gebhart/patrepeval huggingface dataset:
Photonic-Band-Gap Traveling-Wave Gyrotron Amplifier (2013)

We report the experimental demonstration of a gyrotron traveling-wave-tube amplifier at 250 GHz that uses a photonic band gap (PBG) interaction circuit. The gyrotron amplifier achieved a peak small signal gain of 38 dB and 45 W output power at 247.7 GHz with an instantaneous -3 dB bandwidth of 0.4 GHz. The amplifier can be tuned for operation from 245-256 GHz. The widest instantaneous -3 dB bandwidth of 4.5 GHz centered at 253.25 GHz was observed with a gain of 24 dB. The PBG circuit provides stability from oscillations by supporting the propagation of transverse electric (TE) modes in a narrow range of frequencies, allowing for the confinement of the operating TE03-like mode while rejecting the excitation of oscillations at nearby frequencies. This experiment achieved the highest frequency of operation for a gyrotron amplifier; at present, there are no other amplifiers in this frequency range that are capable of producing either high gain or high output power. This result represents the highest gain observed above 94 GHz and the highest output power achieved above 140 GHz by any conventional-voltage vacuum electron device based amplifier.
Comment on “Absence of a Slater Transition in the Two-Dimensional Hubbard Model” (2003)

In a recent paper, Phys. Rev. Lett. 87, 167010/1-4 (2001), Moukouri and Jarrell presented evidence that in the two-dimensional (d=2) Hubbard model at half-filling there is a metal-insulator transition (MIT) at finite temperature even in weak coupling. While we agree with the numerical results of that paper, we arrive at different conclusions: The apparent gap at finite-temperature can be understood, at weak-coupling, as a crossover phenomenon involving large (but not infinite) antiferromagnetic (AFM) correlation length. Phase-space effects on the self-energy in d=2 are crucial, as are the ratio between AFM correlation length and single-particle thermal de Broglie wavelength. In weak coupling, d=2, there is in general no finite-temperature MIT transition in the thermodynamic sense.
On the Optimization of Regression-Based Spectral Reconstruction (2021)

Spectral reconstruction (SR) algorithms attempt to recover hyperspectral information from RGB camera responses. Recently, the most common metric for evaluating the performance of SR algorithms is the Mean Relative Absolute Error (MRAE)-an ℓ1 relative error (also known as percentage error). Unsurprisingly, the leading algorithms based on Deep Neural Networks (DNN) are trained and tested using the MRAE metric. In contrast, the much simpler regression-based methods (which actually can work tolerably well) are trained to optimize a generic Root Mean Square Error (RMSE) and then tested in MRAE. Another issue with the regression methods is-because in SR the linear systems are large and ill-posed-that they are necessarily solved using regularization. However, hitherto the regularization has been applied at a spectrum level, whereas in MRAE the errors are measured per wavelength (i.e., per spectral channel) and then averaged. The two aims of this paper are, first, to reformulate the simple regressions so that they minimize a relative error metric in training-we formulate both ℓ2 and ℓ1 relative error variants where the latter is MRAE-and, second, we adopt a per-channel regularization strategy. Together, our modifications to how the regressions are formulated and solved leads to up to a 14% increment in mean performance and up to 17% in worst-case performance (measured with MRAE). Importantly, our best result narrows the gap between the regression approaches and the leading DNN model to around 8% in mean accuracy.
The biochemical properties and transforming potential of human Wnt-2 are similar to Wnt-1. (1992)

Wnt-2 is a member of the Wnt gene family that includes the proto-oncogene Wnt-1 (formerly Int-1). Although the predicted protein product of the Wnt-2 gene has only 38% amino acid identity with Wnt-1, it exhibits significant conservation of structural properties, including a hydrophobic signal sequence and invariant spacing and conservation of 22 cysteine residues. We have sought to characterize the biological and biochemical properties of Wnt family members and here present a characterization of Wnt-2 protein and a comparison with Wnt-1. We demonstrate, using both CHO and AtT-20 cells transfected with human Wnt-2 cDNA, that Wnt-2 encodes a 33 kDa protein that is modified by N-linked glycosylation to a 35 kDa species. Secreted Wnt-2 protein was detected in the culture medium only after cells were treated with suramin indicating that, like Wnt-1 protein, Wnt-2 is tightly associated with the cell surface. Expression of Wnt-2 cDNA in the mammary epithelial cell line C57 mg results in loss of density-inhibited growth and induces a transformed phenotype in monolayer culture similar to the effects produced by Wnt-1. These results indicate that Wnt-2 shares several biochemical and biological characteristics with Wnt-1 and suggests that other Wnt family members, by virtue of conserved structural features, may also exhibit similar properties.
Low-Rank and Locality Constrained Self-Attention for Sequence Modeling (2019)

