gebhart/patrepeval huggingface dataset:
Nanostructured Coatings by Adhesion of Phosphonated Polystyrene Particles onto Titanium Surface for Implant Material Applications (2010)

Titanium that is covered with a native oxide layer is widely used as an implant material; however, it is only passively incorporated in the human bone. To increase the implant-bone interaction, one can graft multifunctional phosphonic compounds onto the implant material. Phosphonate groups show excellent adhesion properties onto metal oxide surfaces such as titanium dioxide, and therefore, they can be used as anchor groups. Here, we present an alternative coating material composed of phosphonate surface-functionalized polystyrene nanoparticles synthesized via free radical copolymerization in a direct (oil-in-water) miniemulsion process. Two types of functional monomers, namely, vinylphosphonic acid (VPA) and vinylbenzyl phosphonic acid (VBPA), were employed in the copolymerization reaction. Using VBPA as a comonomer leads to particles with a higher density of surface phosphonate groups in comparison to those obtained with VPA. VBPA-functionalized particles were used for the coating formation on the titanium surface. The particles monolayer was investigated by scanning electron microscopy (SEM) and atomic force microscopy (AFM) employing titanium and silicium tip with the native OH groups. Force versus distance curves proves the strong adhesion between the phosphonated particles and the titanium (or silicium) surfaces in contrast to the nonfunctionalized polystyrene particles. Finally, as a proof of concept, the particles adhered to the surface were further used to nucleate hydroxyapatite, which has high potential for bioimplants.
Transmutable nanoparticles with reconfigurable surface ligands (2016)

Unlike conventional inorganic materials, biological systems are exquisitely adapted to respond to their surroundings. Proteins and other biological molecules can process a complex set of chemical binding events as informational inputs and respond accordingly via a change in structure and function. We applied this principle to the design and synthesis of inorganic materials by preparing nanoparticles with reconfigurable surface ligands, where interparticle bonding can be programmed in response to specific chemical cues in a dynamic manner. As a result, a nascent set of "transmutable nanoparticles" can be driven to crystallize along multiple thermodynamic trajectories, resulting in rational control over the phase and time evolution of nanoparticle-based matter.
Retinal Microvasculature in Alzheimer's Disease (2014)

Although cerebral small vessel disease has been implicated in the development of Alzheimer's disease (AD), the cerebral microcirculation is difficult to visualize directly in vivo. As the retina and the brain share similar embryological origin, anatomical features and physiological properties with the cerebral small vessels, the retinal vessels thus offer a unique and easily accessible "window" to study the correlates and consequences of cerebral small vessel diseases in vivo. Retinal microvasculature can now be visualized, quantified and monitored non-invasively using state-of-the-art retinal imaging technology. Recent clinic- and population-based studies have demonstrated a link between retinal vascular changes and dementia, in particular AD, and cerebral small vessel disease. In this review, we summarize the current findings on retinal vascular changes such as retinopathy signs and changes in novel retinal vascular network parameters and retinal vascular caliber with dementia, cognitive dysfunction and cerebral small vessel disease, and discuss possible future research to further evaluate whether retinal vascular imaging might help to elucidate vascular mechanisms contributing to the development of AD and provide additional value in predicting who may be at risk of developing AD.
Bone Marrow-Derived Stem Cell Therapy for Metastatic Brain Cancers (2015)

