gebhart/patrepeval huggingface dataset:
Synthesis and characterization of the monomeric phosphinogallanes But2GaPR′R″(R′, R″= bulky aryl or silyl groups) and related compounds (1993)

The use of bulky substituent groups has allowed the isolation and spectroscopic and structural characterization of several monomeric phosphinogallanes wherein gallium and phosphorus are three-co-ordinate. These new compounds have the formula But2GaP(R)(SiPh3)(R = C6H2But3-2,4,6 1, C6H2Pri3-2,4,6 2, C6H2Me3-2,4,6 3 or SiMe34). Variable-temperature 1H NMR studies indicate that there is a rotational barrier of ca. 12.7 kcal mol–1 around the Ga–P bond in 1 which has been attributed to weak Ga–P π bonding. The synthesis and structures of the related aluminium–phosphorus species But2Al(Et2O)-P(C6H2Pri3-2,4,6)(SiPh3)5 and the gallium–arsenic species But2GaAs[CH(SiMe3)2](SiPh3)6 are also reported. In addition, variable-temperature 1H NMR studies of the precursor asymmetric phosphines (Ph3Si)P(R)H (R = C6H2But3-2,4,6 7, C6H2Pri3-2,4,6 8 or C6H2Me3-2,4,6 9) as well as the X-ray structures of (Ph3Si)P(C6H2But3-2,4,6)H 7 and (Ph3Si)P(SiMe3)210 are discussed. Crystal data with Mo-Kα radiation (λ= 0.710 69 Å) at 130 K: 2, monoclinic, space group P21/c, a= 18.499(5), b= 10.028(4), c= 20.746(6)Å, β= 90.45(1)°, Z= 4, R= 0.043; 5, triclinic, space group P, a= 9.488(3), b= 11.416(5), c= 20.383(6)Å, α= 92.07(3), β= 96.80(2), γ= 103.17(3)°, Z= 2, R= 0.079; 6, triclinic, space group P, a= 12.219(3), b= 14.174(3), c= 21.831(5)Å, α= 92.95(2), β= 99.73(2), γ= 99.47(2)°, Z= 4, R= 0.053; 7, monoclinic, space group P21/c, a= 17.710(6), b= 16.635(5), c= 10.838(4)Å, β= 97.43(3)°, Z= 4, R= 0.044; 10, orthorhombic, space group Pbca, a= 16.092(5), b= 16.841(5), c= 18.778(5)Å, Z= 8 and R= 0.050.
Theoretical Analysis on the Band Structure Variance of the Electron Doped 1111 Iron-based Superconductors (2014)

We perform first principles band calculation of electron doped iron-based superconductors adopting the virtual crystal approximation. We find that when electrons are doped by element substitution in the blocking layer, the band structure near the Fermi level is affected due to the increase of the positive charge in the layer. On the other hand, when Fe in the conducting layer is substituted by Co, the band structure is barely affected. This difference should be a key factor in understanding the phase diagram of the heavily doped electron doped systems LnFeAsO1-xHx.
Role of the CAI-1 Fatty Acid Tail in the Vibrio cholerae Quorum Sensing Response (2012)

Quorum sensing is a mechanism of chemical communication among bacteria that enables collective behaviors. In V. cholerae, the etiological agent of the disease cholera, quorum sensing controls group behaviors including virulence factor production and biofilm formation. The major V. cholerae quorum-sensing system consists of the extracellular signal molecule called CAI-1 and its cognate membrane bound receptor called CqsS. Here, the ligand binding activity of CqsS is probed with structural analogues of the natural signal. Enabled by our discovery of a structurally simplified analogue of CAI-1, we prepared and analyzed a focused library. The molecules were designed to probe the effects of conformational and structural changes along the length of the fatty acid tail of CAI-1. Our results, combined with pharmacophore modeling, suggest a molecular basis for signal molecule recognition and receptor fidelity with respect to the fatty acid tail portion of CAI-1. These efforts provide novel probes to enhance discovery of antivirulence agents for the treatment of V. cholerae.
Delay and Offset Compensated Relaxation Oscillator Core with Replica Integrator (2022)

