gebhart/patrepeval huggingface dataset:
Corresponding Orbitals Derived from Periodic Bloch States for Electron Transfer Calculations of Transition Metal Oxides (2018)

An approach for modeling electron transfer in solids and at surfaces of iron-(oxyhydr)oxides and other redox active solids has been developed for electronic structure methods (i.e., plane-wave density functional theory) capable of performing calculations with periodic cells and large system sizes efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, V <sub>AB</sub>, and the electron transfer transmission factor, κ<sub>el</sub>. This method is an extension of the valence bond theory electron transfer method for molecules and clusters implemented by Dupuis and others and used extensively by Rosso and co-workers in which scaled corresponding orbitals derived from the Bloch states are used to calculate the off-diagonal matrix elements H <sub>AB</sub> and S <sub>AB</sub>. A key development of the present work is the formulation of algorithms to improve the accuracy of the integration of the exact exchange integral in periodic boundary conditions. This method is demonstrated on model systems for electron small polaron transfer in iron-(oxyhydr)oxides, including bare Fe<sup>2+</sup>-Fe<sup>3+</sup> ions, and in [Fe<sup>3+</sup>(OH<sub>2</sub>)<sub>2</sub> (OH<sup>-</sup>)<sub>2</sub>)] <sub>n</sub><sup>n+</sup> chains representing the common edge-sharing Fe octahedral motif in these materials.
Cytogenetic polyclonality in hematologic malignancies (1999)

The present study was undertaken to ascertain the frequency of cytogenetic polyclonality in various hematologic malignancies and to investigate whether morphologic subgroup, age, gender, or previous genotoxic exposure influences the incidence. Among 2,243 cytogenetically investigated hematologic malignancies, 10 acute myeloid leukemias (AML), 5 myelodysplastic syndromes (MDS), 2 acute lymphoblastic leukemias (ALL), 1 acute undifferentiated leukemia (AUL), 1 atypical Philadelphia chromosome-negative (Ph-) chronic myeloid leukemia (CML), 1 chronic myeloproliferative disorder (CMD), and 1 chronic lymphoproliferative disorder (CLD) with karyotypically unrelated clones were identified, constituting 2.6% of AML, 1.6% of MDS, 0.8% of ALL, 13% of AUL, 9.1% of Ph- CML, 1.5% of CMD, and 2.8% of CLD with chromosomal abnormalities. In contrast to the cytogenetic features, the X-inactivation pattern was monoclonal in the two informative female patients that could be investigated. Among 17,733 karyotypically aberrant published cases surveyed, significant frequency differences (P < 0.001) were discerned: 1.7% of 6,526 AML, 3.4% of 2,391 MDS, 0.4% of 1,920 Ph+ CML, 2.9% of 856 CMD, 0.9% of 4,226 ALL, and 5.8% of 1,814 CLD displayed unrelated clones. The incidence of cytogenetic polyclonality did not differ significantly among the MDS, CMD, or ALL subgroups, between males and females, between children (<16 years) and adults, or between B- and T-cell ALL, whereas the frequencies varied among the AML FAB types (P < 0.05), among the different CLD entities (P < 0.001), and between B- and T-cell CLD (P < 0.001). Furthermore, the incidence was higher in therapy-related AML and MDS than in de novo AML and MDS (P < 0.001 and P < 0.01, respectively). Genes Chromosomes Cancer 24:222–229, 1999. © 1999 Wiley-Liss, Inc.
Antibacterial mechanism of silver nanoparticles in Pseudomonas aeruginosa: proteomics approach (2018)