Self-attention mechanism becomes more and more popular in natural language processing (NLP) applications. Recent studies show the Transformer architecture which relies mainly on the attention mechanism achieves much success on large datasets. But a raised problem is its generalization ability is weaker than CNN and RNN on many moderate-sized datasets. We think the reason can be attributed to its unsuitable inductive bias of the self-attention structure. In this paper, we regard the self-attention as matrix decomposition problem and propose an improved self-attention module by introducing two linguistic constraints: low-rank and locality. We further develop the low-rank attention and band attention to parameterize the self-attention mechanism under the low-rank and locality constraints. Experiments on several real NLP tasks show our model outperforms the vanilla Transformer and other self-attention models on moderate size datasets. Additionally, evaluation on a synthetic task gives us a more detailed understanding of working mechanisms of different architectures.
Pathophysiology of NASH: Insulin Resistance, Free Fatty Acids and Oxidative Stress (2006)

Nonalcoholic steatohepatitis (NASH) is a clinicopathological condition that comprises a wide spectrum of liver damage, ranging from steatohepatitis, advanced fibrosis and cirrhosis. NASH is the most common liver disease in the United States, with a high prevalence in the obese, type 2 diabetic population and metabolic syndrome. Although the pathophysiology of NASH remains to be clarified, insulin resistance, free fatty acids and oxidative stress are the most important causes. In this review article, I focused on insulin resistance, free fatty acids and oxidative stress as main causes of NASH, and described the outlines of the pathophysiology of NASH.
Ultrahigh Conductivity Umbilicals: Polymer Nanotube Umbilicals (2014)

Abstract This document describes the work performed and scheduled to satisfy the terms of the Research Partnership to Secure Energy for America (RPSEA) contract number 10121-4302-01. NanoRidge Materials, Inc., located in Houston, Texas, is the prime contractor and has subcontracted Rice University and DUCO, Inc. to participate in this endeavor. Representatives from Shell, Baker Hughes, Total, and DUCO, the project's cost share partners, comprise the Steering Committee and Working Project Group. The ultimate goal is to form a power cable umbilical and perform a demonstration for the subsea community. The umbilical, instead of copper, shall have a carbon nanotube cable as the conductor. The difficulties with copper include a) corrosion, particularly at wire terminations, and b) strength, in some applications the weight of copper exceeds its tenacity. The conductor formed in this effort shall overcome these difficulties. The technology under development is the continuous production of CNT wire with in-line post processing steps to form the bare conductor. The resistivity of the carbon nanotube wire shall be equal to copper at one sixth the weight. Once the conductivity is achieved, the wire shall be jacketed with polymer. This material we have termed the polymer nanotube umbilical (PNU®) cable. Since the wire is carbon-based, we anticipate minimal saltwater corrosion. Also, the CNT conductor shall have greater tensile strength than copper. The following is described in this paper:our technical approach and progress,specialty equipment, andPhase I results.
Probing the RNA structure within the yeast 5 S RNA.L1a protein complex by fluorescence and enzymatic digestion. (1988)

