gebhart/patrepeval huggingface dataset:
Photon pathlength based self-calibrated pulse oximetry (2022)

In pulse oximetry, arterial oxygen saturation (SpO2) is calculated from near-infrared spectroscopy (NIRS) data using the modified Beer-Lambert Law. Tissue homogeneity is assumed, and the photon mean pathlength (〈L〉) needs to be known or calibrated for. We aim to develop a transabdominal fetal pulse oximeter, where SpO2 = 40-70% and the homogeneity assumption and experimental calibration cannot be applied. Our approach relies on spectral fitting of normalized 〈L〉 from NIRS measurements with analytical description of 〈L〉. Data from simulations and human subjects are presented. Our preliminary results show that the self-calibrated algorithm can accurately extract SpO2 changes in homogenous tissue.
Integrated 1 × 3 MEMS silicon nitride photonics switch (2022)

We present a 1 × 3 optical switch based on a translational microelectromechanical system (MEMS) platform with integrated silicon nitride (SiN) photonic waveguides. The fabricated devices demonstrate efficient optical signal transmission between fixed and suspended movable waveguides. We report a minimum average insertion loss of 4.64 dB and a maximum average insertion loss of 5.83 dB in different switching positions over a wavelength range of 1530 nm to 1580 nm. The unique gap closing mechanism reduces the average insertion loss across two air gaps by a maximum of 7.89 dB. The optical switch was fabricated using a custom microfabrication process developed by AEPONYX Inc. This microfabrication process integrates SiN waveguides with silicon-on-insulator based MEMS devices with minimal stress related deformation of the MEMS platform.
Architectures and Circuit Techniques for Multi-Purpose Digital Phase Lock Loops (2013)

This paper discusses novel architectures and circuit techniques for DPLLs. These include: methods to have a wide temperature range in the digitally controlled oscillator (DCO) for ring-oscillator based DPLLs, re-circulating time to digital converter (TDC) architecture to support a large input phase error range, efficient, modular, divider architectures that provide 50% output duty cycle, while allowing dynamic programmability of the division ratio, and fractional DPLL approaches for spur cancellation and low power operation. The techniques described in the paper have been used to build DPLLs for serializer-deserializer (SerDes), processor clock generation, and wireless connectivity applications in 65 nm and 45 nm CMOS. These implementations are briefly discussed and representative silicon results are presented.
Diels‐Alder reaction of 6‐demethoxy‐β‐dihydrothebaine with methyl vinyl ketone using microwave heating; preparation and pharmacology of 3‐hydroxy‐α,α, 17‐trimethyl‐6β,14β‐ethenomorphinan‐7β‐methanol, a novel deoxygenated diprenorphine analogue (chemistry of opium alkaloids, part XXV (1988)

Abstract Diels‐Alder reaction of 6‐demethoxy‐β‐dihydrothebaine 6 with methyl vinyl ketone (3‐buten‐2‐one) yielded, in a 3:2 ratio, (+)‐7β‐acetyl‐3‐methoxy‐17‐methyl‐6β,14β‐ethenomorphinan‐4‐ol (7) and the novel (+)‐8β‐acetyl‐3‐methoxy‐17‐methyl‐6β,14β‐ethenomorphinan‐4‐ol (8). Performing the reaction in a microwave oven resulted in a faster and cleaner reaction. 1 H NMR and mass spectra of 8 were studied and the structure was finally established by single‐crystal X‐ray analysis of its 4‐ O ‐phenyl ether 13. In contrast to thebaine and 6‐demethoxythebaine, the cyclo‐addition reaction of 6‐demethoxy‐β‐dihydrothebaine with methyl vinyl ketone occurred at the α‐face of the diene system. Ullmann reaction of 7 with bromobenzene, followed by Grignard reaction with methylmagnesium bromide and removal of the phenoxyl group using sodium in liquid ammonia, afforded the tertiary alcohol 11. O ‐Demethylation of 11 by potassium hydroxide in boiling glycol, using microwave heating, afforded (+)‐3‐hydroxy‐α,α,17‐trimethyl‐6β,14β‐ethenomorphinan‐7β‐methanol 12. The structure of 12 was confirmed by 1 H NMR and single‐crystal X‐ray analysis. Compound 12 showed morphine‐like activity in the PPQ assay.
Avian Influenza a H9N2 Viruses in Morocco, 2018–2019 (2022)