Silver nanoparticles (AgNPs) are the nanomaterials most widely used as antimicrobial agents in a range of consumer products, due to the environmental release of either the AgNPs themselves or silver ions. Although AgNPs appear to be more potent than silver ions, the mechanism behind the activity is not fully elucidated yet. The most common mechanism of toxicity of AgNPs proposed to date is the release of silver ions and/or the particle-specific functions. In this study, Pseudomonas aeruginosa (a model for Gram-negative bacteria) was treated with AgNPs, and its proteomic response was comprehensively characterized to elucidate the antimicrobial mechanism of AgNPs in the microorganism. In total, 59 silver-regulated proteins (27 up-regulated and 32 down-regulated proteins) and 5 silver-binding proteins were identified. Bioinformatic analysis revealed that interference with the cell-membrane function and generation of intracellular reactive oxygen species (ROS) were the main pathways for the antibacterial effect. The pattern of membrane proteins regulated by AgNPs was similar to that found for silver ions. In addition, the same silver-binding proteins were obtained with both AgNPs and silver ions, which indicated that AgNPs probably affect the cell membrane and react with proteins by releasing silver ions. The elevation of intracellular ROS relative to that with silver ions confirmed oxidative damage caused by AgNPs, which may be ascribed to the nano-characteristics and higher uptake efficiency of the particles. These results demonstrate that the antimicrobial activity of AgNPs is due to the synergistic action of release of dissolved silver ions and particle-specific effects. The proteomic analysis of silver-binding and silver-regulated proteins in the present study provides insight into the mechanism of antimicrobial activity of such nanomaterials.
Folate Receptor–Targeted Single-Photon Emission Computed Tomography/Computed Tomography to Detect Activated Macrophages in Atherosclerosis: Can It Distinguish Vulnerable from Stable Atherosclerotic Plaques? (2014)

The need for noninvasive imaging to distinguish stable from vulnerable atherosclerotic plaques is evident. Activated macrophages play a role in atherosclerosis and express folate receptor folate receptor β (FR-β). The feasibility of folate targeting to detect atherosclerosis was demonstrated in human and mouse plaques, and it was suggested that molecular imaging of FR-β through folate conjugates might be a specific marker for plaque vulnerability. However, these studies did not allow differentiation between stable and vulnerable atherosclerotic plaques. We investigated the feasibility of a folate-based radiopharmaceutical (111)In-EC0800) with high-resolution animal single-photon emission computed tomography/computed tomography (SPECT/CT) to differentiate between stable and vulnerable atherosclerotic plaques in apolipoprotein E(−/−) mice in which we can induce plaques with the characteristics of stable and vulnerable plaques by placing a flow-modifying cast around the common carotid artery. Both plaques showed (111)In-EC0800 uptake, with higher uptake in the vulnerable plaque. However, the vulnerable plaque was larger than the stable plaque. Therefore, we determined tracer uptake per plaque volume and demonstrated higher accumulation of (111)In-EC0800 in the stable plaque normalized to plaque volume. Our data show that (111)In-EC0800 is not a clear-cut marker for the detection of vulnerable plaques but detects both stable and vulnerable atherosclerotic plaques in a mouse model of atherosclerosis.
Towards Brain-Computer Interface Control of a 6-Degree-of-Freedom Robotic Arm Using Dry EEG Electrodes (2013)

Introduction . Development of a robotic arm that can be operated using an exoskeletal position sensing harness as well as a dry electrode brain-computer interface headset. Design priorities comprise an intuitive and immersive user interface, fast and smooth movement, portability, and cost minimization. Materials and Methods . A robotic arm prototype capable of moving along 6 degrees of freedom has been developed, along with an exoskeletal position sensing harness which was used to control it. Commercially available dry electrode BCI headsets were evaluated. A particular headset model has been selected and is currently being integrated into the hybrid system. Results and Discussion . The combined arm-harness system has been successfully tested and met its design targets for speed, smooth movement, and immersive control. Initial tests verify that an operator using the system can perform pick and place tasks following a rather short learning curve. Further evaluation experiments are planned for the integrated BCI-harness hybrid setup. Conclusions . It is possible to design a portable robotic arm interface comparable in size, dexterity, speed, and fluidity to the human arm at relatively low cost. The combined system achieved its design goals for intuitive and immersive robotic control and is currently being further developed into a hybrid BCI system for comparative experiments.
Unexpected atazanavir-associated biliary lithiasis in an HIV-infected patient (2011)