Conformational states of the ribosomal 5 S RNA molecule and its associated protein L1a in the yeast RNA-protein (RNP) complex were determined using controlled RNase T1 digestion in conjunction with fluorescence probes, ethidium bromide and bisanilinonaphthalenesulfonic acid. Fluorescence measurements indicated that the RNA molecule in the RNP complex appeared to exhibit a slightly lower degree of secondary structure than that in the free form. Controlled digestion of the intact RNP complex with RNase T1 resulted in an initial increase in ethidium fluorescence followed by a gradual decrease. In free RNA, a similar profile, except that a larger increase in ethidium fluorescence at the initial stage of digestion, was observed. During digestion of the RNP complex, increases in bisanilinonaphthalenesulfonic acid fluorescence and in light scattering were observed. These findings implied that as regions of the 5 S RNA molecule were perturbed, hydrophobic regions in the protein became exposed. Polyacrylamide gel analysis of the digestion products revealed a temporal appearance of discrete RNA fragments. Sequence analysis of these fragments generated information about the structural arrangement of the RNA molecule within the RNP complex. Results from the present investigation indicate that interactions between the 5 S RNA and protein L1a can stabilize functionally relevant conformations of the components that are individually labile. Properties of the separated components also suggest that special conditions, such as those suggested by Steitz et al. (Steitz, J. A., Berg, C., Hendrick, J. P., LaBranche-Chabot, H., Metspalu, A., Rinke, J., and Yario, T. (1988) J. Cell Biol. 106, 545-556) may be involved for these components to associate during ribosomal assembly.
Improvement of Current Collapse in Deeply Recessed Gate AlGaN/GaN High Electron Mobility Transistors without Field Modulating Structure (2011)

2011 International Conference on Solid State Devices and Materials,Improvement of Current Collapse in Deeply Recessed Gate AlGaN/GaN High Electron Mobility Transistors without Field Modulating Structure
Characterization of voltage degradation in dynamic field gradient focusing (2008)

Dynamic field gradient focusing (DFGF) is an equilibrium gradient method that utilizes an electric field gradient to simultaneously separate and concentrate charged analytes based on their individual electrophoretic mobilities. This work describes the use of a 2-D nonlinear, numerical simulation to examine the impact of voltage loss from the electrodes to the separation channel, termed voltage degradation, and distortions in the electric field on the performance of DFGF. One of the design parameters that has a large impact on the degree of voltage degradation is the placement of the electrodes in relation to the separation channel. The simulation shows that a distance of about 3 mm from the electrodes to the separation channel gives the electric field profile with least amount of voltage degradation. The simulation was also used to describe the elution of focused protein peaks. The simulation shows that elution under constant electric field gradient gives better performance than elution through shallowing of the electric field. Qualitative agreement between the numerical simulation and experimental results is shown. The simulation also illustrates that the presence of a defocusing region at the cathodic end of the separation channel causes peak dispersion during elution. The numerical model is then used to design a system that does not suffer from a defocusing region. Peaks eluted under this design experienced no band broadening in our simulations. Preliminary experimental results using the redesigned chamber are shown.
Development of Moderate Intensity Focused Ultrasound (MIFU) for Ocular Drug Delivery (2022)

The purpose of this study is to develop a method for delivering antiinflammatory agents of high molecular weight (e.g., Avastin) into the posterior segment that does not require injections into the eye (i.e., intravitreal injections; IVT). Diseases affecting the posterior segment of the eye are currently treated with monthly to bimonthly intravitreal injections, which can predispose patients to severe albeit rare complications like endophthalmitis, retinal detachment, traumatic cataract, and/or increased intraocular. In this study, we show that one time moderate intensity focused ultrasound (MIFU) treatment can facilitate the penetration of large molecules across the scleral barrier, showing promising evidence that this is a viable method to deliver high molecular weight medications not invasively. To validate the efficacy of the drug delivery system, IVT injections of vascular endothelial growth factor (VEGF) were used to create an animal model of retinopathy. The creation of this model allowed us to test anti-VEGF medications and evaluate the efficacy of the treatment. In vivo testing showed that animals treated with our MIFU device improved on the retinal tortuosity and clinical dilation compared to the control group while evaluating fluorescein angiogram (FA) Images.
Case study: Control design of an anaerobic digestion system using simulation-based synchronization (2011)

