both proteins would have hydrophobic N-terminal domains and highly acidic C-terminal domains and were predicted to span the cell membrane. An early promoter (ED-L2) is located in the 3' untranslated region of the above genes and was predicted to lead to expression of a 6.5-kilodalton polypeptide containing a C-terminal hydrophobic region.
A Highly Active Aqueous Olefin Metathesis Catalyst Bearing a Quaternary Ammonium Group (2007)

A polar olefin metathesis catalyst that bears a quaternary ammonium group was prepared from commercially available reagents. The electron-withdrawing quaternary ammonium group not only activates the Ru catalyst electronically but at the same time makes the catalyst more hydrophilic. The catalyst can therefore be efficiently used both in traditional media, such as dichloromethane and toluene, as well as in technical-grade alcohols, alcohol-water mixtures and in neat water. Various metathesis reactions, including ring-closing, cross- and enyne metathesis, were conducted in these solvents in the presence of air. In addition, the Ru catalyst can act as an inisurf (initiator and surfactant) molecule, promoting metathesis under heterogeneous aqueous conditions.
DISTORTION OF TRACKS IN BUBBLE CHAMBER (1959)

Dexmedetomidine has clinically relevant benefits compared with midazolam in facilitating extubation due to its shorter time to extubation, more hemodynamic stability, easy arousability, and lack of respiratory depression.
Constitutively active receptor tyrosine kinases as oncogenes in preclinical models for cancer therapeutics (2006)

Receptor tyrosine kinases (RTK) remain an area of therapeutic interest because of their role in epithelial tumors, and experimental models specific to these targets are highly desirable. Chimeric receptors were prepared by in-frame fusion of the CD8 extracellular sequence with the cytoplasmic sequences of RTKs. A CD8HER2 fusion protein was shown to form disulfide-mediated homodimers and to transform fibroblasts and epithelial cells. CD8RTK fusion proteins transform rat kidney epithelial cells and impart phenotypes that may reflect signaling specificity inherent in the native receptors. Transgenic expression of CD8HER2 and CD8Met in mice resulted in the formation of salivary and mammary gland tumors. The transgenic tumors allow the derivation of allograft tumors and cell lines that are sensitive to inhibition by small molecule kinase inhibitors. This approach provides excellent cell and tumor models for the characterization of signaling properties of diverse RTKs and for the evaluation of rationally designed antagonists targeting these kinases.
Biomedical Informatics in the Desert - A New and Unique Program at Arizona State University (2008)

As one of the newest academic BMI programs is taking shape in Arizona, it is embarking on a wide-ranging educational program and a broad research agenda that are now in their earliest stages.
Overexpression of Interleukin-4 in the Thyroid of Transgenic Mice Upregulates the Expression of Duox1 and the Anion Transporter Pendrin (2016)

This is the first study to show that ectopic expression of IL-4 in thyroid tissue upregulates Duox1/Duoxa1 and Slc26a4 expression in the thyroid. The present data demonstrate that IL-4 could affect thyroid morphology and function, mainly by downregulating Slc5a5 expression, while maintaining a normal euthyroid phenotype.
Shoot4U (2016)

Virtual Machine based approaches to workload consolidation, as seen in IaaS cloud as well as datacenter platforms, have long had to contend with performance degradation caused by synchronization primitives inside the guest environments. These primitives can be affected by virtual CPU preemptions by the host scheduler that can introduce delays that are orders of magnitude longer than those primitives were designed for. While a significant amount of work has focused on the behavior of spinlock primitives as a source of these performance issues, spinlocks do not represent the entirety of synchronization mechanisms that are susceptible to scheduling issues when running in a virtualized environment. In this paper we address the virtualized performance issues introduced by TLB shootdown operations. Our profiling study, based on the PARSEC benchmark suite, has shown that up to 64% of a VM's CPU time can be spent on TLB shootdown operations under certain workloads. In order to address this problem, we present a paravirtual TLB shootdown scheme named Shoot4U. Shoot4U completely eliminates TLB shootdown preemptions by invalidating guest TLB entries from the VMM and allowing guest TLB shootdown operations to complete without waiting for remote virtual CPUs to be scheduled. Our performance evaluation using the PARSEC benchmark suite demonstrates that Shoot4U can reduce benchmark runtime by up to 85% compared an unmodified Linux kernel, and up to 44% over a state-of-the-art paravirtual TLB shootdown scheme.
High-brightness fiber-coupled diode laser module (1998)

