gebhart/patrepeval huggingface dataset:
Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1 (2016)

The Mycobacterium tuberculosis H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many M. tuberculosis P450s remain uncharacterized, suggesting that their further analysis may provide new insights into M. tuberculosis metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands. A survey of azole antifungal drugs showed that CYP126A1 is inhibited strongly by azoles containing an imidazole ring but not by those tested containing a triazole ring. To further explore the molecular preferences of CYP126A1 and search for probes of enzyme function, we conducted a high throughput screen. Compounds containing three or more ring structures dominated the screening hits, including nitroaromatic compounds that induce substrate-like shifts in the heme spectrum of CYP126A1. Spectroelectrochemical measurements revealed a 155-mV increase in heme iron potential when bound to one of the newly identified nitroaromatic drugs. CYP126A1 dimers were observed in crystal structures of ligand-free CYP126A1 and for CYP126A1 bound to compounds discovered in the screen. However, ketoconazole binds in an orientation that disrupts the BC-loop regions at the P450 dimer interface and results in a CYP126A1 monomeric crystal form. Structural data also reveal that nitroaromatic ligands "moonlight" as substrates by displacing the CYP126A1 distal water but inhibit enzyme activity. The relatively polar active site of CYP126A1 distinguishes it from its most closely related sterol-binding P450s in M. tuberculosis, suggesting that further investigations will reveal its diverse substrate selectivity.
Characterizing local anisotropy of coercive force in motor laminations with the moving magnet hysteresis comparator (2014)

Non oriented silicon steels are widely used within rotating electrical machines and are assumed to have no anisotropy. There exists a need to detect the anisotropic magnetic properties and to evaluate the local changes in magnetic material properties due to manufacturing cutting processes. In this paper, the so called moving magnet hyteresis comparator is applied to non destructively detect directional variations in coercive force in a variety of local regions of rotor and stator laminations of two materials commonly used to construct induction motors cores. Maximum to minimum coercive force ratios were assessed, varying from 1.4 to 1.7.
Phase II Trial of Gemcitabine as First Line Chemotherapy in Patients With Metastatic or Unresectable Soft Tissue Sarcoma (2006)

Gemcitabine has minimal activity as a single agent at this dose and schedule in advanced STS. The low response rate does not justify further investigation of gemcitabine as a single agent in STS.
Supplementary Table 2 from Serum Antibodies to Blood Group A Predict Survival on PROSTVAC-VF (2023)

&lt;p&gt;PDF file - 112K, Summary of survival correlations for pre-vaccination antibody levels&lt;/p&gt;
Power control optimization for tone reservation based PAPR reduction algorithms (2014)

Orthogonal Frequency Division Multiplexing (OFDM) systems are characterized by a high Peak to Average Power Ratio (PAPR), which results in performance degradation due to High Power Amplifiers' nonlinearities. Multiple algorithms have been proposed to deal with this problem, among them the Tone Reservation (TR) technique adopted in the second generation of Digital Video Broadcasting for Terrestrial transmission (DVB-T2). In this paper we analyze the power control schemes used in TR algorithms by assessing both their performance and complexity. We then propose two novel solutions to improve the performance without requiring additional complexity. The first is based on an enhanced selection of the peaks to be processed by the TR algorithm, and the second is based on a dynamic computation of the threshold used. We show that the proposed techniques outperform the TR algorithm adopted in DVB-T2 by 0.77 dB in terms of CCDF gain at 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> and by 0.33 dB in terms of Input Back Off (IBO) gain for an MER of -40dB.
Through-silicon-via technology for 3D integration (2010)

Major efforts are currently underway throughout the IC industry to develop the capability to integrate device chips by stacking them vertically and using through-silicon vias (TSVs). The resulting interconnect density, bandwidth, and compactness achievable by TSV technology exceed what is currently possible by other packaging approaches. Market-driven applications of TSV involving memory include multi-chip high-performance DRAM, integration of memory and logic functions for enhanced video on handheld devices, and stacked NAND flash for solid-state drives. High-volume commercial implementation of 3D TSV is imminent but faced by special challenges of design, fabrication, bonding, test, reliability, know-good die, standards, logistics, and overall cost. The main focus of this paper is the unit-process and process-integration technology required for TSV fabrication at the wafer level: deep silicon etching, dielectric via isolation, metallization, metal fill, and chemical-mechanical polishing.
Granularity based flow control (2014)