Low pathogenic H9N2 avian influenza (LPAI H9N2) is considered one of the most important diseases found in poultry (broiler, laying hens, breeding chickens, and turkeys). This infection causes considerable economic losses. The objective of this work was to monitor and assess the presence of avian influenza virus (AIV) H9N2 in eight different regions of Morocco using real-time RT-PCR, and to assess the phylogenetic and molecular evolution of the H9N2 viruses between 2016 and 2019. Field samples were collected from 108 farms suspected of being infected with LPAI H9N2 virus. Samples were analyzed using H9N2-specific real-time RT-PCR. Highly positive samples were subjected to virus isolation and seven isolates were fully sequenced. Low pathogenic H9N2 avian influenza virus was introduced in Morocco in 2016. We show that in 2018-2019, the virus was still present irrespective of vaccination status. Phylogenetic and molecular analyses showed mutations related to virulence, although our viruses were related to 2016 Moroccan viruses and grouped in the G1 lineage. Specific amino acid substitutions were identified in Moroccan H9N2 viruses that are believed to lead to increased resistance to antiviral drugs.
Stimulated Emission Depletion Nanoscopy Reveals Time-Course of Human Immunodeficiency Virus Proteolytic Maturation (2016)

Concomitant with human immunodeficiency virus type 1 (HIV-1) budding from a host cell, cleavage of the structural Gag polyproteins by the viral protease (PR) triggers complete remodeling of virion architecture. This maturation process is essential for virus infectivity. Electron tomography provided structures of immature and mature HIV-1 with a diameter of 120-140 nm, but information about the sequence and dynamics of structural rearrangements is lacking. Here, we employed super-resolution STED (stimulated emission depletion) fluorescence nanoscopy of HIV-1 carrying labeled Gag to visualize the virion architecture. The incomplete Gag lattice of immature virions was clearly distinguishable from the condensed distribution of mature protein subunits. Synchronized activation of PR within purified particles by photocleavage of a caged PR inhibitor enabled time-resolved in situ observation of the induction of proteolysis and maturation by super-resolution microscopy. This study shows the rearrangement of subviral structures in a super-resolution light microscope over time, outwitting phototoxicity and fluorophore bleaching through synchronization of a biological process by an optical switch.
Influence of Inter Carrier Interference on Link Adaptation Algorithms in OFDM Systems (2007)

The performance of Link Adaptation (LA) under the influence of inter carrier interference (ICI), which is cause by carrier frequency offset (CFO) and Doppler frequency spread due to mobility, in orthogonal frequency division multiplexing (OFDM) based wireless systems is analyzed in this work. LA maximizes throughput while maintaining a target bit error rate (BER) or Block Error Rate (BLER) at the receiver using the signal to noise ratio (SNR) fed back from the receiver to the transmitter. Since ICI power is proportional to the signal strength, the implications of such an impairment on LA OFDM systems is not obvious and has not received much attention till now. It is seen that when ICI is not captured in the SNR measured then the LA system fails to meet the target error rate. However, it is shown that with suitable modification to the SNR switching threshold for changing the adaptive modulation can over the problem. It is also noted that ICI severely reduces the spectral efficiency of OFDM systems even when LA is used.
Canadian Heart Rhythm Society and Canadian Association of Radiologists Consensus Statement on Magnetic Resonance Imaging with Cardiac Implantable Electronic Devices (2014)

Magnetic resonance imaging (MRI) has historically been considered contraindicated for individuals with cardiac implantable electronic devices (CIEDs) such as pacemakers and implantable defibrillators. Magnetic resonance scanners produce magnetic fields that can interact negatively with the metallic components of CIEDs. However, as CIED technology has advanced, newer MRI conditional devices have been developed that are now in clinical use and these systems have had demonstrated safety in the MRI environment. Despite the supportive data of such CIED systems, physicians remain reluctant to perform MRI scanning of conditional devices. This joint statement by the Canadian Heart Rhythm Society and the Canadian Association of Radiologists describes a collaborative process by which CIED specialists and clinics can work with radiology departments and specialists to safely perform MRI in patients with MRI conditional CIED systems. The steps required for patient and scanning preparation and the roles and responsibilities of the CIED and radiology departments are outlined. We also briefly outline the risks and a process by which patients with nonconditional CIEDs might also receive MRI in highly specialized centres. This document supports MRI in patients with MRI conditional CIEDs and offers recommendations on how this can be implemented safely and effectively.
Assessing mucociliary transport of single particles in vivo shows variable speed and preference for the ventral trachea in newborn pigs (2014)

