gebhart/patrepeval huggingface dataset:
Somatic mosaicism in the central nervous system in spinocerebellar ataxia type 1 and machado‐joseph disease (1996)

Spinocerebellar ataxia type 1 and Machado-Joseph disease are two autosomal dominant cerebellar ataxias caused by expansions of unstable CAG repeats in the coding region of the causative genes. The selectivity of cell death and the resulting characteristic neuropathological features in each of these diseases are not explained by the gene expression patterns. Since the repeat size correlates with age at onset and severity of these diseases, somatic mosaicism, the result of mitotic instability of the CAG repeat, could be the basis for specificity of neurodegeneration; brain structures with larger expanded repeats would be more severely affected. To study the association between neuropathological changes and somatic mosaicism of the CAG repeat size in the central nervous system of patients with these two ataxias, we determined the size of the (CAG)n expansion in 20 different regions of the brain, brainstem, cerebellum, and spinal cord from 3 patients with spinocerebellar ataxia type 1 and 3 with Machado-Joseph disease; these regions were selected for their differential neuropathological involvement in the two disorders. We observed a considerable homogeneity of repeat size ranges in all but 1 of the 20 regions examined: The cerebellar cortex showed slightly smaller (CAG)n tracts in all specimens from both groups of patients. Our results suggest that the pattern of repeat size mosaicism, similar in spinocerebellar ataxia type 1 and Machado-Joseph disease, reflects the developmental pathways and cell composition of different central nervous system regions and is not the cause of selective cell death in these disorders.
Expert System Synthesis for Evolutionary Decoupling Capacitor Optimization (2019)

Power delivery network of an electronic system requires proper component selection and component location choices to achieve a target impedance specification. Typical genetic algorithm optimization requires many evaluations to converge on optimized solutions. This paper investigates using expert systems to accelerate convergence of evolutionary algorithms.
Software Coherence Management on Non-coherent Cache Multi-cores (2016)

The design complexity and power consumption of hardware cache coherence logic increase considerably with the increase in number of cores. Although skipping coherence can simplify hardware and make it more power-efficient, programming becomes more challenging as programmers have to manually insert DMA instructions to ensure that there is coherence of shared data between cores. To reduce the burden of parallel programming, we propose program transformations and a runtime library that will enable correct execution of data-race-free multi-threaded programs. Our scheme manages coherence at byte granularity rather than conventional page-granularity. We further optimize the performance by introducing the concept of private write notice for each core and combining write notices in our coherence implementation. Experimental results of running multi-threaded signal processing benchmarks on the 8-core non-cache coherent Texas Instruments processor TMS320C6678 demonstrates that our technique achieves 12X performance improvement over naive scheme of disabling caches, and 2X performance improvement over the state-of-art technique.
Unambiguous reconstruction of network structure using avalanche dynamics (2015)

A robust method for inferring the structure of networks is presented based on the one-to-one correspondence between the expected composition of cascades of bursts of activity, called crackling noise or avalanches, and the weight matrix. Using a model of neuronal avalanches as a paradigmatic example, we derive this correspondence exactly by calculating the closed-form expression of the joint probability distribution of avalanche sizes obtained by counting separately the number of elements active in each subnetwork during avalanches.
High Efficiency Transfection of iCell Cardiomyocytes and Stem Cell Relevant Cell Sources (2012)

revolutionizing therapy for a myriad of diseases. Researchers can utilize stem cells for elucidating disease models through differentiation of both normal and diseased cells into biologically relevant and homogenous cellular lineages. Transfection of nucleic acids such as plasmid DNA, mRNA and siRNA serves as a vital tool in stem cell reprogramming and differentiation processes. TransIT Transfection Reagents and Ingenio Electroporation Solution will be highlighted for high efficiency delivery of plasmid DNA and siRNA to iCell Cardiomyocytes and induced pluripotent stem (iPS) cells. High Efficiency Transfection of iCell Cardiomyocytes and Stem Cell Relevant Cell Sources Miguel Dominguez1, Chuenchanok Khodthong1, Anthony Lauer1, Elizabeth Dominguez2, Michael McLachlan2, Laura Juckem1 1 Mirus Bio, Madison, WI 2 Cellular Dynamics International, Madison, WI
Delayed Bone Infarct in the Ilium Following a Pelvic Crush Injury and Embolization (2017)

