gebhart/patrepeval huggingface dataset:
Mycobacterium tuberculosis DNA gyrase ATPase domain structures suggest a dissociative mechanism that explains how ATP hydrolysis is coupled to domain motion (2013)

DNA gyrase, a type II topoisomerase, regulates DNA topology by creating a double-stranded break in one DNA duplex and transporting another DNA duplex [T-DNA (transported DNA)] through this break. The ATPase domains dimerize, in the presence of ATP, to trap the T-DNA segment. Hydrolysis of only one of the two ATPs, and release of the resulting Pi, is rate-limiting in DNA strand passage. A long unresolved puzzle is how the non-hydrolysable ATP analogue AMP-PNP (adenosine 5'-[β,γ-imido]triphosphate) can catalyse one round of DNA strand passage without Pi release. In the present paper we discuss two crystal structures of the Mycobacterium tuberculosis DNA gyrase ATPase domain: one complexed with AMP-PCP (adenosine 5'-[β,γ-methylene]triphosphate) was unexpectedly monomeric, the other, an AMP-PNP complex, crystallized as a dimer. In the AMP-PNP structure, the unprotonated nitrogen (P-N=P imino) accepts hydrogen bonds from a well-ordered 'ATP lid', which is known to be required for dimerization. The equivalent CH2 group, in AMP-PCP, cannot accept hydrogen bonds, leaving the 'ATP lid' region disordered. Further analysis suggested that AMP-PNP can be converted from the imino (P-N=P) form into the imido form (P-NH-P) during the catalytic cycle. A main-chain NH is proposed to move to either protonate AMP-P-N=P to AMP-P-NH-P, or to protonate ATP to initiate ATP hydrolysis. This suggests a novel dissociative mechanism for ATP hydrolysis that could be applicable not only to GHKL phosphotransferases, but also to unrelated ATPases and GTPases such as Ras. On the basis of the domain orientation in our AMP-PCP structure we propose a mechanochemical scheme to explain how ATP hydrolysis is coupled to domain motion.
Human Serum Contains Detectable Levels of the Hsp70 Cochaperone HspBP1 and Antibodies Bound to HspBP1 (2006)

The identification of the proteins that comprise the serum proteome is a current major research goal that will provide useful information for the diagnosis and treatment of various diseases. It is well established that Hsp70 and Hsp70 antibodies are present in human serum. This study reports on the development of an ELISA assay for the Hsp70 co-chaperone, HspBP1. HspBP1 is present in human serum at concentrations ranging between 0.74 to 3.98 ng/mL. No gender or age differences in the HspBP1 levels were identified. It was also found that human serum contained antibodies to HspBP1, and there were no gender or age differences in these levels. In addition, there was no correlation between the level of HspBP1 in a sample and the antibody titer. Finally, we found that HspBP1 in serum is complexed to anti-HspBP1 antibodies. This report provides initial baseline data on HspBP1 in human serum and provides the methods for future studies to determine if these levels are altered in response to disease.
A study on miniaturization of folded monopole antenna for handsets using a reactance slit (2005)

The latest trends in mobile phone handset units is to reduce their size and weight. Antennas used for such handsets must also follow the handset downsizing and yet keep the antenna performance unchanged or even improved. Furthermore, built-in antennas are becoming a more intense requirement for handsets. In order to make a low profile and small size, the built-in folded monopole antenna (BFMA) has been introduced. In order to confirm the basic antenna characteristics of BFMA, an FMA with a slit has been analyzed on the infinite ground plane (GP). The infinite GP has been used so that the analysis of the antenna does not depend on the size of the GP. In addition, the VSWR characteristics of the FMA with a slit have been compared with those of the BFMA and the PIFA. It has been confirmed that the folded part of the BFMA has a reactance loading effect like the slit of the FMA, and the FMA with a slit is miniaturized up to approximately 37% of the PIFA.
CYTOLYTIC AND NON-CYTOLYTIC T-CELL LINES AGAINST COLORECTAL CARCINOMA (1994)

JACOB, L.; Somasundaram, R.; Monos, D.; Peritt, D.; Mastrangelo, M.; Hart, E.; Herlyn, D. Author Information
Comparison of the Hypersensitive Response Induced by the Tomato Cf-4 and Cf-9 Genes in Nicotiana spp. (2000)