We propose that stem cell therapy may be a potent treatment for metastatic melanoma in the brain. Here we discuss the key role of a leaky blood-brain barrier (BBB) that accompanies the development of brain metastases. We review the need to characterize the immunological and inflammatory responses associated with tumor-derived BBB damage in order to reveal the contribution of this brain pathological alteration to the formation and growth of brain metastatic cancers. Next, we discuss the potential repair of the BBB and attenuation of brain metastasis through transplantation of bone marrow-derived mesenchymal stem cells with the endothelial progenitor cell phenotype. In particular, we review the need for evaluation of the efficacy of stem cell therapy in repairing a disrupted BBB in an effort to reduce neuroinflammation, eventually attenuating brain metastatic cancers. The demonstration of BBB repair through augmented angiogenesis and vasculogenesis will be critical to establishing the potential of stem cell therapy for the treatment/prevention of metastatic brain tumors. The overarching hypothesis we advanced here is that BBB breakdown is closely associated with brain metastatic cancers of melanoma, exacerbating the inflammatory response of the brain during metastasis, and ultimately worsening the outcome of metastatic brain cancers. Abrogating this leaky BBB-mediated inflammation via stem cell therapy represents a paradigm-shifting approach to treating brain cancer. This review article discusses the pros and cons of cell therapy for melanoma brain metastases.
Resonance Raman Cross‐Sections and Vibronic Analysis of Rhodamine 6G from Broadband Stimulated Raman Spectroscopy (2008)

Molecular resonance quantified: The resonance Raman spectrum of rhodamine 6G is obtained at 532 nm and the scattering cross-sections are quantified using resonance broadband stimulated Raman spectroscopy. Thus, the molecular resonance and surface-enhanced effects in SERRS are quantified for the first time. The surface enhancement is ∼107–108 in typical SERRS experiments.
Comment on “Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies” (2011)

Everett et al. recently reported on a statistical bias that arises in the target-decoy approach to false discovery rate estimation in two-pass proteomics search strategies as exemplified by X!Tandem. This bias can cause serious underestimation of the false discovery rate. We argue here that the "unbiased" solution proposed by Everett et al., however, is also biased and under certain circumstances can also result in a serious underestimate of the FDR, especially at the protein level.
Analysis of the spectrum characteristics of a super linear optical modulator (2009)

We demonstrate the superior RF spectrum characteristics of an ultra-linear modulator. This modulator exhibits excellent linearity (Spurious Free Dynamic Range, SFDR ~ 133 dB at 1Hz bandwidth), wider linearization bandwidth (an order of magnitude wider), and flatter RF modulation frequency dependence characteristics (linearized 3dB bandwidth ~ 20% of central RF frequency) when compared with Resonator- Assisted Mach Zehnder (RAMZ) modulators. The modulator is based on a traveling-wave electrode design, in which a phase modulator (PM) is on the upper arm of a Mach Zehnder (MZ) interferometer and a ring resonator (RR) is located on the lower arm. This modulator design is also shown to have flexible control of the power split ratio of an RF input to both the PM and the RR, in addition to the RF phase bias between the RR and PM - which enables better manufacturing tolerance.
Phospholipid–porphyrin conjugates: deciphering the driving forces behind their supramolecular assemblies (2022)

Phospholipid-porphyrin conjugates (PL-Por) are nowadays considered as a unique class of building blocks that can self-assemble into supramolecular structures that possess multifunctional properties and enhanced optoelectronics characteristics compared to their disassembled counterparts. However, despite their versatile properties, little is known about the impact of the packing parameter of PL-Por conjugates on their assembling mechanism and their molecular organization inside these assemblies. To gain a better understanding on their assembling properties, we synthesized two new series of PL-Por conjugates with different alkyl sn2-chain lengths linked <i>via</i> an amide bond to either pheophorbide-a (Ph<sub><i>x</i></sub>LPC) or pyropheophorbide-a (Pyr<sub><i>x</i></sub>LPC). By combining a variety of experimental techniques with molecular dynamics (MD) simulations, we investigated both the assembling and optical properties of the PL-Por either self-assembled or when incorporated into lipid bilayers. We demonstrated that independently of the linker length, Ph<sub><i>x</i></sub>LPC assembled into closed ovoid structures, whereas Pyr<sub><i>x</i></sub>LPC formed rigid open sheets. Interestingly, Pyr<sub><i>x</i></sub>LPC assemblies displayed a significant red shift and narrowing of the Q-band indicating the formation of ordered J-aggregates. The MD simulations highlighted the central role of the interaction between porphyrin cores rather than the length difference between the two phospholipid chains in controlling the structure of the lipid bilayer membranes and thus their optical properties. Indeed, while Ph<sub><i>x</i></sub>LPC have the tendency to form inter-leaflet π-stacked dimers, Pyr<sub><i>x</i></sub>LPC conjugates formed dimers within the same leaflet. Altogether, this work could be used as guidelines for the design of new PL-Por conjugates that self-assemble into bilayer-like supramolecular structures with tunable morphology and optical properties.
Synthesis and enzymatic resolution of carbocyclic 2′-ara-fluoro-guanosine: a potent new anti-herpetic agent (1988)