The symptoms from osteonecrosis of the ilium may simulate sacroiliitis or other conditions. It is important to keep the differential diagnosis in mind when considering additional management for posterior pelvic pain in the setting of prior trauma and preexisting hardware.
Salvage of pelvic recurrence of colorectal cancer (2010)

Although the incidence of locally recurrent colorectal cancer has been reduced by improved surgical techniques and the frequent use of multimodality therapy, pelvic recurrence remains a significant problem. Radiation or chemotherapy may provide palliation but it is often short-lived. For fit candidates without evidence of extrapelvic disease, surgical resection (anterior resection, abdominoperineal resection, pelvic exenteration, or abdominosacral resection) may be the most appropriate treatment. For patients with unresectable disease, isolated pelvic perfusion may provide effective palliation.
Single-Post Inductive Obstacle in Rectangular Waveguide (1983)

A rapidly converging moment solution for electromagnetic scattering by a single inductive post in a rectangular waveguide is obtained. The numerical results show good agreement with Marcuvitz's data as far as this data goes. Furthermore, Marcuvitz's curves are extended to cover data for large posts. This new data should aflow one to design a simply constructed new type of narrow bandpass filter, namely, a filter consisting of large single posts. The successful use of this straightforward moment solution in solving the single-post problem suggests that this technique should prove useful in solving a variety of microwave discontinuities such as those involving thin or thick irises and posts of arbitrary shape.
[Structure and function of IL-2 receptor subunits]. (1994)

IL-2 regulates growth and differentiation of various types of cells in the immune system via its interaction with IL-2 receptor (IL-2R). The high and intermediate-affinity IL-2Rs, which consist of the alpha beta gamma heterotrimer complex and the beta gamma heterodimer complex, respectively, harbor the function of the intracellular signal transduction, indicating that the beta and gamma chains are indispensable for the signal transduction but not the alpha chain. The reconstitution studies of IL-2Rs with alpha, beta and gamma chain genes demonstrated that each subunit has potential for altering the affinity of the receptor, and the cytoplasmic domains of the beta and gamma chains participate in signal transduction in terms of cell growth, activation of alpha tyrosine kinase and enhancement of c-myc, c-fos and c-jun transcription. The region containing the SH2 homologous sequence of the gamma chain should have a critical function for signal transduction. On the other hand, common subunits are known to be shared among receptors for IL-3, IL-5 and GM-CSF, and receptors for IL-6, LIF, OSM and LIF. We have demonstrated that the monoclonal antibody specific for the IL-2R gamma chain completely inhibited not only IL-2-dependent cell growth but also IL-4-dependent, IL-7-dependent, and IL-9-dependent cell growth, suggesting that the gamma chain is possibly shared among receptors for IL-2, IL-4, IL-7 and IL-9. Impairment of the gamma chain function is considered to be closely related to human XSCID characterized by profound T cell defect.(ABSTRACT TRUNCATED AT 250 WORDS)
Congestion avoidance for unicast and multicast traffic (2002)

This paper proposes a congestion avoidance mechanism that addresses unicast (TCP or UDP) as well as multicast (UDP) best effort flows. Our mechanism originally combine explicit congestion notification (ECN) based on router active queue management to detect congestion, with ICMP source quench messages to inform the involved sources of the network congestion state. The fairness achieved is a trade-off between TCP-like and max-min fairness. We demonstrate through simulation that the proposed mechanism enforces fairness and provides an efficient and simple solution to congestion avoidance.
Reaction of 4-picoline(2,2′ :6′,2″-terpyridine)platinum(<scp>II</scp>) with nucleosides (1996)