One of the problems for development of industrial controls programs is the availability of the actual equipment to be controlled. Availability of the equipment may be due to project timing, cost issues, and even location. By using a simulation tool, integrated with the control programming environment, the control engineer can test the control program functionality to reduce the amount of time required to commission and deploy the system. Dependent upon the complexity of the system and simulation, diagnostic programs can be developed and tested. Additionally, as new control system capabilities are developed, the corresponding simulation model can be adapted to test those new capabilities. In this paper, we describe the development, use, and validation of an integrated control and simulation tool for an anaerobic digester lab system. Results of the validation tests are discussed, as well as the methods used to develop and deploy the control program. Finally, future work is described to use the capabilities of the control and simulation tool as a formal validation step in the control system design and commissioning.
A variable-rate Viterbi decoder in 130-nm CMOS: design, measurements, and cost of flexibility (2008)

This paper discusses design and measurements of a flexible Viterbi decoder fabricated in 130-nm digital CMOS. Flexibility was incorporated by providing various code rates and modulation schemes to adjust to varying channel conditions. Based on previous trade-off studies, flexible building blocks were carefully designed to cause as little area penalty as possible. The chip runs down to a minimal core supply of 0.8V. It turns out that striving for more modulation schemes is beneficial in terms of power consumption once the price is paid for accepting different code rates viz. radices in the trellis and survivor path units.
Data from Targeting Cellular Iron Homeostasis with Ironomycin in Diffuse Large B-cell Lymphoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Diffuse large B-cell lymphoma (DLBCL) is the most common hematological malignancy. Although more than half of patients with DLBCL achieve long-term remission, the majority of remaining patients succumb to the disease. As abnormal iron homeostasis is implicated in carcinogenesis and the progression of many tumors, we searched for alterations in iron metabolism in DLBCL that could be exploited to develop novel therapeutic strategies. Analysis of the iron metabolism gene expression profile of large cohorts of patients with DLBCL established the iron score (IS), a gene expression–based risk score enabling identification of patients with DLBCL with a poor outcome who might benefit from a suitable targeted therapy. In a panel of 16 DLBCL cell lines, ironomycin, a promising lysosomal iron-targeting small molecule, inhibited DLBCL cell proliferation at nanomolar concentrations compared with typical iron chelators. Ironomycin also induced significant cell growth inhibition, ferroptosis, and autophagy. Ironomycin treatment resulted in accumulation of DNA double-strand breaks, delayed progression of replication forks, and increased RPA2 phosphorylation, a marker of replication stress. Ironomycin significantly reduced the median number of viable primary DLBCL cells of patients without major toxicity for nontumor cells from the microenvironment and presented low toxicity in hematopoietic progenitors compared with conventional treatments. Significant synergistic effects were also observed by combining ironomycin with doxorubicin, BH3 mimetics, BTK inhibitors, or Syk inhibitors. Altogether, these data demonstrate that a subgroup of high-risk patients with DLBCL can be identified with the IS that can potentially benefit from targeting iron homeostasis.&lt;/p&gt;Significance:&lt;p&gt;Iron homeostasis represents a potential therapeutic target for high-risk patients with DLBCL that can be targeted with ironomycin to induce cell death and to sensitize tumor cells to conventional treatments.&lt;/p&gt;&lt;/div&gt;
Vaccination via Chloroplast Genetics: Affordable Protein Drugs for the Prevention and Treatment of Inherited or Infectious Human Diseases (2016)

Plastid-made biopharmaceuticals treat major metabolic or genetic disorders, including Alzheimer's, diabetes, hypertension, hemophilia, and retinopathy. Booster vaccines made in chloroplasts prevent global infectious diseases, such as tuberculosis, malaria, cholera, and polio, and biological threats, such as anthrax and plague. Recent advances in this field include commercial-scale production of human therapeutic proteins in FDA-approved cGMP facilities, development of tags to deliver protein drugs to targeted human cells or tissues, methods to deliver precise doses, and long-term stability of protein drugs at ambient temperature, maintaining their efficacy. Codon optimization utilizing valuable information from sequenced chloroplast genomes enhanced expression of eukaryotic human or viral genes in chloroplasts and offered unique insights into translation in chloroplasts. Support from major biopharmaceutical companies, development of hydroponic production systems, and evaluation by regulatory agencies, including the CDC, FDA, and USDA, augur well for advancing this novel concept to the clinic and revolutionizing affordable healthcare.
P1‐081: OPTIMIZED LITHIUM THERAPEUTIC, LIPROSAL™, MITIGATES ALZHEIMER‐LIKE NEUROPATHOLOGY, COGNITIVE‐ AND NEUROPSYCHIATRIC‐BEHAVIORAL DEFICITS IN PRECLINICAL RODENT STUDIES (2019)

