gebhart/patrepeval huggingface dataset:
Adaptive slope compensation for high bandwidth digital current mode controller (2015)

An adaptive slope compensation method for digital current mode control of dc-dc converters is proposed in this paper. The compensation slope is used for stabilizing the inner current loop in peak current mode control. In this method, the compensation slope is adapted with the variations in converter duty cycle. The adaptive slope compensation provides optimum controller operation in term of bandwidth over wide range of operating points. In this paper operation principle of the controller is discussed. The proposed controller is implemented in an FPGA to control a 100 W buck converter. The experimental results of measured loop-gain at different operating points are presented to validate the theoretical performance of the controller.
Asymmetric Catalysis with Organic Azides and Diazo Compounds Initiated by Photoinduced Electron Transfer (2016)

Electron-acceptor-substituted aryl azides and α-diazo carboxylic esters are used as substrates for visible-light-activated asymmetric α-amination and α-alkylation, respectively, of 2-acyl imidazoles catalyzed by a chiral-at-metal rhodium-based Lewis acid in combination with a photoredox sensitizer. This novel proton- and redox-neutral method provides yields of up to 99% and excellent enantioselectivities of up to >99% ee with broad functional group compatibility. Mechanistic investigations suggest that an intermediate rhodium enolate complex acts as a reductive quencher to initiate a radical process with the aryl azides and α-diazo carboxylic esters serving as precursors for nitrogen and carbon-centered radicals, respectively. This is the first report on using aryl azides and α-diazo carboxylic esters as substrates for asymmetric catalysis under photoredox conditions. These reagents have the advantage that molecular nitrogen is the leaving group and sole byproduct in this reaction.
852 Differential expression of surface protein-encoding genes highlights therapeutic vulnerabilities of four SCLC subtypes (2020)

<h3>Background</h3> Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine malignancy that accounts for 15% of lung cancer diagnoses. The severity of this disease is exacerbated by the fact that there are few therapeutic options, which mostly offer limited clinical benefit, culminating in a 5-year survival rate of <h3>Methods</h3> To identify transcriptional subtypes, we used non-negative matrix factorization of gene expression data from 81 SCLC tumors and identified four subtypes largely based on differential expression of the transcription factors ASCL1, NEUROD1, and POU2F3. We hypothesized that these subtypes may underlie unique therapeutic vulnerabilities. We examined differential expression of genes that encode surface-expressed proteins that may be targetable by reagents such as therapeutic antibodies or antibody-drug conjugates (ADCs). <h3>Results</h3> Our four subtypes are defined either by high expression of ASCL1 (SCLC-A), NEUROD1 (SCLC-N), POU2F3 (SCLC-P), or an absence of those transcription factors and instead a prevalence of immunological factors (SCLC-Inflamed, or SCLC-I). We curated a list of approximately 60 candidate genes encoding surface proteins that are differentially expressed across the four subtypes. Within these 60 candidates, we have identified a few specific to each subtype for which there exist clinically available, targeted ADCs. The most prevalent subtype, SCLC-A, showed high expression of targets such as DLL3 (SCLC-A) and CEACAM5 (SCLC-A). SCLC-N highly expressed SSTR2, a somatostatin receptor that is being actively targeted in SCLC clinical trials. The two non-neuroendocrine subtypes, SCLC-P and SCLC-I shared some common hits such as the NK cell ligand MICA and B7H6. All of the identified and highlighted hits have been or are actively being pursued in clinical trials, highlighting the importance of understanding their expression levels pre- and post-treatment so that novel therapies can be developed that will be effective over the course of disease progression <h3>Conclusions</h3> The underlying biology defining our four identified subtypes of SCLC has revealed a striking number of targetable, differentially expressed surface protein encoding genes many of which already have clinically available reagents that could be repurposed for treatment of SCLC on a subtype-specific basis.
The evolution of bacterial cell size: the internal diffusion-constraint hypothesis (2017)