Many models, methods, techniques, and systems have been developed to preserve the integrity of data and guarantee an acceptable level of security over networks. Protection from illegitimate data access and control of information flow are two main goals. This paper presents new techniques that address two main issues: information protection at various levels of granularity and data flow control We first investigate challenges and limits of established access control models regarding flow control. We then introduce a new flow control model based on granularity, the GBFC. GBFC is capable of guaranteeing flow control under reasonable assumptions. In addition, it offers advantages such as adaptability, full control, reliability and compatibility amongst others. Essentially, in GBFC classified information at suitable levels of granularity is accessible through references and information flow control is applied on the references. We also introduce the concepts of views for information access and Noise Injection that represent building blocks for the Granularity Based Flow Control. With noise injection, a document can be transformed into different views to erase or replace protected information and this transformation can be made almost undetectable to the unauthorized reader. Therefore, inference can be made much more difficult with this method. The GBFC model is intended to complement, rather than replace, existing access control methods.
Supplementary Table 1 from Exposure to a Histone Deacetylase Inhibitor Has Detrimental Effects on Human Lymphocyte Viability and Function (2023)

&lt;p&gt;PDF file - 26KB, Antibody Cocktails for Phosphoproteomic at single cell level.&lt;/p&gt;
Prognostic value of texture analysis from cardiac magnetic resonance imaging in patients with Takotsubo syndrome: a machine learning based proof-of-principle approach (2020)

Cardiac magnetic resonance (CMR) imaging has become an important technique for non-invasive diagnosis of takotsubo syndrome (TTS). The long-term prognostic value of CMR imaging in TTS has not been fully elucidated yet. This study sought to evaluate the prognostic value of texture analysis (TA) based on CMR images in patients with TTS using machine learning. In this multicenter study (InterTAK Registry), we investigated CMR imaging data of 58 patients (56 women, mean age 68 ± 12 years) with TTS. CMR imaging was performed in the acute to subacute phase (median time after symptom onset 4 days) of TTS. TA of the left ventricle was performed using free-hand regions-of-interest in short axis late gadolinium-enhanced and on T2-weighted (T2w) images. A total of 608 TA features adding the parameters age, gender, and body mass index were included. Dimension reduction was performed removing TA features with poor intra-class correlation coefficients (ICC ≤ 0.6) and those being redundant (correlation matrix with Pearson correlation coefficient r > 0.8). Five common machine-learning classifiers (artificial neural network Multilayer Perceptron, decision tree J48, NaïveBayes, RandomForest, and Sequential Minimal Optimization) with tenfold cross-validation were applied to assess 5-year outcome including major adverse cardiac and cerebrovascular events (MACCE). Dimension reduction yielded 10 TA features carrying prognostic information, which were all based on T2w images. The NaïveBayes machine learning classifier showed overall best performance with a sensitivity of 82.9% (confidence interval (CI) 80-86.2), specificity of 83.7% (CI 75.7-92), and an area-under-the receiver operating characteristics curve of 0.88 (CI 0.83-0.92). This proof-of-principle study is the first to identify unique T2w-derived TA features that predict long-term outcome in patients with TTS. These features might serve as imaging prognostic biomarkers in TTS patients.
Oxidation of Human Copper Chaperone Atox1 and Disulfide Bond Cleavage by Cisplatin and Glutathione (2019)

Cancer cells cope with high oxidative stress levels, characterized by a shift toward the oxidized form (GSSG) of glutathione (GSH) in the redox couple GSSG/2GSH. Under these conditions, the cytosolic copper chaperone Atox1, which delivers Cu(I) to the secretory pathway, gets oxidized, i.e., a disulfide bond is formed between the cysteine residues of the Cu(I)-binding CxxC motif. Switching to the covalently-linked form, sulfur atoms are not able to bind the Cu(I) ion and Atox1 cannot play an antioxidant role. Atox1 has also been implicated in the resistance to platinum chemotherapy. In the presence of excess GSH, the anticancer drug cisplatin binds to Cu(I)-Atox1 but not to the reduced apoprotein. With the aim to investigate the interaction of cisplatin with the disulfide form of the protein, we performed a structural characterization in solution and in the solid state of oxidized human Atox1 and explored its ability to bind cisplatin under conditions mimicking an oxidizing environment. Cisplatin targets a methionine residue of oxidized Atox1; however, in the presence of GSH as reducing agent, the drug binds irreversibly to the protein with ammine ligands <i>trans</i> to Cys12 and Cys15. The results are discussed with reference to the available literature data and a mechanism is proposed connecting platinum drug processing to redox and copper homeostasis.
Photometric registration of indoor real scenes using an RGB-D camera with application to mixed reality (2019)