This work presents a novel relaxation oscillator core architecture using a replica integrator and a chopped comparator, suitable for advanced technology nodes. The oscillator core receives two reference voltages and three reference currents, based on which the output clock is generated having the frequency invariant to delay and offset of the comparators. The oscillator core prototype is designed in 110 nm technology, having an area of 0.045 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and typically consuming 33 µA at 2 MHz. The frequency variation is ±0.5% in the temperature range from −40 to 125°C and ±0.33% in the power supply range from 1.08 to 1.32 V. The core starts up after a single half-cycle.
Targeting FROUNT with disulfiram suppresses macrophage accumulation and its tumor-promoting properties (2020)

Tumor-associated macrophages affect tumor progression and resistance to immune checkpoint therapy. Here, we identify the chemokine signal regulator FROUNT as a target to control tumor-associated macrophages. The low level FROUNT expression in patients with cancer correlates with better clinical outcomes. Frount-deficiency markedly reduces tumor progression and decreases macrophage tumor-promoting activity. FROUNT is highly expressed in macrophages, and its myeloid-specific deletion impairs tumor growth. Further, the anti-alcoholism drug disulfiram (DSF) acts as a potent inhibitor of FROUNT. DSF interferes with FROUNT-chemokine receptor interactions via direct binding to a specific site of the chemokine receptor-binding domain of FROUNT, leading to inhibition of macrophage responses. DSF monotherapy reduces tumor progression and decreases macrophage tumor-promoting activity, as seen in the case of Frount-deficiency. Moreover, co-treatment with DSF and an immune checkpoint antibody synergistically inhibits tumor growth. Thus, inhibition of FROUNT by DSF represents a promising strategy for macrophage-targeted cancer therapy.
Architectures and algorithms for synthesizable embedded programmable logic cores (2003)

As integrated circuits become more and more complex, the ability to make post-fabrication changes will become more and more attractive. This ability can be realized using programmable logic cores. Currently, such cores are available from vendors in the form of a "hard" layout. In this paper, we focus on an alternative approach: vendors supply a synthesizable version of their programmable logic core (a "soft" core) and the integrated circuit designer synthesizes the programmable logic fabric using standard cells. Although this technique suffers increased speed, density, and power overhead, the task of integrating such cores is far easier than the task of integrating "hard" cores into an ASIC. For very small amounts of logic, this ease of use may be more important than the increased overhead. This paper presents two synthesizable programmable logic core architectures, describes the associated place and route CAD tools, and compares the two architectures to each other, and to a "hard" programmable logic core. It also shows how these cores can be made more efficient by creating a non-rectangular architecture, an option not available to "hard" core vendors.
Visual map-making and guided reinforcement learning for mobile robot navigation: a neurocomputational approach (1996)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Through-Silicon-Via Interposers with Cu-Level Electrical Conductivity and Si-Level Thermal Expansion Based on Carbon Nanotube-Cu Composites for Microelectronic Packaging Applications (2020)

Through-silicon-via (TSV) interposers using silicon and copper represent a critical element in microelectronic packaging, as they bridge between fine-pitch inputs/outputs at the integrated circuit chips to the coarser-pitch packages at the substrate. High electrical conductivity is one of the required properties, but as with the continued miniaturization of electronics, thermal expansion match between the substrate (typically silicon) and copper becomes increasingly important to avoid device failure. A CNT-Cu composite TSV interposer was fabricated envisioning microelectronic packaging applications, which demonstrates both copper-level electrical conductivity (∼2.5 × 105 S/cm) and Si-level coefficient of thermal expansion (CTE) (∼7 × 10–6/K). The CTE mismatch between CNT-Cu and Si was measured to be less than 1/5 compared with that between Cu and Si. To realize this, numerous technologies were combined. Specifically, this included the precision synthesis of vertically aligned pillars perfectly normal to the growth substrate, structural reinforcement of the CNT bundles to retain alignment during processing, electrodeposition of Cu into the interstitial spaces of the CNT pillars, and insertion of the CNT-Cu pillar arras into a prefabricated TSV substrate. Finally, the functionality of the prepared CNT-Cu TSV interposer was demonstrated for several configurations.
A dual zeroth-order resonance antenna (2009)