Growing preclinical and clinical evidence suggests that lithium can reduce neuropathology and cognitive decline associated with Alzheimer's disease (AD). While FDA approved lithium carbonate (Li2CO3) has been widely prescribed in the US since the 1970's as a treatment for bipolar disorder and suicide, it has a narrow therapeutic window due, in part, to undesirable pharmacokinetics. In an effort to optimize lithium therapeutics for AD, we have developed a novel ionic co-crystal composed of lithium salicylate and l-proline called LiProSal™, which appears to have an improved therapeutic profile relative to Li2CO3 when compared in a series of in vitro and in vivo studies conducted in both rats and mice. Preclinical studies were conducted comparing the efficacy and safety of LiProSal™ against Li2CO3 in ameliorating AD-like neuropathology, cognitive impairment, and associated neuropsychiatric symptoms employing a variety of transgenic mouse models. We found that 8-week oral treatment with LiProSal™ significantly reduced β-amyloid plaques and tau phosphorylation by reducing neuroinflammation and inactivating glycogen synthase kinase 3β in transgenic Tg2576 mice. Specifically, cytokine profiles from the brain, plasma, and splenocytes indicated that LiProSal™ down regulates pro-inflammatory while up-regulating anti-inflammatory cytokines. Pharmacokinetic analyses indicated that LiProSal™ provides higher brain to blood ratios of lithium and more stable plasma lithium levels in rats (acute oral treatment 72 hrs) and in mice, B6129SF2/J (2-week oral treatment) and transgenic Tg2576 (8-week oral treatment) compared with Li2CO3. Oral administration of LiProSal™ for 28 weeks in 3XTg-AD transgenic mice significantly reduced β-amyloid plaques and tau-phosphorylation, while significantly elevating pre-synaptic (synaptophysin) and post-synaptic protein (post synaptic density protein 95) expression in the brain. Following oral treatment with LiProSal™ for 9 months in APP/PS1 transgenic and B6C3F1/J control mice, no significant differences were found in body weight, brain, heart, lung, spleen, liver or kidney between LiProSal™ treated- and untreated cohorts. However, LiProSal™ treatment produced significant improvements in cognitive function, depression-like behavior and irritability when compared to untreated APP/PS1 mice. Taken together, our data suggest that LiProSal™ represents optimized lithium therapeutics over Li2CO3 for the treatment for AD with fast track development potential.
Fabrication and electrical characteristics of TFTs based on chemically deposited CdS films, using glycine as a complexing agent (2011)

In this work, we report on the fabrication and electrical characteristics of thin film transistors (TFTs) using chemically deposited cadmium sulfide (CdS) thin films as the semiconductor active layer in back-gated devices. The CdS thin films were deposited by the chemical bath deposition (CBD) technique using glycine as the complexing agent. The CdS layers were deposited on SiO2/Si-n substrates and lift-off was used to define the source and drain contacts (Au) on top of these layers. The Si-n wafer with a chromium-gold back contact served as the common gate for the transistors. Several devices with different channel lengths ranging from 10 to 80 μm were fabricated by this process. We studied the properties of the CdS layers deposited by this glycine-based CBD process and the electrical behavior of the transistors as a function of the channel length. The experimental results show that as-deposited CdS are n-type in character and devices exhibit typical pinch-off in drain current versus source–drain voltage (IDS–VDS) curves for several gate voltages. The values of the threshold voltage of the devices were in the range from 8.5 to 8.9 V, depending on the channel length. Channel mobility was between 4.3 and 5.2 cm 2 V −1 s −1 . This research implies that CdS TFTs produced by a simple and low-cost technique could be applicable to electronic devices. (Some figures in this article are in colour only in the electronic version)