Size is one of the most important biological traits influencing organismal ecology and evolution. However, we know little about the drivers of body size evolution in unicellulars. A long-term evolution experiment (Lenski's LTEE) in which Escherichia coli adapts to a simple glucose medium has shown that not only the growth rate and the fitness of the bacterium increase over time but also its cell size. This increase in size contradicts prominent 'external diffusion' theory (EDC) predicting that cell size should have evolved toward smaller cells. Among several scenarios, we propose and test an alternative 'internal diffusion-constraint' (IDC) hypothesis for cell size evolution. A change in cell volume affects metabolite concentrations in the cytoplasm. The IDC states that a higher metabolism can be achieved by a reduction in the molecular traffic time inside of the cell, by increasing its volume. To test this hypothesis, we studied a population from the LTEE. We show that bigger cells with greater growth and CO<sub>2</sub> production rates and lower mass-to-volume ratio were selected over time in the LTEE. These results are consistent with the IDC hypothesis. This novel hypothesis offers a promising approach for understanding the evolutionary constraints on cell size.
On approximating the depth and related problems (2005)

In this paper, we study the problem of finding a disk covering the largest number of red points, while avoiding all the blue points. We reduce it to the question of finding a deepest point in an arrangement of pseudodisks and provide a near-linear expected-time randomized approximation algorithm for this problem. As an application of our techniques, we show how to solve linear programming with violations approximately. We also prove that approximate range counting has roughly the same time and space complexity as answering emptiness range queries.
2,3,4-Trioxo-1-(1H-pyrrolo[2,3-b]pyridin-7-ium-7yl)-cyclobutan-1-ide (2018)

2,3,4-Trioxo-1-(1H-pyrrolo[2,3-b]pyridin-7-ium-7-yl)-cyclobutan-1-ide was obtained by reaction of squaric acid with 7-azaindole in acetic anhydride.
Enhancement of the optomechanical coupling and Kerr nonlinearity using the Josephson Capacitance of Cooper-pair box (2020)

We propose a scheme for enhancing the optomechanical coupling between microwave and mechanical resonators by up to seven orders of magnitude to the ultrastrong coupling limit in a circuit optomechanical setting. The tripartite system considered here consists of a Josephson junction Cooper-pair box that mediates the coupling between the microwave cavity and the mechanical resonator. The optomechanical coupling can be modified by tuning the gate charge and the magnetic flux bias of the Cooper-pair box which in turn affect the Josephson capacitance of the Cooper-pair box. We additionally show that with suitable choice of tuning parameters, the optomechanical coupling vanishes and the system exhibits purely a cross-Kerr type of nonlinearity between the cavity and the mechanical resonator. This allows the system to be used for phonon counting.
Implementation of a Transformer-Less Common Mode Active Filter for Off-Line Converter Systems (2006)

This work presents a study and practical implementation of an active filter employing a HF power amplifier and passive filter components to be connected to the AC power lines in order to mitigate common mode conducted emissions of PWM converter systems. The filter topology is chosen from different possibilities listed in a literature survey and studied regarding practical implementation issues. Special attention is put on the stability analysis where the challenges for the feedback structure are discussed and a simple feedback structure is proposed. A prototype is designed and built, from which mathematical and experimental results are obtained demonstrating the potential and limitations of such a system.
Can change in phase angle predict the risk of morbidity and mortality during an 18-year follow-up period? A cohort study among adults (2023)

The larger the decrease in PhA, the higher the risk of early mortality and incident CVD over the subsequent 18 years. PhA is a reliable and easy measure that may help identify those apparently healthy individuals who may be at increased risk of future CVD or dying prematurely. More studies are needed to confirm our results before it can be definitively concluded that PhA changes can improve clinical risk prediction.
An Observational Study of Deep Learning and Automated Evaluation of Cervical Images for Cancer Screening (2018)

The results support consideration of automated visual evaluation of cervical images from contemporary digital cameras. If achieved, this might permit dissemination of effective point-of-care cervical screening.
Dynamic Load Balancing of Dispatch Scheduling for Solid State Disks (2016)