In this paper, a dual ZOR antenna is demonstrated. The equivalent circuit model of general CRLH-TL is modified and the shunt inductances and capacitances that determine each of the ZOR frequencies are analyzed. The simulation result and the measured result of the fabricated antenna are presented, and the results are in good agreement. In addition, the ZOR frequencies with various lengths of the spiral-shaped slot of the patches are observed through simulation. From the result, it is verified that each of the ZOR frequencies can be controlled separately.
Shearography for Non-Destructive Evaluation with Applications to Bat Mask Tile Adhesive Bonding and Specular Surface Honeycomb Panels (2013)

In this report we examine the applicability of shearography techniques for nondestructive inspection and evaluation in two unique application areas. In the first application, shearography is used to evaluate the quality of adhesive bonds holding lead tiles to the BAT gamma ray mask for the NASA Swift program. By exciting the mask with a vibration, the more poorly bonded tiles can be distinguished by their greater displacement response, which is readily identifiable in the shearography image. A quantitative analysis is presented that compares the shearography results with a destructive pull test measuring the force at bond failure. Generally speaking, the results show good agreement. Further investigation would be useful to optimize certain test parameters such as vibration frequency and amplitude. The second application is to evaluate the bonding between the skin and core of a honeycomb structure with a specular (mirror-like) surface. In standard shearography techniques, the object under test must have a diffuse surface to generate the speckle patterns in laser light, which are then sheared. A novel configuration using the specular surface as a mirror to image speckles from a diffuser is presented, opening up the use of shearography to a new class of objects that could not have been examined with the traditional approach. This new technique readily identifies large scale bond failures in the panel, demonstrating the validity of this approach. For the particular panel examined here, some scaling issues should be examined further to resolve the measurement scale down to the very small size of the core cells. In addition, further development should be undertaken to determine the general applicability of the new approach and to establish a firm quantitative foundation.
Combination bortezomib and rituximab treatment affects multiple survival and death pathways to promote apoptosis in mantle cell lymphoma (2009)

Mantle cell lymphoma (MCL) is a distinct histologic subtype of B cell non-Hodgkins lymphoma (NHL) associated with an aggressive clinical course. Inhibition of the ubiquitin-proteasome pathway modulates survival and proliferation signals in MCL and has shown clinical benefit in this disease. This has provided rationale for exploring combination regimens with B-cell selective immunotherapies such as rituximab. In this study, we examined the effects of combined treatment with bortezomib and rituximab on patient-derived MCL cell lines (Jeko, Mino, SP53) and tumor samples from patients with MCL where we validate reversible proteasome inhibition concurrent with cell cycle arrest and additive induction of apoptosis. When MCL cells were exposed to single agent bortezomib or combination bortezomib/rituximab, caspase dependent and independent apoptosis was observed. Single agent bortezomib or rituximab treatment of Mino and Jeko cell lines and patient samples resulted in decreased levels of nuclear NFkappaB complex(es) capable of binding p65 consensus oligonucleotides, and this decrease was enhanced by the combination. Constitutive activation of the Akt pathway was also diminished with bortezomib alone or in combination with rituximab. On the basis of in vitro data demonstrating additive apoptosis and enhanced NFkappaB and phosphorylated Akt depletion in MCL with combination bortezomib plus rituximab, a phase II trial of bortezomib-rituximab in patients with relapsed/refractory MCL is underway.
End-to-end Differentiable Clustering with Associative Memories (2023)

Clustering is a widely used unsupervised learning technique involving an intensive discrete optimization problem. Associative Memory models or AMs are differentiable neural networks defining a recursive dynamical system, which have been integrated with various deep learning architectures. We uncover a novel connection between the AM dynamics and the inherent discrete assignment necessary in clustering to propose a novel unconstrained continuous relaxation of the discrete clustering problem, enabling end-to-end differentiable clustering with AM, dubbed ClAM. Leveraging the pattern completion ability of AMs, we further develop a novel self-supervised clustering loss. Our evaluations on varied datasets demonstrate that ClAM benefits from the self-supervision, and significantly improves upon both the traditional Lloyd's k-means algorithm, and more recent continuous clustering relaxations (by upto 60% in terms of the Silhouette Coefficient).
Transparent Insertion of Custom Logic in HTTP(S) Streams Using PbProxy (2010)