s of the Twelfth Conference on Retroviruses and Opportunistic infections, Boston, MA, USA, 2005. Abstract 645. Foundation for Retrovirology and Human Health, Alexandria, VA, USA. 6 Verdon R, Daudon M, Albessard F et al. Indinavir-induced cholelithiasis in a patient infected with human immunodeficiency virus. Clin Infect Dis 2002; 35: e57–9. 200 400 600 M1 M5 M8 M15 M20 M25 M34 M41 Month CD 4 (/m m 3 ) , pV L (c op ie s/ m L) a nd e GF R (m L/ m in ) 1 10 100 1000 10 000 100 000 Pl as m a co nc en tr at io ns (l og 10 , n g/ m L) : ATV C24h (ng/mL) : TFV C24h (ng/mL) : eGFR (mL/min) : CD4 (/mm3) : pVL (copies/mL) : ATV C24h therapeutic range (150-850 ng/mL5) Figure 1. Follow-up of patient. Plasma concentrations of atazanavir at 24 h (ATV C24h) and tenofovir at 24 h (TFV C24h), estimated glomerular filtration rate (eGFR), CD4 cell count and plasma viral load (pVL). Research letter
Digitally adjustable resistors in CMOS for high-performance applications (1992)

Methods by which CMOS circuits can be adjusted digitally to generate controlled impedances for use in high-performance circuits are described. Since digital signals are the only inputs to these circuits, on-chip DC power dissipation can be reduced, the circuit can be made more robust, and the impedance of the circuit can be adjusted by manipulating the input digital information. A design of a CMOS series terminated line driver is discussed, and the utilization of the controlled impedance in terminating transmission lines on-chip, constant delay lines, and controlled di/dt output buffers is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hierarchical overlapped tiling (2012)

This paper introduces hierarchical overlapped tiling, a transformation that applies loop tiling and fusion to conventional loops. Overlapped tiling is a useful transformation to reduce communication overhead, but it may also generate a significant amount of redundant computation. Hierarchical overlapped tiling performs overlapped tiling hierarchically to balance communication overhead and redundant computation, and thus has the potential to provide better performance.
Response to BRAF/MEK Inhibition After Progression With BRAF Inhibition in a Patient With Anaplastic Pleomorphic Xanthoastrocytoma (2018)

Pleomorphic xanthoastrocytoma (PXA) is a rare primary central nervous system tumor which frequently harbors mutations in BRAF. Anaplastic PXA follow a more aggressive course than their nonanaplastic counterparts. We present the case of an anaplastic PXA initially treated with the BRAF inhibitor vemurafenib. After progression of disease the MEK inhibitor trametinib was added to the regimen leading to radiographic improvement. The rationale for combined BRAF and MEK inhibition in PXA is reviewed.
Signaling and Policy Enforcement for Co-operative Firewalls (2013)

The Internet environment has been changing dramatically during the recent years. Plenty of new requirements and problems such as the IPv4 address shortage, traversing middle boxes and mobility that cannot be solved with the current Internet architecture have emerged. Among those problems, the IPv4 address exhaustion is recognized as one of the key challenges in the original Internet design. The reason is the unprecedented growth in the number of user devices and regular network nodes which are addressed with IPv4 locators. Several solutions including Network Address Translator (NAT) and IPv6 (a new version of IP) have been proposed to alleviate the scalability problem. NAT postpones the depletion of the IP address space by reusing the IPv4 address space and isolating customer networks from the public network; it makes hosts in the private address space unreachable from the public Internet. To be exact, a NAT, like a strict firewall, filters out all inbound data flows while outbound traffic from private hosts can go through it. The proposed NAT traversal techniques by IETF have many disadvantages. The Customer Edge Switching aims to replace NAT with a new device called co-operative firewall and eliminate the problems of existing NAT traversal solutions. A CES device provides global connectivity over the Internet using different types of identifiers, global unique domain names and private addresses. In this thesis, Customer Edge Traversal Protocol (CETP) is introduced as an edge-to-edge protocol and prototyped so as to tunnel data and control information while transporting the source and destination IDs from one customer network to another. This work also includes the policy management of co-operative firewalls. The testing results assure the suitability of CETP for inter-CES communication and edge-to-edge signaling.
Development of O2 tolerance in rabbits with no increase in antioxidant enzymes (1989)