Providing low-latency and high-throughput is an important design feature of an I/O scheduler. Especially, when multiple applications share and compete for a storage resource, the operating system is required to schedule the IO requests for the maximum throughput. Recently, the flash-based storage, solid-state drive (SSD) has been popularly used in various computing systems and traditional scheduling algorithms have been researched and tuned for the emerging flash-based storages. However, the SSDs suffer from the contention problem caused by multiple I/O requests and experience significant performance degradation. This is mainly due to the concurrently accesses to a finite set of flash memory chips. In this paper we propose Dynamic Load Balanced Queuing (DLBQ) that reorders the I/O requests and evenly distributes the accesses on flash memory chips to avoid contention. For that purpose, we have introduced a virtual time method which chases the run-time status of the SSD. We have evaluated the throughput and latency of DLBQ versus the four I/O schedulers with micro benchmarks and server benchmarks. The experimental results show that the throughput of DLBQ is improved by 11 percent on a 128 GB SSD and 15 percent on a 256 GB SSD while ensuring a bounded latency.
A Numerical Study of Absorption by Multilayered Biperiodic Structures (1998)

10 pages, revtex, osa aps sty, 13 eps figures
ChemInform Abstract: Cobalt‐Catalyzed Synthesis of Tertiary Azides from α,α‐Disubstituted Olefins under Mild Conditions Using Commercially Available Reagents. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Physical Link Maintenance and Logical Message Routing Integration for Robotic Network Connectivity (2019)

Network connectivity maintenance is essential for efficient robotic team operations. Achieving robust robotic ad hoc network connectivity requires a capable link maintenance mechanism, especially if the network experiences expected intermittent connectivity. Although various routing protocols for wireless ad hoc networks have been proposed, they deal with the message routing and the link maintenance problems separately, resulting in additional overhead costs and long network latency. These limitations motivate us to develop a new routing mechanism for a robotic network, which we called Meta-Routing. Meta-Routing expands current routing protocols to include not only the normal routing of packets, but also the maintenance of broken links in robotic networks. This paper presents a method to achieve Meta-Routing by controlling robot motion based on gradient descent method augmented with the radio frequency (RF) environment recognition method. The RF recognition method utilizes hidden Markov models (HMMs) to categorize "RF shadows" into a set of RF obstacle primitives from partial information. The motion control algorithm utilizes the gradient estimations augmented with HMM results through RF recognition to determine the robot movement direction for achieving connectivity maintenance. The numerical experimental results demonstrate promising RF recognition and gradient estimations results as well as confirm their abilities in robot motion control for link maintenance, reduction of the total path cost and network latency for achieving Meta-Routing.
GrapHD: Graph-Based Hyperdimensional Memorization for Brain-Like Cognitive Learning (2022)

Memorization is an essential functionality that enables today's machine learning algorithms to provide a high quality of learning and reasoning for each prediction. Memorization gives algorithms prior knowledge to keep the context and define confidence for their decision. Unfortunately, the existing deep learning algorithms have a weak and nontransparent notion of memorization. Brain-inspired HyperDimensional Computing (HDC) is introduced as a model of human memory. Therefore, it mimics several important functionalities of the brain memory by operating with a vector that is computationally tractable and mathematically rigorous in describing human cognition. In this manuscript, we introduce a brain-inspired system that represents HDC memorization capability over a graph of relations. We propose GrapHD, hyperdimensional memorization that represents graph-based information in high-dimensional space. GrapHD defines an encoding method representing complex graph structure while supporting both weighted and unweighted graphs. Our encoder spreads the information of all nodes and edges across into a full holistic representation so that no component is more responsible for storing any piece of information than another. Then, GrapHD defines several important cognitive functionalities over the encoded memory graph. These operations include memory reconstruction, information retrieval, graph matching, and shortest path. Our extensive evaluation shows that GrapHD: (1) significantly enhances learning capability by giving the notion of short/long term memorization to learning algorithms, (2) enables cognitive computing and reasoning over memorization graph, and (3) enables holographic brain-like computation with substantial robustness to noise and failure.
Three-Dimensional Biomimetic Mineralization of Dense Hydrogel Templates (2009)