(±)-Carbocyclic-9-(2′-deoxy-2′-β-fluoroarabinofuranosyl) guanine (8) and the corresponding furanose compound (12) have been synthesised; the former compound [which was resolved by formation of the monophosphate (20) and enantioselective hydrolysis using a 5′-nucleotidase] is an extremely potent inhibitor of herpes simplex viruses types 1 and 2.
Some physicochemical properties of plasma membrane vesicles (1976)

Abstract The plasma membranes of many animal cells can be disrupted into small sealed vesicles that can be purified centrifugally and utilized for studies on membrane transport. The vesicles behave as micro‐osmometers. However, the presence of charges fixed at the internal and external surfaces of the membrane walls produce pH levels at these surfaces that deviate considerably from bulk pH. Transverse symmetry of charge distribution further leads to transverse asymmetry of surface pH. Finally, charges fixed at the internal membrane surface produce significant Donnan osmotic effects that depend upon membrane composition and ionic environment.
Higher-yield water-splitting catalyst found (1980)

A method has been developed to detect dense clusters of residue side-chains in proteins, where contact is based upon the percentage of the maximum possible for a given residue type. The clusters represent protein sites with the highest degree of interaction amongst their member residues, while contacts with the environment surrounding the cluster are lower in number. The method has been applied to three distinct structural sets of proteins to check for consistency: mixed alpha-helical/beta-sheet proteins, all beta-strand proteins, and all alpha-helical proteins. A number of cluster features generated from these sets are of general interest for protein folding. (1) A majority of the clusters, comprising three to four residues on average, are localized near the protein surfaces and not within the protein cores. (2) The clusters have preferences for the N- and C-terminal ends of alpha-helices and beta-strands in alpha/beta and alpha-proteins, while beta-proteins utilize the middle strand regions more often. A number of clusters connect three or more beta-strands and/or alpha-helices. (3) More than half of the clusters display residue pairs with oppositely charged atoms within 4.5 A of each other. (4) The residue composition of the clusters does not show correlation with hydrophobicity measures but rather with side-chain volume and surface. The highly preferred cluster residues are (in order of decreasing preference) Trp, His, Arg, Tyr, Glu, Gln and Phe. Clusters with extensive internal contacts in related haemoglobin and immunoglobulin tertiary structures show respective conservation. Several examples illustrate "strategic" folding positions in proteins that often bring together a number of sheets and/or helices, suggesting a folding model in which largely preformed secondary structures are joined together in a cluster induced collapse. Alternatively, the clusters may form at some stage in the folding process to reduce considerably the searchable conformational space and help maintain the proper folding pathway. The clusters also provide hints for site-directed mutagenesis and protein engineering experiments as they are also suggested to be important for structural stability.
A high-speed technique for timeinterleaving continuous-time delta-sigma modulators (2005)

A technique for increasing the speed of time-interleaved continuous-time /spl Delta//spl Sigma/ modulators is presented. Extra feedback paths allow the DAC pulse to enter the adjacent clock period without deteriorating the SNR of the /spl Delta//spl Sigma/ modulator. With the added feedback paths, an extra summer needs to be added to the modulator to attain an equivalent impulse response, but the critical path of the modulator is able to operate twice as fast. Also, with the inclusion of non-idealities such as finite gain and finite bandwidth opamps and DAC clock jitter, the modulator is able to attain a higher SNR with the new technique.
makeSense: Simplifying the Integration of Wireless Sensor Networks into Business Processes (2017)