Based on a pair of step-mirrors for beam rearranging we coupled the emission of three high-power diode laser arrays into an optical fiber of 800 micrometer diameter. We compressed the fast axis collimated beams of three diode lasers in respect to their fast axes by means of a step prism and symmetrized the beam parameter product by reordering the radiation which is focused into a fiber then. By simple optimization a coupling efficiency of 70% can be obtained.
Microstructures of YBa2Cu3O7−x superconducting thin films grown on a SrTiO3(100) substrate (1988)

We report microstructures of superconducting YBa2Cu3O7−x thin films epitaxially grown on a SrTiO3(100) substrate. Transmission electron microscopy studies reveal epitaxial, highly ordered grains ∼5000 Å in size for both types of films with either the a or c axis perpendicular to the film. Defects due to out-of-phase boundaries are observed in the former case. The high density of twin boundaries found in the latter case seems to correlate with the higher Jc observed in thin-film samples.
3D Star Skeleton For Fast Human Posture Representation (2008)

In this paper, we propose an improved 3D star skeleton technique, which is a suitable skeletonization for human posture representation and reflects the 3D information of human posture. Moreover, the proposed technique is simple and then can be performed in real-time. The existing skeleton construction techniques, such as distance transformation, Voronoi diagram, and thinning, focus on the precision of skeleton information. Therefore, those techniques are not applicable to real-time posture recognition since they are computationally expensive and highly susceptible to noise of boundary. Although a 2D star skeleton was proposed to complement these problems, it also has some limitations to describe the 3D information of the posture. To represent human posture effectively, the constructed skeleton should consider the 3D information of posture. The proposed 3D star skeleton contains 3D data of human, and focuses on human action and posture recognition. Our 3D star skeleton uses the 8 projection maps which have 2D silhouette information and depth data of human surface. And the extremal points can be extracted as the features of 3D star skeleton, without searching whole boundary of object. Therefore, on execution time, our 3D star skeleton is faster than the "greedy" 3D star skeleton using the whole boundary points on the surface. Moreover, our method can offer more accurate skeleton of posture than the existing star skeleton since the 3D data for the object is concerned. Additionally, we make a codebook, a collection of representative 3D star skeletons about 7 postures, to recognize what posture of constructed skeleton is.
<title>Innovation of laser ITT with specially developed integrated laser accessories</title> (1998)

One of the most successful methods for the treatment of malignant and benign tumors is the thermal denaturation of tissue induced by absorbed light from a laser. Our LITT fiber products are emitting a spherical light profile along the entire length of up to 35 mm. A special spherical laser power meter was designed to measure the integral laser power. An exact coagulation zone can be obtained by varying laser power and application time. For faster treatment a beam splitter is built to apply up to four fibers with one laser unit. This allows the treatment of larger or metastatic tumors. In combination with a stable laser system a maximum of patients safety is obtained and the physical strain is reduced.
DNA Tests for Genetic Genealogy (2020)

Abstract This chapter covers the different types of direct to consumer DNA tests for genealogy. They are technically similar but a bit different from those used for medical and health conditions, as genealogy tests focus on identifying “matches,” or relatives who’ve also tested based on shared SNPs or other similarities. Consumers can choose from autosomal DNA, Y-chromosome, and mtDNA tests, depending on their interests and research goals. Unlike the other tests, genealogy DNA tests compare your results with those of others and predict a relationship based on the amount of DNA you share. This adds an extra layer of complexity but is no less rewarding, and the findings can be no less surprising. Understanding how these tests work and what they show enables consumers to choose the specific ones that will be most helpful in compiling their genetic genealogy.
Thermal donors formation via isothermal annealing in magnetic Czochralski high resistivity silicon (2006)