Cost and testing considerations limit the acceptance and deployment of technologies that make information exchanges more secure, reliable, semantically understandable, and self-improving. PbProxy is a flexible proxy that enables transparent insertion of custom logic into HTTP and HTTPS interactions. It has successfully been used to facilitate behavior-based prevention of phishing attacks, machine learning of Web service procedures, and Web browsing over disruption-tolerant networks by injecting custom logic into existing applications and communication streams. PbProxy encapsulates common functionality into a proxy base and supports customizable plugins to foster code reuse.
Optimization of organic tandem solar cells based on small molecules (2010)

Organic solar cells (OSC) have attracted growing attention in recent years and their development has reached a stage at which several companies are preparing to make them commercially available either as standalone products or integrated into other device. There are different production routes for OSC: one very promising approach uses thermal evaporation of small organic molecules in vacuum, i.e. the same approach that is used in all current commercial manufacturing of organic LEDs. We use vacuum processing to create an organic stack in the p-i-n concept. In this concept the intrinsic absorber layers are sandwiched between p- and n-doped wide gap transport layers which leads to a nearly ideal solar cell structure and offers a stable platform both for investigation of fundamental processes and device optimization. In recent years it was found that the device operation crucially depends on the morphology of the bulk heterojunction and that optical interference effects in the organic stack play an important role for light absorption. We show here how the morphology of the organic layers can be controlled in vacuum deposited layers, and describe the optical optimization of tandem solar cells, for which an efficient recombination contact and current matching are essential requirements. Applying these principles and subsequently combining two complementary absorbing subcells lead to a tandem organic solar cell with an independently certified efficiency of 6.07% on 2cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> device area, i.e. the first OSC over 6% on module relevant dimensions.
Image Modeling and Enhancement via Structured Sparse Model Selection (2010)

An image representation framework based on structured sparse model selection is introduced in this work.The corresponding modeling dictionary is comprised of a family of learned orthogonal bases.For an image patch, a model is first selected from this dictionary through linear approximation in a best basis, and the signal estimation is then calculated with the selected model.The model selection leads to a guaranteed near optimal denoising estimator.The degree of freedom in the model selection is equal to the number of the bases, typically about 10 for natural images, and is significantly lower than with traditional overcomplete dictionary approaches, stabilizing the representation.For an image patch of size √ N × √ N, the computational complexity of the proposed framework is O(N 2 ), typically 2 to 3 orders of magnitude faster than estimation in an overcomplete dictionary.The orthogonal bases are adapted to the image of interest and are computed with a simple and fast procedure.State-of-the-art results are shown in image denoising, deblurring, and inpainting.
Modified Mayo score versus Mayo score for evaluation of treatment efficacy in patients with ulcerative colitis: data from the tofacitinib OCTAVE program (2022)

ClinicalTrials.gov identifiers: NCT01465763; NCT01458951; NCT01458574.
Process for electrospinning chitin fibers from chitinous biomass solution (2023)

Disclosed are methods for electrospinning chitinous biomass solution to form chitin fibers, using ionic liquids or other ion-containing liquids as solvent. Chitin fibers produced thereby and articles containing such chitin fibers are also disclosed. The chitin fiber thus obtained has very high surface area and improved strength over currently commercially available chitin materials.
Effects of iron-oxide nanoparticles and magnetic fields on oral biofilms (2017)

Human mouth is a host of a large gamut of bacteria species, with over 700 of different bacteria strains identified. Most of these bacterial species are harmless, some are beneficial (such as probiotics assisting in food digestion), but some are responsible for various diseases, primarily tooth decay and gum diseases such as gingivitis and periodontitis. For example, Streptococus mutans produces enamel-eroding acids, while Porphyromonas gingivalis is strongly linked to periodontitis. In this paper, we report on the effects of exposure of oral biofilms to iron oxide nanoparticles and static magnetic fields as possible bactericidal agent.
Ribotoxic Stress through p38 Mitogen-activated Protein Kinase Activates in Vitro the Human Pyrin Inflammasome (2013)