We have previously shown that tomato Cf-9 induces an Avr9-dependent hypersensitive response (HR) in Nicotiana tabacum and potato. We show here that Cf-4 also induces an Avr4-dependent HR in two tobacco species (N. tabacum and N. benthamiana). The HR induced by Cf-4 and Cf-9 was compared in stable tobacco transgenics by a seedling lethal assay and resistance to recombinant Potato virus X expressing Avr4 or Avr9. We also compared HR induction with Agrobacterium-mediated transient expression. The Cf-4/Avr4 combination induced a more rapid HR than Cf-9/Avr9. Sensitive assays for Cf-9 and Cf-4 function should prove useful for structure/function analyses of these resistance proteins in tobacco.
Instant Places: Using Bluetooth for Situated Interaction in Public Displays (2008)

Instant Places is an investigation into the role of Bluetooth presence and naming as techniques for situated interaction around public displays. The authors' utilization of Bluetooth naming extends beyond identity representation, introducing the use of a simple instruction mechanism in which the system can recognize parts of the Bluetooth device name as explicit instructions to trigger the generation of pervasive content on situated displays. The study specifically addresses the suitability of these techniques and the type of social practices that emerges from their availability in a real setting. The results of the study, which involved the deployment of a fully functional prototype in a bar for several weeks, suggest that, despite their simplicity, these techniques were effective in their ability to sustain situated interaction around a public display and were easily and creatively appropriated for new forms of social practices.
Figure S2 from BET Inhibitors Suppress ALDH Activity by Targeting <i>ALDH1A1</i> Super-Enhancer in Ovarian Cancer (2023)

&lt;p&gt;JQ1 synergizes with cisplatin and downregulates ALDH1A1.&lt;/p&gt;
Uncertainty Estimations for Particle Image Velocimetry in a Medical Device Analog (Nozzle) Model (2013)

Particle Image Velocimetry (PIV) is currently the most widely used and well-established tool for non-invasive flow field velocity measurements, and a valuable method for validating computational fluid dynamics (CFD) models of medical devices. One of the critical steps in the CFD validation process is quantification of the experimental uncertainties. This work utilizes a new uncertainty estimation methodology developed by Charonko et al.1 for quantifying the PIV cross-correlation uncertainties. Uncertainties from experimental sources, including image magnification and acquisition timing, were propagated using Taylor series expansion for PIV data within the FDA benchmark Nozzle model2.
Cyclophosphamide Induces Differentiation of Th17 Cells in Cancer Patients (2010)

Low doses of the alkylating agent cyclophosphamide (CTX) mediate antiangiogenic and immunostimulatory effects, leading to potent tumoricidal activity in association with various immunotherapeutic strategies. Here, we show in rodents and cancer patients that CTX markedly promotes the differentiation of CD4(+) T helper 17 (Th17) cells that can be recovered in both blood and tumor beds. However, CTX does not convert regulatory T cells into Th17 cells. Because Th17 are potent inducers of tissue inflammation and autoimmunity, these results suggest impact on the clinical management of various types of malignancies treated with alkylating agents and a potential need to optimize CTX-based immunotherapy in patients.
A Clinical Trial to Verify the Efficiency of the LC-1000 Exfoliative Cell Analyzer as a New Method of Cervical Cancer Screening (2019)

LC-1000 may be useful for cervical cancer screening as an index to qualitatively evaluate CIN and cancer based on the changes in characteristics of cells.
Seamless-walk: Novel Natural Virtual Reality Locomotion Method with a High-Resolution Tactile Sensor (2022)

Natural movement is a challenging problem in virtual reality locomotion. However, existing foot-based locomotion methods lack naturalness due to physical limitations caused by wearing equipment. Therefore, in this study, we propose Seamless-walk, a novel virtual reality (VR) locomotion technique to enable locomotion in the virtual environment by walking on a high-resolution tactile carpet. The proposed Seamless-walk moves the user&#x0027;s virtual character by extracting the users&#x0027; walking speed and orientation from raw tactile signals using machine learning techniques. We demonstrate that the proposed Seamless-walk is more natural and effective than existing VR locomotion methods by comparing them in VR game-playing tasks.
Stereoselective synthesis and characterization of new enantiomerically pure phosphoric acids (2009)