Mucociliary transport (MCT) is an innate defense mechanism that removes particulates, noxious material, and microorganisms from the lung. Several airway diseases exhibit abnormal MCT, including asthma, chronic bronchitis, and cystic fibrosis. However, it remains uncertain whether MCT abnormalities contribute to the genesis of disease or whether they are secondary manifestations that may fuel disease progression. Limitations of current MCT assays and of current animal models of human disease have hindered progress in addressing these questions. Therefore, we developed an in vivo assay of MCT, and here we describe its use in newborn wild-type pigs. We studied pigs because they share many physiological, biochemical, and anatomical features with humans and can model several human diseases. We used X-ray multidetector-row-computed tomography to track movement of individual particles in the large airways of newborn pigs. Multidetector-row-computed tomography imaging provided high spatial and temporal resolution and registration of particle position to airway anatomy. We discovered that cilia orientation directs particles to the ventral tracheal surface. We also observed substantial heterogeneity in the rate of individual particle movement, and we speculate that variations in mucus properties may be responsible. The increased granularity of MCT data provided by this assay may provide an opportunity to better understand host defense mechanisms and the pathogenesis of airway disease.
Silicones (2002)

Abstract Silicon are a class of materials with unique properties that make them useful in a variety of applications of commercial interest and support a thriving global industry. This article updates a comprehensive survey of the chemistry and technology of silicones last published in Kirk‐Othmer Encyclopedia of Chemical Technology in 1997. The update contains more than 235 references not cited in the previous version and includes literature published through 2001. A new section dealing with fiber finishing applications has been included in the current version. The review provides an excellent primary reference for this interesting area of chemistry and technology.
Single-EV analysis (sEVA) of mutated proteins allows detection of stage 1 pancreatic cancer (2022)

Tumor cell-derived extracellular vesicles (EVs) are being explored as circulating biomarkers, but it is unclear whether bulk measurements will allow early cancer detection. We hypothesized that a single-EV analysis (sEVA) technique could potentially improve diagnostic accuracy. Using pancreatic cancer (PDAC), we analyzed the composition of putative cancer markers in 11 model lines. In parental PDAC cells positive for KRAS<sup>mut</sup> and/or P53<sup>mut</sup> proteins, only ~40% of EVs were also positive. In a blinded study involving 16 patients with surgically proven stage 1 PDAC, KRAS<sup>mut</sup> and P53<sup>mut</sup> protein was detectable at much lower levels, generally in <0.1% of vesicles. These vesicles were detectable by the new sEVA approach in 15 of the 16 patients. Using a modeling approach, we estimate that the current PDAC detection limit is at ~0.1-cm<sup>3</sup> tumor volume, below clinical imaging capabilities. These findings establish the potential for sEVA for early cancer detection.
Presentation by a major histocompatibility complex class I molecule of nucleoprotein peptide expressed in two different genes of an influenza virus transfectant. (1995)

Major histocompatibility (MHC) class I glycoproteins are specialized to present to CD8+ T cells, peptides that originate from proteins synthesized within the cytoplasm. Conventional killed vaccines are unable to get into the cell cytoplasm and therefore fail to expand the CD8+ T cell population. We have created a novel influenza transfectant virus, R10, which carries an immunogenic peptide from the nucleoprotein (NP) of PR8 influenza virus in its hemagglutinin (HA) and another similar peptide in its HK influenza virus NP. The two peptides are both presented by H-2Db and bind with approximately equal affinity. They can compete with one another for binding to H-2Db. Yet in cells infected with R10, both peptides are presented efficiently enough to expand the respective cytotoxic T lymphocyte (CTL) precursors in vivo and to serve as targets for CTL lysis in vitro. It has been proposed that proteins bearing signal sequences may be processed by a transporter-independent pathway. To investigate this, we infected the transporter-deficient cell line RMA-S with the R10 virus to see if the NP peptide expressed by the HA would be presented. The result shows that even the presence of a signal peptide in the HA does not overcome the lack of a transporter function, suggesting that the presentation of both peptides is dependent on functional transporter proteins. Our data also suggest the feasibility of creating by genetic engineering, recombinant vaccines expressing multiple epitopes that can effectively stimulate a cellular immune response.
Contour-Based Dead-Time Harmonic Analysis in a Three-Level Neutral-Point-Clamped Inverter (2014)