Human pyrin with gain-of-function mutations in its B30.2/SPRY domain causes the autoinflammatory disease familial Mediterranean fever by assembling an ASC-dependent inflammasome that activates caspase-1. Wild-type human pyrin can also form an inflammasome complex with ASC after engagement by autoinflammatory PSTPIP1 mutants. How the pyrin inflammasome is activated in the absence of disease-associated mutations is not yet known. We report here that ribotoxic stress triggers the assembly of the human pyrin inflammasome, leading to ASC oligomerization and caspase-1 activation in THP-1 macrophages and in a 293T cell line stably reconstituted with components of the pyrin inflammasome. Knockdown of pyrin and selective inhibition of p38 MAPK greatly attenuated caspase-1 activation by ribotoxic stress, whereas expression of the conditional mutant ΔMEKK3:ER* allowed the activation of caspase-1 without ribotoxic stress. Disruption of microtubules by colchicine also inhibited pyrin inflammasome activation by ribotoxic stress. Together, our results indicate that ribotoxic stress activates the human pyrin inflammasome through a mechanism that requires p38 MAPK signaling and microtubule stability.
Recent Advances in Therapeutic Delivery Systems of Bacteriophage and Bacteriophage-Encoded Endolysins (2017)

Antibiotics have been the cornerstone of clinical management of bacterial infection since their discovery in the early 20th century. However, their widespread and often indiscriminate use has now led to reports of multidrug resistance becoming globally commonplace. Bacteriophage therapy has undergone a recent revival in battle against pathogenic bacteria, as the self-replicating and co-evolutionary features of these predatory virions offer several advantages over conventional therapeutic agents. In particular, the use of targeted bacteriophage therapy from specialized delivery platforms has shown particular promise owing to the control of delivery location, administration conditions and dosage of the therapeutic cargo. This review presents an overview of the recent formulations and applications of such delivery vehicles as an innovative and elegant tool for bacterial control.
New methods for quantifying rapidity of action potential onset differentiate neuron types (2021)

Two new methods for quantifying the rapidity of action potential onset have lower relative standard deviations and better distinguish neuron cell types than current methods. Action potentials (APs) in most central mammalian neurons exhibit sharp onset dynamics. The main views explaining such an abrupt onset differ. Some studies suggest sharp onsets reflect cooperative sodium channels activation, while others suggest they reflect AP backpropagation from the axon initial segment. However, AP onset rapidity is defined subjectively in these studies, often using the slope at an arbitrary value on the phase plot. Thus, we proposed more systematic methods using the membrane potential's second-time derivative ([Formula: see text]) peak width. Here, the AP rapidity was measured for four different cortical and hippocampal neuron types using four quantification methods: the inverse of full-width at the half maximum of the [Formula: see text] peak (IFWd2), the inverse of half-width at the half maximum of the [Formula: see text] peak (IHWd2), the phase plot slope, and the error ratio method. The IFWd2 and IHWd2 methods show the smallest variation among neurons of the same type. Furthermore, the AP rapidity, using the [Formula: see text] peak width methods, significantly differentiates between different types of neurons, indicating that AP rapidity can be used to classify neuron types. The AP rapidity measured using the IFWd2 method was able to differentiate between all four neuron types analyzed. Therefore, the [Formula: see text] peak width methods provide another sensitive tool to investigate the mechanisms impacting the AP onset dynamics.
The Hybrid Simplified Kalman Filter for Adaptive Feedback Cancellation (2018)

Numerous adaptive feedback cancellation (AFC) algorithms are used in open-fitting and in-ear hearing aid devices (HADs) in order to avoid the possible annoying howling sounds. Recently, a hybrid AFC (H-AFC) scheme that shortened the recovering time from howling was proposed. It consists of a switched combination adaptive filter controlled by a stability detector that chooses either the standard normalized least mean squares (NLMS) algorithm or the prediction-error method (PEM) NLMS algorithm. In this paper a hybrid simplified Kalman filter (H -SKF) that uses a modified stability detector and a switch between NLMS and (PEM) SKF algorithms is proposed. It is shown that the proposed approach improves the convergence properties and shortens the howling periods for both speech and music signals compared with the hybrid NLMS (H-NLMS) algorithm.