The four nucleosides found in DNA react with 4-picoline(2,2′ :6′,2″-terpyridine)platinum(II). Guanosine and 2′-deoxyguanosine are platinated at N7. Adenosine and 2′-deoxyadenosine are platinated at both N1 and N6 with loss of a proton and there is no evidence of monoplatinated intermediates. It is proposed that platination occurs initially at N1, the most nucleophilic site, which leads to loss of a proton from the N6 amino function and subsequent rapid platination at this site. This conclusion is supported by NMR and mass spectral evidence. 2′-Deoxycytidine is similarly platinated at N3 and N4 and a similar explanation is proposed. Platination of thymidine is very slow and the product(s) has not been characterised.
Melecular Dynamics Study of Stress Effects on Raman Frequencies of Crystalline Silicon. (1997)

The effects of stress on the Raman frequencies of crystalline silicon are studied using molecular dynamics simulation, both for uniaxial stress along the [100] direction and for biaxial stress which is isotropic in the (001) plane. The Tersoff potential is used to represent the interaction among the silicon atoms. Simulation results showed that the stress causes the Raman frequencies to shift. The phenomenological coefficients which are needed to calculate the stress from the shifts of the Raman frequencies were obtained by comparing the simulation results with the dynamical equations for optical modes. The values obtained for the coefficients agreed well with the experimental values obtained by Chandrasekhar et al. [Phys. Rev., B17. (1978), 1623]. The obtained relationship between the uniaxial stress and the Raman frequency for vibration in the [001] direction also agreed well with the experimental result we obtained using microscopic Raman spectroscopy.
Further Investigation of the Nature of the C‐Li Bond. Structures of a Phenylthiomethyllithium Complex and ofa Methylthiomethyllithium Complex (1984)

Abstract Phenylthiomethyllithium/ N , N , N ′, N ′‐tetramethylethylenediamine (TMEDA) (1:1) is shown by X‐ray analysis to be dimeric in the crystalline state. The structural unit contains a six‐membered ring in which each Li is bonded to the terminal C atom of one thioanisole and to the S atom of the other, as well as to the two N atoms of a TMEDA. Methylthiomethyllithium/TMEDA (1:1) is also dimeric, but the structural unit contains a four‐membered ring in which each Li is bonded to two C atoms and to the two TMEDA N atoms. An error has been detected in an earlier published electron‐density difference map for 2‐lithio‐2‐phenyl‐1, 3‐dithiane/TMEDA/THF (1:1:1). The conclusion drawn then that this complex exists as a tight ion‐pair in the crystal is now retracted.
Electrical resistivity imaging for long-term autonomous monitoring of hydrocarbon degradation: Lessons from the Deepwater Horizon oil spill (2014)

ABSTRACT Conceptual models for the geophysical responses associated with hydrocarbon degradation suggest that the long-term evolution of an oil plume will result in a more conductive anomaly than the initial contamination. In response to the Deepwater Horizon (DH) oil spill into the Gulf of Mexico in 2010, an autonomous resistivity monitoring system was deployed on Grand Terre, Louisiana, in an attempt to monitor natural degradation processes in hydrocarbon-impacted beach sediments of this island. A 48-electrode surface array with a 0.5-m spacing was installed to obtain twice-daily images of the resistivity structure of the shallow subsurface impacted by oil. Over the course of approximately 18 months, we observed a progressive decrease in the resistivity of the DH spill-impacted region. Detailed analysis of pixel/point resistivity variation within the imaged area showed that long-term decreases in resistivity were largely associated with the DH-impacted sediments. A microbial diversity survey revealed the presence of hydrocarbon-degrading organisms throughout the test site. However, hydrocarbon degradation activity was much higher in the DH-impacted locations compared to nonimpacted locations, suggesting the presence of active hydrocarbon degraders, supporting biodegradation processes. The results of this long-term monitoring experiment suggested that resistivity might be used to noninvasively monitor the long-term degradation of crude oil spills.
Development of a new high-throughput screening model for human high density lipoprotein receptor (CLA-1) agonists. (2005)

Human HDL receptor CLA-1 was successfully expressed in Sf9 insect cells and a novel high-throughput screening model for CLA-1 agonists was developed. Utilization of this model allows us to identify potent and selective CLA-1 agonists which might possibly be used as therapeutics for atherosclerosis.
Cover Image (2015)