An electric-current-assisted method was used to mineralize dense hydrogels and create hydroxyapatite/hydrogel composites with unique hierarchical structures. The microstructure of the final material can be controlled by the mineralization technique and the chemistry of the organic matrix. A hydroxyapatite/hydrogel composite was obtained with a large inorganic content (approximately 60% of the weight of the organics). After being heated to 1050 degrees C, the sintered inorganic phase has a very uniformly distributed porosity and its Brunauer-Emmett-Teller (BET) surface area is 0.68 m(2)/g.
Aristolochic acid I determine the phenotype and activation of macrophages in acute and chronic kidney disease (2018)

Acute and chronic kidney injuries are multifactorial traits that involve various risk factors. Experimental animal models are crucial to unravel important aspects of injury and its pathophysiological mechanisms. Translating knowledge obtained from experimental approaches into clinically useful information is difficult; therefore, significant attention needs to be paid to experimental procedures that mimic human disease. Herein, we compared aristolochic acid I (AAI) acute and chronic kidney injury model with unilateral ischemic-reperfusion injury (uIRI), cisplatin (CP)- or folic acid (FA)-induced renal damage. The administration of AAI showed significant changes in serum creatinine and BUN upon CKD. The number of neutrophils and macrophages were highly increased as well as AAI-induced CKD characterized by loss of tubular epithelial cells and fibrosis. The in vitro and in vivo data indicated that macrophages play an important role in the pathogenesis of AA-induced nephropathy (AAN) associated with an excessive macrophage accumulation and an alternative activated macrophage phenotype. Taken together, we conclude that AA-induced injury represents a suitable and relatively easy model to induce acute and chronic kidney injury. Moreover, our data indicate that this model is appropriate and superior to study detailed questions associated with renal macrophage phenotypes.
Crystallization and 2.2 Å resolution structure of R-phycoerythrin from<i>Gracilaria chilensis</i>: a case of perfect hemihedral twinning (2001)

R-phycoerythrin, a light-harvesting component from the red algae Gracilaria chilensis, was crystallized by vapour diffusion using ammonium sulfate as precipitant agent. Red crystals grew after one week at 293 K and diffracted to 2.70 A resolution. Three serial macroseeding assays were necessary to grow a second larger crystal to dimensions of 0.68 x 0.16 x 0.16 mm. This crystal diffracted to 2.24 A resolution using synchrotron radiation at beamline BM14 of the European Synchrotron Radiation Facility (ESRF) at Grenoble, France and was used for structure determination. Data were collected at 100 K to a completeness of 98.6%. The crystal was trigonal, space group R3, with unit-cell parameters a = b = 187.3, c = 59.1 A, alpha = beta = 90, gamma = 120 degrees. Data treatment using the CCP4 suite of programs indicated that the crystal was twinned ((I(2))/(I)(2) = 1.41). Molecular replacement was performed with AMoRe using the R-phycoerythrin from Polysiphonia urceolata [Chang et al. (1996), J. Mol. Biol. 249, 424-440] as a search model. In order to overcome the twinning problem, SHELX97 was used for the crystallographic refinement. The twin fraction was 0.48, indicating a nearly perfect hemihedrally twinned crystal. The final R(work) and R(free) factors are 0.16 and 0.25, respectively. All the residues and chromophores of the alpha- and beta-chains are well defined in the electron-density maps. Some residues belonging to the gamma-linker are also recognizable.
Pupil-plane filtering for improved signal detection in an optical data-storage system incorporating a solid immersion lens (1999)

A pupil-plane filtering technique is applied to data-signal detection in an optical data-storage system that uses a solid immersion lens (SIL) and a four-layered phase-change recording medium. We have confirmed by numerical calculations and experiment that the technique improves signal contrast and makes the contrast less sensitive to the gap width between the bottom surface of the SIL and the top surface of the recording medium. Light that is incident upon the objective lens that is used with the SIL is linearly polarized, and the full vectorial feature of the light is considered in the calculations.
Trial of Upadacitinib and Adalimumab for Psoriatic Arthritis (2021)

The percentage of patients with psoriatic arthritis who had an ACR20 response at week 12 was significantly higher with 15-mg or 30-mg upadacitinib than with placebo. The 30-mg dose but not the 15-mg dose was superior to adalimumab. Adverse events were more frequent with upadacitinib than with placebo. (Funded by AbbVie; SELECT-PsA 1 ClinicalTrials.gov number, NCT03104400.).
EFA6B regulates a stop signal for collective invasion in breast cancer (2020)