Starting from (R)-6,6'-dimethyldiphenyl-2,2'-dicarboxylic acid, a novel class of enantiomerically pure cyclic dialkyl phosphates was synthesized and properly characterized. The absolute configuration was determined by 2D NOESY experiments. The catalytic behavior of the new chiral Bronsted acids was investigated in the stereoselective addition of a silyl keteneacetal to aldimines. The Mannich-type reaction was promoted in up to 94% yields and enantioselectivities up to 55%. On the basis of preliminary molecular mechanic calculations, a model of stereoselection was also proposed to explain the sense of the enantioselectivity observed in the reaction.
Tunnel barriers on Pb–In–Au alloy films (1983)

Tunnel barrier oxides consisting primarily of In2O3 formed on Pb–In–Au alloys by various thermal and rf-plasma oxidation techniques were characterized in situ using ellipsometry and Auger Electron Spectroscopy (AES). The results were compared to measurements of the Josephson critical current density j1 and the specific capacitance of tunnel junctions fabricated on the same wafers. It was found for junctions with oxides consisting entirely of In2O3 that j1 exceeded 3 KA/cm2 and did not depend strongly on oxide thickness from about 3 nm (for thermally-grown oxides) to 4.5–7 nm (for rf-grown oxides). The addition of a thin layer of PbOx at the top of the barrier, either by backscattering during rf oxidation or by deposition onto a thermal oxide, caused by a substantial decrease in j1, while the presence of PbO in the bulk of the oxide had little effect. The specific capacitance of the lower current density junctions was essentially the same for either 3- or 4.5–6-nm thick oxides and was consistent with a barrier thickness of order 2 nm. These results are interpreted as evidence that tunneling occurs through a Schottky barrier in the indium oxide at the interface with the counterelectrode. Such a barrier, which is consistent with the known behavior of In2O3 as a degenerately-doped semiconductor, would account for effective tunneling and capacitive thicknesses less than the physical oxide thickness.
Visco-Elastic Analysis for Warpage of Electronic Package Considering Change in Material Properties of Mold Resin Caused by Reflow Heating (2011)

BGA（Ball Grid Array）半導体パッケージのリフロー加熱時反り挙動を検討した。パッケージを実装基板にリフロー接続する工程での反りによる接続不良発生の懸念があるため，反り挙動を把握することは重要である。検討の結果，反り挙動は加熱履歴によって変化する場合があることを明らかにした。また，この場合，封止樹脂の線膨張挙動も加熱履歴によって変化することを明らかにした。この加熱履歴に伴う封止樹脂の線膨張挙動の変化を考慮した反り粘弾性解析を実施したところ，解析結果は実際の反り挙動とよく一致し，前述の加熱に伴う反り挙動の変化は，主に封止樹脂の線膨張挙動の変化に起因した現象であることを明らかにした。
Charge analysis for Li-ion battery pack state of health estimation for electric and hybrid vehicles (2019)

The aging monitoring of Lithium-ion batteries (LIBs) represents a critical point for electrified vehicle applications. Consumers may expect their vehicle to have a steady autonomy range and available power throughout the lifetime of their cars. Several embedded solutions exist in the literature. In this paper two new approaches are suggested to enrich the existing solutions. To that extent, capacity fading is studied using exchanged energy during charging events. What's more, power fading is assessed using direct current resistance (DCR) and voltage measurement at the beginning of charge events. Both solutions produce reliable state of health measurements SoH with significantly good accuracy.
Fully Dynamic Discrete-Time ΔΣ ADC Using Closed-Loop Two-Stage Cascoded Floating Inverter Amplifiers (2021)

This brief proposes a fully dynamic discrete-time <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${\Delta }{\Sigma }$ </tex-math></inline-formula> ADC using closed-loop two-stage cascoded floating inverter amplifiers (FIA). The proposed FIA uses a non-cascoded FIA as the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1^{\mathrm{ st}}$ </tex-math></inline-formula> stage and a cascoded one as the 2 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$^{\mathrm{ nd}}$ </tex-math></inline-formula> . By using this arrangement as well as applying metal-insulator-metal (MIM) capacitors for floating reservoir capacitors, it stably achieves high gain even with the input common-mode voltage fluctuation without an additional CMFB nor calibrations. The proposed ADC fabricated in a 65nm standard CMOS process realizes a fully dynamic operation without calibration and achieves 88.5dB SNDR, 97.9dB SFDR with an OSR of 256. It consumes 43.5 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${\mu }\text{W}$ </tex-math></inline-formula> from a 1V supply at a 10MHz sampling frequency.
Collaborative Sensing in Perceptive Mobile Networks: Opportunities and Challenges (2022)