ABSTRACT Background The regrowth of amputated appendage extremities and the distal tips of digits represent models of tissue regeneration in multiple vertebrate taxa. In humans, digit tip injuries, including traumatic amputation and crush injuries, are among the most common type of injury to the human hand. Despite clinical reports demonstrating natural regeneration of appendages in lower vertebrates and human digits, current treatment options are suboptimal, and are complicated by the anatomical complexities and functions of the different tissues within the digits. Results : In light of these challenges, we focus on recent advancements in understanding appendage regeneration from model organisms. We pay special attention to the cellular programs underlying appendage regeneration, where cumulative data from salamanders, fish, frogs, and mice indicate that regeneration occurs by the actions of lineage‐restricted precursors. We focus on pathologic states and the interdependency that exists, in both humans and animal models, between the nail organ and the peripheral nerves for successful regeneration. Conclusions : The increased understanding of regeneration in animal models may open new opportunities for basic and translational research aimed at understanding the mechanisms that support limb regeneration, as well as amelioration of limb abnormalities and pathologies. Developmental Dynamics 244:641–650, 2015 . © 2015 Wiley Periodicals, Inc.
Advanced envelope detection method with novel optical PLL for optical sampling trigger (2005)

An advanced envelope detection method has been developed with a novel optical PLL without electrical 10 MHz timebase synchronisation. The principle of this method and the results of 160 Gbit/s far-end measurements using this technique are presented.
Influence of ATF Dynamics and Controls on Jet Engine Performance (2007)

Current and future requirements in the verification and validation of the performance of modern aircraft engines lead to continuously increasing requirements on the transient performance capability and flexibility of Altitude Test Facilities (ATF). These requirements have been investigated via numerical simulations of a medium size turbofan and a modern core engine. The simulations using the turbofan engine, document a significant influence of the boundary conditions supplied by the ATF on the dynamic behaviour of bypass engines. Variations in engine acceleration times and compressor stability have been identified. This leads to stability requirements for entry conditions at Fan face and ambient conditions at the nozzle exit. The especially demanding operability tests with core engines, challenge ATF systems due to the additional need to simulate the behaviour of low pressure components. It turns out that the interaction between test vehicle and ATF, in both cases, requires special attention and great care in the design of the ATF control system. Therefore a closed loop simulation model including, ATF, ATF controls system, test vehicle and vehicle control has been developed in order to assess and evaluate the integrated ATF - test vehicle behaviour in advance of the test. The integration of the test vehicle and vehicle control into the modular simulation tool is described. The standardized interface allows integrating different vehicle types without a lot of effort. The application of the simulation in a core engine ATF test is described as an example. The observed vehicle - ATF interaction with and without control is discussed.
Supplementary Figure 6 from Inhibitor-Sensitive FGFR2 and FGFR3 Mutations in Lung Squamous Cell Carcinoma (2023)

&lt;p&gt;PDF file - 147K, FGFR2-P253R functional data.&lt;/p&gt;
A Compact Trench-Assisted Space-Modulated JTE Design for High-Voltage 4H-SiC Devices (2021)

This article proposes a compact trench-assisted space-modulated junction termination extension (TSM-JTE) design for high-voltage 4H-silicon carbide (SiC) devices. In this design, trench structures are introduced into the JTE region to effectively split the termination region into three functional zones. The proposed termination structure is cost effective in terms of the chip area it occupies; for devices rated at 10 kV, the termination structure extends the edge of the device by only 250 μm. Requiring only one implant, it is relatively cheap to fabricate, while a wide implantation dose window endures that is relatively insensitive to variations in dose that may occur during processing. The same advantages occur at 20 kV, the TSM-JTE proving to have the best tradeoff between maximum breakdown voltage and implantation window, compared with other single implant termination designs, achieving this in 500 μm of termination length. At 3.3 kV, a 110-μm TSM-JTE retains its advantages over the other JTE designs, but floating field rings are expected to consume less area, though this is not the case at the higher voltages.
The Ageing of the Low-Frequency Water Disturbances Caused by Swimming Goldfish and Its Possible Relevance to Prey Detection (2000)