Instillation of exogenous surfactant into rabbits exposed to 100% O2 increases survival time and decreases alveolar epithelial injury. In this study we investigated whether rabbits with increased levels of endogenous pulmonary surfactant are more resistant to hyperoxia. Rabbits were exposed to 100% O2 for 64 h and then returned to room air for 8 days (preexposed). At this time, they had normal gas exchange and alveolar permeability to solute and increased levels of lavageable alveolar phospholipids compared with control rabbits breathing air (26 +/- 2 vs. 12 +/- 2 mumol/kg). Preexposed rabbits survived significantly longer than control rabbits when reexposed to 100% O2 (166 +/- 24 vs. 80 +/- 6 h; n = 7; P less than 0.05) and had significantly higher values of total lavageable phospholipids after 72 h in 100% O2 (15 +/- 2 vs. 5 +/- 2 mumol/kg). Controls developed arterial hypoxemia after 72 h in 100% O2. On the other hand, preexposed rabbits maintained arterial PO2 values greater than 100 Torr throughout the hyperoxic exposure and developed progressive respiratory acidosis. Specific activities of CuZn and Mn superoxide dismutase, catalase, and glutathione peroxidase in lung homogenates and isolated alveolar type II pneumocytes of preexposed rabbits were unchanged from those of controls before O2 reexposure and after 72 h in 100% O2. We concluded that 1) increases in pulmonary antioxidant enzyme specific activities are not necessary for the development of O2 tolerance in rabbits and 2) pulmonary surfactant may play a role in O2 adaptation.
Joint Communication, Computation, Caching, and Control in Big Data Multi-Access Edge Computing (2019)

The concept of Multi-access Edge Computing (MEC) has been recently introduced to supplement cloud computing by deploying MEC servers to the network edge so as to reduce the network delay and alleviate the load on cloud data centers. However, compared to the resourceful cloud, MEC server has limited resources. When each MEC server operates independently, it cannot handle all computational and big data demands stemming from users devices. Consequently, the MEC server cannot provide significant gains in overhead reduction of data exchange between users devices and remote cloud. Therefore, joint Computing, Caching, Communication, and Control (4C) at the edge with MEC server collaboration is needed. To address these challenges, in this paper, the problem of joint 4C in big data MEC is formulated as an optimization problem whose goal is to jointly optimize a linear combination of the bandwidth consumption and network latency. However, the formulated problem is shown to be non-convex. As a result, a proximal upper bound problem of the original formulated problem is proposed. To solve the proximal upper bound problem, the block successive upper bound minimization method is applied. Simulation results show that the proposed approach satisfies computation deadlines and minimizes bandwidth consumption and network latency.
Exercise-induced enhancement of synaptic function triggered by the inverse BAR protein, Mtss1L (2019)

Abstract Exercise is a potent enhancer of learning and memory, yet we know little of the underlying mechanisms that likely include alterations in synaptic efficacy in the hippocampus. To address this issue, we exposed mice to a single episode of voluntary exercise, and permanently marked mature hippocampal dentate granule cells that were specifically activated during exercise using conditional Fos-TRAP mice. Only a few dentate granule cells were active at baseline, but two hours of voluntary exercise markedly increased the number of activated neurons. Activated neurons (Fos-TRAPed) showed an input-selective increase in dendritic spines and excitatory postsynaptic currents at 3 days post-exercise, indicative of exercise-induced structural plasticity. Laser-capture microdissection and RNASeq of activated neurons revealed that the most highly induced transcript was Mtss1L, a little-studied gene in the adult brain. Overexpression of Mtss1L in neurons increased spine density, leading us to hypothesize that its I-BAR domain initiated membrane curvature and dendritic spine formation. shRNA-mediated Mtss1L knockdown in vivo prevented the exercise-induced increases in spines and excitatory postsynaptic currents. Our results link short-term effects of exercise to activity-dependent expression of Mtss1L, which we propose as a novel effector of activity-dependent rearrangement of synapses. One Sentence Summary Single episodes of voluntary exercise induced a functional increase in hippocampal synapses mediated by activity-dependent expression of the BAR protein Mtss1L, acting as a novel early effector of synapse formation.
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE) (2019)