A wide gap exists between the state of the art in developing Wireless Sensor Network (WSN) software and current practices concerning the design, execution, and maintenance of business processes. WSN software is most often developed based on low-level OS abstractions, whereas business process development leverages high-level languages and tools. This state of affairs places WSNs at the fringe of industry. The makeSense system addresses this problem by simplifying the integration of WSNs into business processes. Developers use BPMN models extended with WSN-specific constructs to specify the application behavior across both traditional business process execution environments and the WSN itself, which is to be equipped with application-specific software. We compile these models into a high-level intermediate language-also directly usable by WSN developers-and then into OS-specific deployment-ready binaries. Key to this process is the notion of meta-abstraction, which we define to capture fundamental patterns of interaction with and within the WSN. The concrete realization of meta-abstractions is application-specific; developers tailor the system configuration by selecting concrete abstractions out of the existing codebase or by providing their own. Our evaluation of makeSense shows that i) users perceive our approach as a significant advance over the state of the art, providing evidence of the increased developer productivity when using makeSense; ii) in large-scale simulations, our prototype exhibits an acceptable system overhead and good scaling properties, demonstrating the general applicability of makeSense; and, iii) our prototype-including the complete tool-chain and underlying system support-sustains a real-world deployment where estimates by domain specialists indicate the potential for drastic reductions in the total cost of ownership compared to wired and conventional WSN-based solutions.
Perceptually motivated spatial and temporal integration of pixel based video quality measures (2007)

In the evaluation of video quality often a full reference approach is used, thus calculating some measure of difference between the reference frames and the distorted frames. Often this measure returns one value per pixel, in the simplest case the squared difference. Conventionally, this pixel based measure is averaged over space and time. This paper introduces a psychophysically derived algorithm for this step. It uses the distribution of the cells in the fovea and the assumption that in a subjective test the part with the highest distortion is most important. Additionally, a temporal integration step is proposed which models the recency and forgiveness effect. Different video quality measures are enhanced with these two steps and their performance is evaluated using the results of a subjective test.
Time and frequency synchronization for CoMP with FBMC (2013)

Filter Bank Multicarrier (FBMC) is a multicarrier modulation technique characterized by a prototype filter that can be optimized either in time or in frequency, depending on the target application and/or on the dispersion of the channel. FBMC is often referred as a non- orthogonal modulation technique as symbols overlap in the time domain and as adjacent subcarriers overlap in the frequency domain. This structural absence of orthogonality at the transmitter implies no need for Cyclic Prefix (CP), increasing the bandwidth efficiency of FBMC systems. In cellular systems, Multi-User (MU) downlink cooperation between cells (CoMP) enables to provide a good quality of service to cell edge users while maintaining a high spectral efficiency in the system. For MU-CoMP, time and frequency synchronization between cooperating Base Stations (BSs) and the User Equipment (UE) is a crucial mandatory step. In this study, where synchronization for CoMP with FBMC is considered, it is demonstrated that the UE can robustly estimate very large delays and arbitrary high carrier frequency offsets. The correction of the delays requires only few bits of feedback and the correction of the frequency offset can be entirely realized at the UE side. These results demonstrate that FBMC is a suitable technique for DL CoMP cellular systems.
Low Level of Antifungal Resistance in Iranian Isolates of Candida glabrata Recovered from Blood Samples in a Multicenter Study from 2015 to 2018 and Potential Prognostic Values of Genotyping and Sequencing of PDR1 (2019)