The overarching goal of Mixed Reality (MR) is to provide the users with the illusion that virtual and real objects coexist indistinguishably in the same space. An effective illusion requires an accurate registration between both worlds. This registration must be geometrically and photometrically coherent. In this thesis, we propose novel photometric registration methods to estimate the illumination and reflectance of real scenes. Specifically, we propose new approaches which address three main challenges: (1) use of a single RGB-D camera. (2) estimation of both diffuse and specular reflectance properties. (3) estimation of the 3D position and color of multiple dynamic light sources. Within our first contribution, we consider indoor real scenes where both geometry and illumination are static. As the sensor browses the scene, specular reflections can be observed throughout a sequence of RGB-D images. These visual cues are very informative about the illumination and reflectance of scene surfaces. Hence, we model these cues to recover both diffuse and specular reflectance properties as well as the 3D position of multiple light sources. Our algorithm allows convincing MR results such as realistic virtual shadows and correct real specularity removal. Shadows are omnipresent and result from the occlusion of light by existing geometry. They therefore represent interesting cues to reconstruct the photometric properties of the scene. Presence of texture in this context is a critical scenario. In fact, separating texture from illumination effects is often handled via approaches which require user interaction or do not satisfy mixed reality processing time requirements. We address these limitations and propose a method which estimates the 3D position and intensity of light sources. The proposed approach handles dynamic light sources and runs at an interactive frame rate. The existence of a light source is more likely if it is supported by more than one cue. We therefore address the problem of estimating illumination and reflectance properties by jointly analysing specular reflections and cast shadows. The proposed approach takes advantage of information brought by both cues to handle a large variety of scenes. Our approach is capable of handling any textured surface and considers both static and dynamic light sources. Its effectiveness is demonstrated through a range of applications including real-time mixed reality and retexturing. Since the detection of cast shadows and specular reflections are at the heart of this thesis, we further propose a deep-learning framework to jointly detect both cues in indoor real scenes.
Electrodynamics of oxide superconductors (1994)

We present a brief review of results on the surface impedance of cuprate superconductors, focusing mainly on YBa<SUB>2</SUB>Cu<SUB>3</SUB>O<SUB>7-(delta</SUB> ) (YBCO) and evidence of d-wave superconductivity in that material. We then discuss our recent results on Ba-K-Bi-O thin films, and the effects of DC electric fields on the surface impedance of YBCO films. A summary of our data on high quality thin films and single crystals of the electron-doped Nd<SUB>1.85</SUB>Ce<SUB>0.15</SUB>CuO<SUB>4-(delta</SUB> ) (NCCO) cuprate superconductor follows. Surprisingly, the measurements on NCCO are consistent with the behavior of an s-wave BCS superconductor, in striking contrast to recent results on YBCO. Finally we discuss some of the interesting potential implications of d-wave superconductivity for microwave applications of the cuprates.
A 95% Peak Efficiency Modified KY (Boost) Converter for IoT with Continuous Flying Capacitor Charging in DCM (2021)

DC-DC converters are required to achieve high efficiency over wide loading range and compact size for loT applications as shown in Fig. 1(a). However, many designs applied more than one control method to satisfy such requirements [1,2,4,5], which demands complex control system that involves mode selection subsystem, causing efficiency penalty and large chip area. The conventional boost converter has discontinuous output current, which degrades efficiency and output voltage ripple. As a hybrid converter with switched capacitor and inductor, the KY converter overcomes the above drawbacks. However, the charging time of the flying capacitor is seriously limited by the inner operation logic in discontinuous conduction mode (DCM) operation, resulting in small output loading capability and low efficiency.
Ambient base-free glycerol oxidation over bimetallic PdFe/SiO2 by in situ generated active oxygen species (2021)

Abstract Low temperature oxidation of alcohols over heterogeneous catalysts is exceptionally challenging, particularly under neutral conditions. Herein, we report on an efficient, base-free method to oxidise glycerol over a 0.5%Pd-0.5%Fe/SiO 2 catalyst at ambient temperature in the presence of gaseous H 2 and O 2 . The exceptional catalytic performance was attributed to the in situ formation of highly reactive surface-bound oxygenated species, which promote the dehydrogenation on the alcohol. The PdFe bimetallic catalyst was determined to be significantly more active than corresponding monometallic analogues, highlighting the important role both metals have in this oxidative transformation. Fe leaching was confirmed to occur over the course of the reaction but sequestering experiments, involving the addition of bare carbon to the reactions, confirmed that the reaction was predominantly heterogeneous in nature. Investigations with electron paramagnetic resonance spectroscopy suggested that the reactivity in the early stages was mediated by surface-bound reactive oxygen species; no homogeneous radical species were observed in solution. This theory was further evidenced by a direct H 2 O 2 synthesis study, which confirmed that the presence of Fe in the bimetallic catalyst neither improved the synthesis of H 2 O 2 nor promoted its decomposition over the PdFe/SiO 2 catalyst.
Salt Stress in<i>Desulfovibrio vulgaris</i>Hildenborough: an Integrated Genomics Approach (2006)