The term dead time refers to a prime safety factor for most power electronic converter topologies, and it is included either in the control software or in the gate/base driver hardware, depending on the application as well as the control requirements. In this paper, the authors present a comprehensive numerical analysis of dead-time effects on the output voltage of a three-level neutral-point-clamped (NPC) inverter. To incorporate the dead-time effect in the output voltage, 3-D models of three-level carrier pulse width modulation (PWM) methods are modified for two dead-time implementations. Closed-form expressions of inverter phase voltage harmonics for phase opposition disposition (POD) PWM are derived based on the double Fourier series approach and modified contour plots. The harmonic spectra from numerical evaluations, simulations, and experiments for natural sampling (NS), symmetrical regular sampling (SRS), and asymmetrical regular sampling (ARS) are compared to validate the mathematical models. In addition, the fundamental voltage with respect to the dead time and the load phase angle is presented based on analytical results and simulation.
Ionothermal Synthesis of Polyanionic Electrode Material Na3V2(PO4)2FO2 through a Topotactic Reaction (2020)

Polyanionic Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>2</sub>FO<sub>2</sub> has been successfully prepared for the first time by ionothermal reaction in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM TFSI) ionic liquid. Its structure and elemental stoichiometry are confirmed by X-ray diffraction, NMR spectroscopy, and ICP-OES, respectively. Furthermore, the scanning electron microscopy reveals that the as-obtained material possesses an original platelet-like morphology. A topochemical reaction mechanism is proposed to explain the formation of the 3D framework of Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>2</sub>FO<sub>2</sub> from layered compound α-VOPO<sub>4</sub>·2H<sub>2</sub>O. Galvanostatic electrochemical tests indicate a modification of the desodiation and sodiation mechanism of the as-prepared Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>2</sub>FO<sub>2</sub> compared to those synthesized by conventional solid-state approaches. Furthermore, the electrochemical performance of Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>2</sub>FO<sub>2</sub> obtained at different cycling rates is also discussed.
Large meta-analysis of genome-wide association studies identifies five loci for lean body mass (2017)

A correction to this article has been published and is linked from the HTML version of this article.
Emerging Contact-Killing Antibacterial Strategies for Developing Anti-Biofilm Dental Polymeric Restorative Materials (2020)

Polymeric materials are the first choice for restoring tooth cavities, bonding tooth-colored fillings, sealing root canal systems, and many other dental restorative applications. However, polymeric materials are highly susceptible to bacterial attachment and colonization, leading to dental diseases. Many approaches have been investigated to minimize the formation of biofilms over polymeric restorative materials and at the tooth/material interfaces. Among them, contact-killing compounds have shown promising results to inhibit dental biofilms. Contact-killing compounds can be immobilized within the polymer structure, delivering a long-lasting effect with no leaching or release, thus providing advantages compared to release-based materials. This review discusses cutting-edge research on the development of contact-killing compounds in dental restorative materials to target oral pathogens. Contact-killing compounds in resin composite restorations, dental adhesives, root canal sealers, denture-based materials, and crown cements have all demonstrated promising antibacterial properties. Contact-killing restorative materials have been found to effectively inhibit the growth and activities of several oral pathogens related to dental caries, periodontal diseases, endodontic, and fungal infections. Further laboratory optimization and clinical trials using translational models are needed to confirm the clinical applicability of this new generation of contact-killing dental restorative materials.
Novel immunogenic antigen homologous to hyaluronidase in meningioma (1998)