The Red Blood Cell (RBC) is a metabolically-driven cell vital for processes such a gas transport and homeostasis. RBC possesses at its surface exposing antigens proteins that are critical in blood transfusion. Due to their importance, numerous studies address the cell function as a whole but more and more details of RBC structure and protein content are now studied using massive state-of-the art characterisation techniques. Yet, the resulting information is frequently scattered in many scientific articles, in many databases and specialized web servers. To provide a more compendious view of erythrocytes and of their protein content, we developed a dedicated database called RESPIRE that aims at gathering a comprehensive and coherent ensemble of information and data about proteins in RBC. This cell-driven database lists proteins found in erythrocytes. For a given protein entry, initial data are processed from external portals and enriched by using state-of-the-art bioinformatics methods. As structural information is extremely useful to understand protein function and predict the impact of mutations, a strong effort has been put on the prediction of protein structures with a special treatment for membrane proteins. Browsing the database is available through text search for reference gene names or protein identifiers, through pre-defined queries or via hyperlinks. The RESPIRE database provides valuable information and unique annotations that should be useful to a wide audience of biologists, clinicians and structural biologists. Database URL: http://www.dsimb.inserm.fr/respire.
On the Distribution of Speaker Verification Scores: Generative Models for Unsupervised Calibration (2020)

Speaker verification systems whose outputs can be interpreted as log-likelihood ratios (LLR) allow for cost-effective decisions by comparing the system outputs to application-defined thresholds depending only on prior information. Classifiers often produce uncalibrated scores, and require additional processing to produce well-calibrated LLRs. Recently, generative score calibration models have been proposed, which achieve calibration performance close to that of state-of-the-art discriminative techniques for supervised scenarios, while also allowing for unsupervised training. The effectiveness of these methods, however, strongly depends on their capabilities to correctly model the target and non-target score distributions. In this work we propose theoretically grounded and accurate models for characterizing the distribution of scores of speaker verification systems. Our approach is based on tied Generalized Hyperbolic distributions and overcomes many limitations of Gaussian models. Experimental results on different NIST benchmarks, using different utterance representation front-ends and different back-end classifiers, show that our method is effective not only in supervised scenarios, but also in unsupervised tasks characterized by very low proportion of target trials.
T-cell Recognition of Superantigens: Inside or Outside the Groove? (1989)

Conventional antigens usually stimulate only about one in 104 T cells, and alloantigens provoke a response from approximately 1% of the T-cell repertoire. Both types of antigen are surpassed by a newly recognized class of molecules capable of stimulating as many as one in five T lymphocytes. Included in this class are the staphylococcal enterotoxins (SEA-SEE), other bacterial toxins (toxic shock syndrome toxin, exfoliating toxin), the minor lymphocyte stimulatory antigens (Mls-1a, Mls-2a), and the uncharacterized substances recognized by Vβ17a+, Vβ11+, Vβ5+, and Vβ12+ T-cell receptors (TCRs) (for recent reviews, see Janeway et al. 1988, 1989b; Fleischer 1989; White et al. 1989). These molecules have recently been termed “superantigens” to connote their immunological potency (White et al. 1989). In the following discussion, we will focus on bacterial toxins as representative superantigens, since they, unlike the others listed, have been identified in molecular terms.
Polarimetric radar signatures of precipitation at S and C-bands (1991)

Polarimetric radar measurements in precipitation at S and C-band frequencies are considered. Time series data were obtained from three advanced radars: the National Center for Atmospheric Research (NCAR) CP-2 radar, the National Severe Storms Laboratory&apos;s (NSSL) Cimarron radar, and the C-band Poldirad radar operated by the German Aerospace Research Establishment (DLR). Measurements of radar reflectivity, differential reflectivity ZDR, differential propagation phase (φDP, and the crosscorrelation between horizontal and vertical polarised waves are derived from time series data in rain, rain mixed with ice, and in the stratiform ice phase of convective storms. Raindrops are modelled as oblate in shape with a gamma form for their size distribution. The gamma parameters (No, Do, m) are varied over an entire range encompassing a wide variety of rainfall types. The radar rain measurements are shown to be in good general agreement with the model rain simulations. By combining ZDR and(φDP it is possible to identify regions of mixed particle types, e.g. raindrops and hail, or ice crystals and snowflakes. The differential phase upon backscatter may be identified by examining the range profile of φDP, giving additional clues as to the type and size of particles responsible for the backscatter.