With the development of innovative applications that demand accurate environment information, e.g., autonomous driving, sensing becomes an important requirement for future wireless networks. To this end, integrated sensing and communication (ISAC) provides a promising platform to exploit the synergy between sensing and communication, where perceptive mobile networks (PMNs) were proposed to add accurate sensing capability to existing wireless networks. The well-developed cellular networks offer exciting opportunities for sensing, including large coverage, strong computation and communication power, and most importantly networked sensing, where the perspectives from multiple sensing nodes can be collaboratively utilized for sensing the same target. However, PMNs also face big challenges such as the inherent interference between sensing and communication, the complex sensing environment, and the tracking of high-speed targets by cellular networks. This paper provides a comprehensive review on the design of PMNs, covering the popular network architectures, sensing protocols, standing research problems, and available solutions. Several future research directions that are critical for the development of PMNs are also discussed.
Immunopharmacologic Properties of 1,6-Bis[2–(Diethylamino) Ethoxylxanthen-9-One Dihydrochloride (Wy-15297) (1980)

When tested in a series of immunopharmacologic assays, the interferon inducer, WY-15297, was shown to lack activity in early vascular and humoral phases of the inflammatory response, while it was quite effective against the immunologic phase. The profile of activity of Wy-15927 was, however, unlike those previously described for reference antiinflammatory and immunosuppressive drugs and this may represent one of a new class of immunopharmacologic agents capable of selectively modulating the lymphoreticular system.
Hydrated Arrays of Acidic Surface Groups as Model Systems for Interfacial Structure and Mechanisms in PEMs (2006)

We utilize ab initio quantum mechanical calculations in order to explore structural conformations and cooperative mechanisms at a minimally hydrated 2D array of flexible acidic surface groups. This system serves as a model for rationalizing interactions and correlations of protons and water with ionized side chains that are affixed to hydrophobic polymer aggregates in polymer electrolyte membranes (PEMs). The model exhibits two basic minimum energy configurations upon varying the separation of surface groups from 5 to 12 A. In the "upright" structure at small separation, surface groups are fully dissociated and oriented perpendicular to the basal plane. Together with hydronium ions (H3O+) they form a highly ordered network with long-range correlations. At larger separations we found the transition to a "tilted" structure with cluster-like conformation of surface groups. This structure retains only short-range correlations. Moreover, we investigated the strength of water binding to the minimally hydrated structures. At small separations between surface groups, an additional water molecule interacts only weakly with the minimally hydrated array (binding energy < 0.1 eV) while the energy needed to remove one water molecule exceeds 1 eV. This shows that the minimally hydrated systems are very stable. Ideally, these studies would expedite the design of cheap, highly performing PEMs for fuel cells, with a major focus on membranes that could operate stably at minimal hydration and elevated temperatures (>120 degrees C).
Germline Mutations in CIDEB and Protection against Liver Disease (2022)

Rare germline mutations in <i>CIDEB</i> conferred substantial protection from liver disease. (Funded by Regeneron Pharmaceuticals.).
Evaluation of Lower-Limb Kinematics during Timed Up and Go (TUG) Test in Subjects with Locomotive Syndrome (LS) Using Wearable Gait Sensors (H-Gait System) (2023)

Few studies have dealt with lower-limb kinematics during the timed up and go (TUG) test in subjects with locomotive syndrome (LS). This study aimed to evaluate the characteristics of lower-limb kinematics during the TUG test in subjects with LS using the wearable sensor-based H-Gait system. A total of 140 participants were divided into the non-LS (<i>n</i> = 28), the LS-stage 1 (<i>n</i> = 78), and LS-stage 2 (<i>n</i> = 34) groups based on the LS risk test. Compared with the non-LS group, the LS-stage 1 and LS-stage 2 groups showed significantly smaller angular velocity of hip and knee extension during the sit-to-stand phase. The LS-stage 2 group showed significantly smaller peak angles of hip extension and flexion during the walking-out phase compared to the non-LS group. These findings indicate that the evaluation of the lower-limb kinematics during the TUG test using the H-Gait system is highly sensitive to detect LS, compared with the evaluation of the lower-limb kinematics when simply walking.
Prediction of Human Arm Target for Robot Reaching Movements (2019)