By screening a meningioma expression library with autologous serum we identified four cDNA clones representing a novel gene with striking homology to Caenorhabditis elegans hyaluronidase as indicated by BLASTP analysis. In humans hyaluronidase has been implicated in cancer development and three human genes are known to encode proteins with hyaluronidase activity. None of the human genes, however, showed any homology at the nucleotide or amino acid sequence level to the newly isolated antigen we termed meningioma expressed antigen 5 (MGEA5). Somatic cell hybrid mapping and fluorescence in situ hybridization mapped the gene for MGEA5 to chromosomal band 10q24.1-q24.3. Reverse transcription (RT)-PCR and northern blot hybridization revealed expression of the gene encoding MGEA5 in several meningioma and additional human tissues. Expression analysis also indicated an alternative splicing event giving rise to a shorter and altered transcript termed MGEA5s. The expression of MGEA5 and MGEA5s as fusion proteins revealed an approximate molecular weight of 92 and 54 kDa, respectively. Using heterologous sera we found antibodies against MGEA5s in five out of 23 meningioma patients, whereas no immune reaction was detected in 12 control sera from healthy individuals. Confirmation of hyaluronidase activity was independently achieved by turbidometric analysis and a gel matrix assay. A model for involvement of the novel hyaluronidase gene in meningioma development is proposed.
Chemically Derivatized Semiconductor Photoelectrodes (1980)

Pretreated Au, Pt, n-type Si, and n-type Ge can be derivatized with trichlorosilylferrocene, (1,1′-ferrocenediyl)dichlorosilane, and 1,1′-bis(triethoxysilyl)ferrocene to yield electroactive, surface-attached, oligomeric ferrocene material. Derivatized, n-type semiconductors exhibit photoeffects expected for such an electrode material; irradiated derivatized n-type Si can be used to effect the oxidation of solution reductants by mediated electron transfer, unique proof for which comes from the semiconductor electrode that responds to two stimuli, light and potential. The sustained, mediated oxidation of Fe(CN)64- in aqueous solution in an uphill sense by irradiation of derivatized n-type Si is possible whereas a naked n-type Si undergoes decomposition to SiOx at a rate too fast to allow sustained energy conversion. This establishes the principle of manipulating interfacial charge-transfer kinetics for practical applications.
Mini-circuit cardiopulmonary bypass with vacuum assisted venous drainage: feasibility of an asanguineous prime in the neonate (1999)

Conventional cardiopulmonary bypass (CPB) in neonates results in increased transfusion requirements and hemodilution. There has been little advancement in CPB for the neonatal population. There is evidence that increased priming volumes and blood product transfusion enhances inflammatory response to CPB and increases myocardial and pulmonary dysfunction. We have devised a miniaturized CPB circuit that utilizes vacuum-assisted venous drainage (VAVD) in an effort to decrease priming volume and avoid transfusion requirements. The purpose of this study was to evaluate the safety and efficacy of this miniaturized CPB system and determine the feasibility of an asanguineous prime. Ten 1-week-old piglets were randomized to five mini- and five conventional CPB pump circuits. Subjects were supported with CPB at 100 ml/kg/min, cooled to 28 degrees C, exposed to 10 min aortic crossclamp with cardioplegic arrest, rewarmed to 37 degrees C, weaned from bypass, and subjected to modified-ultrafiltration (MUF) for approximately 10 min. This method was chosen to simulate a situation with all the elements of clinical CPB. Blood transfusion trigger was a hematocrit <15 on CPB. Serum samples were obtained pre-CPB, at 15 min of CPB onset, immediately post-CPB completion, and immediately post-MUF. Indices of hemolysis (SGOT, LDH), production of inflammatory mediators (interleukin (IL)-8, tumor necrosis factor-alpha (TNFalpha)), and physiologic parameters of inflammation were measured. The overall blood requirement was significantly less in the mini-circuit compared to conventional CPB (47.0+/-5.8 ml vs 314.2+/-31.6 ml; p < 0.0001). The only significant blood requirement in the mini-circuit was to replace the volume removed for samples. During the study, mean arterial pressure (MAP) (p = 0.004), static pulmonary compliance (p = 0.04), platelets (p = 0.0003), and white blood cells (p = 0.003) significantly decreased across the groups. Lung water content (p = 0.02), TNFalpha levels (p = 0.05), and SGOT (p = 0.009) increased significantly during the study, across the groups. Among all parameters tested, except for blood requirement and hematocrit post-CPB, there were no significant differences between the two circuits. VAVD makes asanguineous prime in neonates feasible. When used in this study to miniaturize a conventional-CPB circuit, VAVD with a reconfigured neonatal CPB console and circuit resulted in no detrimental effects, and allowed for markedly decreased priming volumes and blood transfusion requirements.