A quantitative study about the thermal activation of oxygen related thermal donors in high resistivity p-type magnetic Czochralski silicon has been carried out. Thermal donor formation has been performed through isothermal annealing at 430°C up to a total time of 120min. Space charge density after each annealing step has been measured by transient current technique. The localized energy levels related to thermal double donors (TD) have been observed and studied in details by thermally stimulated currents (TSCs) in the range of 10–70K, and activation energies E and effective cross sections σ have been determined for both the emissions TD0∕+ (E=75±5meV, σ=4×10−14cm2) and TD+∕+ (E=170±5meV, σ=2×10−12cm2). The evolution of the space charge density caused by annealing has been unambiguously related to the activation of TDs by means of current deep level transient spectroscopy TSC, and current transients at constant temperature i(t,T). Our results show that TDs compensate the initial boron doping, eventually provoking the sign inversion of the space charge density. TD’s generation rate has been found to be linear with the annealing time and to depend critically on the initial interstitial oxygen concentration, in agreement with previous models developed on low resistivity silicon.
Human Immunodeficiency Virus Type 1 Tat Induces Apoptosis and Increases Sensitivity to Apoptotic Signals by Up-Regulating FLICE/Caspase-8 (1999)

Apoptosis contributes to the loss of CD4 cells during human immunodeficiency virus type 1 (HIV-1) infection. Although the product of the env gene, gp160/gp120, is known to play a role in cell death mediated by HIV-1, the role of other HIV-1 genes in the process is unclear. We found that HIV-1 lacking the env gene (HIVDeltaenv) still induced apoptosis in T-cell lines and primary CD4 T cells. The ability to induce apoptosis was attributable to Tat, a viral regulatory protein. Tat induction of apoptosis was separate from the transactivation function of Tat, required expression of the second exon of Tat, and was associated with the increased expression and activity of caspase-8 (casp-8), a signaling molecule in apoptotic pathways. Moreover, induction of apoptosis could be prevented by treating cells with an inhibitor of casp-8. In addition, we show that HIV-1Deltaenv infection and Tat expression increased the sensitivity of cells to Fas-mediated apoptosis, an apoptotic pathway that signals via casp-8. The up-regulation of casp-8 by HIV-1 Tat expression may contribute to the increased apoptosis and sensitivity to apoptotic signals observed in the cells of HIV-1-infected persons.
Direct Synthesis of Indoles from Azoarenes and Ketones with Bis(neopentylglycolato)diboron Using 4,4′-Bipyridyl as an Organocatalyst (2021)

Multifunctionalized indole derivatives were prepared by reducing azoarenes in the presence of ketones and bis(neopentylglycolato)diboron (B<sub>2</sub>nep<sub>2</sub>) with a catalytic amount of 4,4'-bipyridyl under neutral reaction conditions, where 4,4'-bipyridyl acted as an organocatalyst to activate the B-B bond of B<sub>2</sub>nep<sub>2</sub> and form <i>N</i>,<i>N</i>'-diboryl-1,2-diarylhydrazines as key intermediates. Further reaction of <i>N</i>,<i>N</i>'-diboryl-1,2-diarylhydrazines with ketones afforded <i>N</i>-vinyl-1,2-diarylhydrazines, which rearranged to the corresponding indoles via the Fischer indole mechanism. This organocatalytic system was applied to diverse alkyl cyclic ketones, dialkyl, and alkyl/aryl ketones, including heteroatoms. Methyl alkyl ketones gave the corresponding 2-methyl-3-substituted indoles in a regioselective manner. This protocol allowed us to expand the preparation of indoles having high compatibility with not only electron-donating and electron-withdrawing groups but also <i>N</i>- and <i>O</i>-protecting functional groups.
An improved TCAM-based IP lookup engine (2008)

IP lookup is a key task in packet processing to guarantee the high performance of the IP routers. It has been proposed to use TCAMs to implement IP-lookup accelerators for IP forwarding. In the paper, a new TCAM-based IP-lookup scheme MSMB-LPT is proposed and studied. It is shown that MSMB-LPT scheme significantly improve the performance of the state-of-art MSMB-PT scheme in terms of speedup and power consumption by simulations. These performance improvements are achieved with reduced cost.