The raise of collaborative robotics has allowed to create new spaces where robots and humans work in proximity. Consequently, to predict human movements and his/her final intention becomes crucial to anticipate robot next move, preserving safety and increasing efficiency. In this paper we propose a human-arm prediction algorithm that allows to infer if the human operator is moving towards the robot to intentionally interact with it. The human hand position is tracked by an RGB-D camera online. By combining the Minimum Jerk model with Semi-Adaptable Neural Networks we obtain a reliable prediction of the human hand trajectory and final target in a short amount of time. The proposed algorithm was tested in a multi-movements scenario with FANUC LR Mate 200iD/7L industrial robot.
Quantification of Cerenkov Luminescence Imaging (CLI) Comparable With 3-D PET Standard Measurements (2018)

Cerenkov luminescence imaging (CLI) is commonly performed using two-dimensional (2-D) conventional optical imaging systems for its cost-effective solution. However, quantification of CLI comparable to conventional three-dimensional positron emission tomography (PET) is challenging using these systems due to both the high attenuation of Cerenkov radiation (CR) on mouse tissue and nonexisting depth resolution of CLI using 2-D imaging systems (2-D CLI). In this study, we developed a model that estimates effective tissue attenuation coefficient and corrects the tissue attenuation of CLI signal intensity independent of tissue depth and size. To evaluate this model, we used several thin slices of ham as a phantom and placed a radionuclide (<sup>89</sup>Zr and <sup>64</sup>Cu) inside the phantom at different tissue depths and sizes (2, 7, and 12 mm). We performed 2-D CLI and MicroPET/CT (Combined small animal PET and Computed Tomography (CT)) imaging of the phantom and in vivo mouse model after administration of <sup>89</sup>Zr tracer. Estimates of the effective tissue attenuation coefficient (μ<sub>eff</sub>) for <sup>89</sup>Zr and <sup>64</sup>Cu were ∼2.4 and ∼2.6 cm<sup>-1</sup>, respectively. The computed unit conversion factor to %ID/g from 2-D CLI signal was 2.74 × 10<sup>-3</sup> μCi/radiance estimated from phantom study. After applying tissue attenuation correction and unit conversion to the in vivo animal study, an average quantification difference of 10% for spleen and 35% for liver was obtained compared to PET measurements. The proposed model provides comparable quantification accuracy to standard PET system independent of deep tissue CLI signal attenuation.
Charged Nanoparticle Attraction in Multivalent Salt Solution: A Classical-Fluids Density Functional Theory and Molecular Dynamics Study B (2016)

Negatively charged nanoparticles (NPs) in 1:1, 1:2, and 1:3 electrolyte solutions are studied in a primitive ion model using molecular dynamics (MD) simulations and classical density functional theory (DFT). We determine the conditions for attractive interactions between the like-charged NPs. Ion density profiles and NP–NP interaction free energies are compared between the two methods and are found to be in qualitative agreement. The NP interaction free energy is purely repulsive for monovalent counterions, but can be attractive for divalent and trivalent counterions. Using DFT, the NP interaction free energy for different NP diameters and charges is calculated. The depth and location of the minimum in the interaction depend strongly on the NPs’ charge. For certain parameters, the depth of the attractive well can reach 8–10 kBT, indicating that kinetic arrest and aggregation of the NPs due to electrostatic interactions is possible. Rich behavior arises from the geometric constraints of counterion packing at the NP surface. Layering of counterions around the NPs is observed and, as secondary counterion layers form the minimum of the NP–NP interaction free energy shifts to larger separation, and the depth of the free energy minimum varies dramatically. We find that attractive interactions occur with and without NP overcharging.
SIMD divergence optimization through intra-warp compaction (2013)

SIMD execution units in GPUs are increasingly used for high performance and energy efficient acceleration of general purpose applications. However, SIMD control flow divergence effects can result in reduced execution efficiency in a class of GPGPU applications, classified as divergent applications. Improving SIMD efficiency, therefore, has the potential to bring significant performance and energy benefits to a wide range of such data parallel applications.