ABSTRACT The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris . In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.
A survey of QoS routing solutions for mobile ad hoc networks (2007)

In mobile ad hoc networks (MANETs), the provision of quality of service (QoS) guarantees is much more challenging than in wireline networks, mainly due to node mobility, multihop communications, contention for channel access, and a lack of central coordination. QoS guarantees are required by most multimedia and other time- or error-sensitive applications. The difficulties in the provision of such guarantees have limited the usefulness of MANETs. However, in the last decade, much research attention has focused on providing QoS assurances in MANET protocols. The QoS routing protocol is an integral part of any QoS solution since its function is to ascertain which nodes, if any, are able to serve applications‚ requirements. Consequently, it also plays a crucial role in data session admission control. This document offers an up-to-date survey of most major contributions to the pool of QoS routing solutions for MANETs published in the period 1997-2006. We include a thorough overview of QoS routing metrics, resources, and factors affecting performance and classify the protocols found in the literature. We also summarize their operation and describe their interactions with the medium access control (MAC) protocol, where applicable. This provides the reader with insight into their differences and allows us to highlight trends in protocol design and identify areas for future research.
NOMA Enabled Computation and Communication Resource Trade-off for Mobile Edge Computing (2021)

In this paper, we investigate a mobile edge computing (MEC) system in which a set of users with intensive computation tasks, and a set of users with high downlink rate requirement, can cooperate to achieve a mutually-beneficial situation where the task completion time is reduced and the downlink users receive more information from the base station (BS). Specifically, by leveraging uplink and downlink non-orthogonal multiple access (NOMA), the user with an intensive computation task can offload its task bits to the edge cloud and the downlink user. Simultaneously this user relays information to the downlink user from the BS. We consider the joint optimization of computational resource allocation at the edge cloud, communication resource allocation, assignment among the two sets of users, the share of computation, and relay bits to minimize the overall completion time of the tasks while guaranteeing downlink users' incentive requirement. A low complexity iterative algorithm is proposed to find efficient locally optimal solutions by utilizing convex optimization, a graph theory matching algorithm, and block coordinate descent technique. Numerical results show that the proposed technique leads to a significant reduction in users' task completion time and increase in the downlink users rate.
Reciprocity Calibration of TDD MIMO Channel for Interference Alignment (2020)

Interference alignment (IA) is a promising technique to boost the Multiple-input Multiple-output (MIMO) network throughput. Concurrent data transmission links between multiple pairs of transmitters (TX) and receivers (RX) can be established in the same spectrum via cooperation. To make the channel state information (CSI) available on the transmitter side, channel reciprocity in time division duplex (TDD) networks is assumed by a large number of distributed IA algorithms. The physical channel is reciprocal, but nevertheless the channel considered by IA is not, because it also involves the radio frequency (RF) front ends of the transceiver, which are different circuits for transmit and receive modes individually. The difference between the two circuits yields mismatch between the forward and backward channels. Given the mutual coupling effect of the antenna array, the channel's non-symmetry is further complicated. In this paper, we provide the modeling of the non-reciprocity for the TDD MIMO channels and propose a corresponding calibration method to minimize the mismatch. Experimental validation has been conducted with classic distributed IA algorithms. The results highlight the indispensability of the reciprocity calibration for approaching the network capacity gain promised by IA.
Gene expression profiling of replicative and induced senescence (2014)

Cellular senescence is a cell cycle arrest accompanied by high expression of cyclin dependent kinase inhibitors which counteract overactive growth signals, which serves as a tumor suppressive mechanism. Senescence can be a result of telomere shortening (natural or replicative senescence) or DNA damage resulting from exogenous stressors (induced senescence). Here, we performed gene expression profiling through RNA-seq of replicative senescence, adriamycin-induced senescence, H2O2-induced senescence, and 5-aza-2-deoxycytidine-induced senescence in order to profile the pathways controlling various types of senescence. Overall, the pathways common to all 4 types of senescence were related to inflammation and the innate immune system. It was also evident that 5-aza-induced senescence mirrors natural replicative senescence due to telomere shortening. We also examined the prevalence of senescence-associated secretory phenotype (SASP) factors in the RNA-seq data, showing that it is a common characteristic of all 4 types of senescence. In addition, we could discriminate changes in gene expression due to quiescence during cellular senescence from those that were specific to senescence.