Abstract Cancer is initiated by somatic mutations in oncogenes or tumor suppressor genes, however additional mutations provide selective advantages to the tumor cells to resist treatment and develop metastases, therefore identification of secondary mutations is of paramount importance. EFA6B (Exchange Factor for ARF6, B) expression is reduced in breast cancer. To study the pro-tumoral impact of the loss of EFA6B we have invalidated its gene in normal human mammary cells. We found that EFA6B knock-out triggers a transcriptional reprogramming of the cell-to-ECM interaction machinery and unleashes CDC42-dependent collective invasion in collagen. In addition, invasive and metastatic tumors isolated from patients have lower expression of EFA6B and display gene ontology signatures identical to those of EFA6B knock-out cells. Thus, we reveal a new EFA6B-regulated molecular mechanism that controls the invasive potential of mammary cells; this finding opens up new avenues for the treatment of invasive breast cancer.
Formation of Mixed‐Metal Ceria Nanopeapod Composites within Scrolled Hexaniobate Nanosheets (2019)

Abstract Ceria hexaniobate nanopeapods have been prepared and their formation and assembly studied. Various sized ceria nanocubes (5 to 40 nm) were synthesized via a solvothermal approach with oleic acid and oleylamine capping agents. Utilizing a second solvothermal treatment, the nanoparticles were then captured within scrolling hexaniobate nanosheets to produce ceria@hexaniobate nanopeapods. In some instances, peapods were partially filled with ceria so that in a subsequent step, open sites could be filled with Au nanoparticles via in situ growth methods leading to arrangements of gold and ceria NPs within nanoscrolls. Studies on nanoparticle assembly and encapsulation were also carried out. Size‐selective preassembly of nanoparticles on hexaniobate nanosheet surfaces is observed prior to scrolling, after which smaller ceria NPs ( ca . ≤ 10 nm) are efficiently captured inside scrolled nanosheets. Improved understanding and control of this behavior is important for further development of more intricate multicomponent particles assemblies and formations within varieties of tubular structures with different morphological and structural features.
Molecular Mechanisms of Chaperonin GroEL−GroES Function (2001)

The dynamics of the GroEL-GroES complex is investigated with a coarse-grained model. This model is one in which single-residue points are connected to other such points, which are nearby, by identical springs, forming a network of interactions. The nature of the most important (slowest) normal modes reveals a wide variety of motions uniquely dependent upon the central cavity of the structure, including opposed torsional rotation of the two GroEL rings accompanied by the alternating compression and expansion of the GroES cap binding region, bending, shear, opposed radial breathing of the cis and trans rings, and stretching and contraction along the protein assembly's long axis. The intermediate domains of the subunits are bifunctional due to the presence of two hinges, which are alternatively activated or frozen by an ATP-dependent mechanism. ATP binding stabilizes a relatively open conformation (with respect to the central cavity) and hinders the motion of the hinge site connecting the intermediate and equatorial domains, while enhancing the flexibility of the second hinge that sets in motion the apical domains. The relative flexibilities of the hinges are reversed in the nucleotide-free form. Cooperative cross-correlations between subunits provide information about the mechanism of action of the protein. The mechanical motions driven by the different modes provide variable binding surfaces and variable sized cavities in the interior to enable accommodation of a broad range of protein substrates. These modes of motion could be used to manipulate the substrate's conformations.
Laser-induced dehydration of graphite oxide coatings on polymer substrates (2014)

Nanosized graphite has been oxidized by the Hummers method to give high quality graphite oxide. This reaction is characterized by a very fast kinetic behavior and a high yield. The produced graphite oxide has been conveniently used to pattern graphene by using a standard photolithographic method, and the resulting systems have been characterized by optical microscopy (OM), scanning electron microscopy (SEM) and by Fourier transform infrared spectroscopy (FT-IR) and Visible-Near Infrared spectroscopy (Vis-NIR).