Wakes caused by swimming goldfish (Carassius auratus) were measured with a particle image velocimetry system and analyzed using a cross-correlation technique. Particle velocities in a horizontal plane (size of measuring plane 24 cmx32 cm or 20 cmx27 cm) were determined, and the vorticity in the plane was derived from these data. The wake behind a swimming goldfish can show a clear vortex structure for at least 30 s. Particle velocities significantly higher than background noise could still be detected 3 min after a fish (body length 10 cm) had passed through the measuring plane. Within this time span, the lateral spread of fish-generated wakes could exceed 30 cm for a 10 cm fish and 20 cm for a 6 cm fish. Measurements in a man-made open-air pond showed that water velocities in a quasi-natural still water environment can be as small as 1 mm s(-)(1). Background velocities did not exceed 3 mm s(-)(1) as long as no moving animal was present in the measuring plane. The possible advantage for piscivorous predators of being able to detect and analyze fish-generated wakes is discussed.
The Double Calcaneal Osteotomy and Flexor Digitorum Longus Tendon Transfer for Stage II Posterior Tibial Tendon Dysfunction (2003)

The treatment of the acquired pes planovalgus foot deformity that occurs in Johnson stage 2 posterior tibial tendon insufficiency remains controversial. Because the deformities remain flexible in stage 2, osteotomies are thought to be preferable to arthrodeses. It is our contention that operative intervention should address all components of stage 2 posterior tibial tendon dysfunction. Our proposed surgical management combines a lateral column lengthening with a medial displacement calcaneal osteotomy into a double osteotomy technique. The double osteotomy and tendon transfer consists of a flexor digitorum longus to medial cuneiform tendon transfer, lateral column lengthening with iliac crest bone grafting, medial displacement calcaneal osteotomy, and percutaneous heel cord lengthening. Use of the American Orthopaedic Foot and Ankle Society Ankle-Hindfoot Scale shows significant improvement in postoperative scores and correlates with a high patient satisfaction rate. This combination of surgical procedures provides clinical and radiographic correction of the stage 2 pes planovalgus deformity and symptomatic pain relief at intermediate follow-up.
Electron neutral elastic collision frequency measurement with the hairpin resonator probe (2017)

Electron neutral elastic collision frequency is measured over pressures ranging from 0.1-2.5 Torr in Ar, He, O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , Ar-He and Ar-O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> plasmas. Measurements are made with both grounded and fully floating hairpin resonator probes in a symmetric parallel plate capacitively coupled system driven at 13 MHz. Results are compared to hybrid plasma equipment module (HPEM) simulations, showing good agreement with simulated collision frequency. Results between grounded and floating probes are also compared.
TCR strength of signal is upstream of and dominates over cytokine effects in controlling CD4+ T cell polarization in vivo (IRC2P.449) (2014)

Abstract Both quantitative antigenic signal strength and the qualitative effects of cytokine signaling have been reported to direct the polarization of CD4+ T cells into effectors with distinct patterns of cytokine secretion. Most current models of the polarization process attribute a dominant role to the effects of cytokines, with polarizing adjuvants presumed to work mainly through elicitation of the relevant cytokines. Here we have varied both the adjuvants used for DC activation and the strength of TCR signaling to examine whether quantitative or qualitative aspects of CD4+ T cell activation play the primary role in effector choice in vivo. Using two-photon intravital microscopy we compared DC stimulated with TH1 or TH2 promoting adjuvants and found that it is the duration of interaction and the strength of signal that dominates in controlling CD4+ T cell fate. Adjustments to antigen level that affect interaction duration can reverse the fate outcome irrespective of the adjuvant used to treat the DC, clearly pointing to the quantitative aspects of signaling as dominant over qualitative effects arising from adjuvant-induced cytokine production. Indicating that cytokines operate as a secondary step in a developmental system in which the strength of initial CD4+ T cell signaling regulates the capacity of the cells to respond to cytokine mediators.