Establishing an effective empirical antifungal therapy requires that national surveillance studies be conducted. Herein, we report the clinical outcome of infections with and the microbiological features of Iranian isolates of <i>Candida</i><i>glabrata</i> derived from patients suffering from candidemia. <i>C. glabrata</i> isolates were retrospectively collected from four major cities in Iran; identified by a 21-plex PCR, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and large subunit of ribosomal DNA sequencing; and genotyped by amplified fragment length polymorphism (AFLP). Mutations in <i>PDR1</i>, <i>ERG11</i>, and hot spot 1 (HS1) of <i>FKS1</i> and <i>FKS2</i> were investigated, and antifungal susceptibility testing (AFST) was performed (by the CLSI M27-A3 and M27-S4 methods). Seventy isolates of <i>C. glabrata</i> were collected from 65 patients with a median age of 58 years. Fluconazole was the most widely used (29.23%) and least effective antifungal agent. The overall crude mortality rate was 35.4%. Only one strain was resistant to fluconazole, and 57.7% and 37.5% of the isolates were non-wild type (non-WT) for susceptibility to caspofungin and voriconazole, respectively. All isolates showed the WT phenotype for amphotericin B, posaconazole, and itraconazole. HS1 of <i>FKS1</i> and <i>FKS2</i> did not harbor any mutations, while numerous missense mutations were observed in <i>PDR1</i> and <i>ERG11</i> AFLP clustered our isolates into nine genotypes; among them, genotypes 1 and 2 were significantly associated with a higher mortality rate (<i>P</i> = 0.034 and <i>P</i> = 0.022, α < 0.05). Moreover, 83.3% of patients infected with strains harboring a single new mutation in <i>PDR1</i>, T745A, died despite treatment with fluconazole or caspofungin. Overall, Iranian isolates of <i>C. glabrata</i> were susceptible to the major antifungal drugs. Application of genotyping techniques and sequencing of a specific gene (<i>PDR1</i>) might have prognostic implications.
NeutRAN: An Open RAN Neutral Host Architecture for Zero-Touch RAN and Spectrum Sharing (2023)

Obtaining access to exclusive spectrum, cell sites, Radio Access Network (RAN) equipment, and edge infrastructure imposes major capital expenses to mobile network operators. A neutral host infrastructure, by which a third-party company provides RAN services to mobile operators through network virtualization and slicing techniques, is seen as a promising solution to decrease these costs. Currently, however, neutral host providers lack automated and virtualized pipelines for onboarding new tenants and to provide elastic and on-demand allocation of resources matching operators' requirements. To address this gap, this paper presents NeutRAN, a zero-touch framework based on the O-RAN architecture to support applications on neutral hosts and automatic operator onboarding. NeutRAN builds upon two key components: (i) an optimization engine to guarantee coverage and to meet quality of service requirements while accounting for the limited amount of shared spectrum and RAN nodes, and (ii) a fully virtualized and automated infrastructure that converts the output of the optimization engine into deployable micro-services to be executed at RAN nodes and cell sites. NeutRAN was prototyped on an OpenShift cluster and on a programmable testbed with 4 base stations and 10 users from 3 different tenants. We evaluate its benefits, comparing it to a traditional license-based RAN where each tenant has dedicated physical and spectrum resources. We show that NeutRAN can deploy a fully operational neutral host-based cellular network in around 10 seconds. Experimental results show that it increases the cumulative network throughput by 2.18x and the per-user average throughput by 1.73x in networks with shared spectrum blocks of 30 MHz. NeutRAN provides a 1.77x cumulative throughput gain even when it can only operate on a shared spectrum block of 10 MHz (one third of the spectrum used in license-based RANs).
Possible Markers of Venous Sinus Pressure Elevation in Multiple Sclerosis: Correlations with Gender and Disease Progression (2021)

In this larger cohort, worse outcomes in both males and progressive forms of MS were associated with larger sagittal sinuses. The possible cause of the altered sinus pressure in females was narrower transverse sinuses. In males, higher jugular bulbs may be associated with increased venous sinus pressure.
Efficient channel reservation for backup paths in optical mesh networks (2002)

In an optical mesh network, backup channels are shared between multiple lightpaths to reduce restoration capacity overhead. The sharability of channels is usually constrained by the mandate to provide 100% recovery of all lightpaths affected by any single event failure in the network. This paper proposes a pool based channel reservation scheme that is optimal when the set of primary and backup paths (specified at link level without channel allocation) is given. In the online case, our simulations on representative network topologies show that this method improves over the existing (more restrictive) method of allocating shared backup channels using primary path diversity.