gebhart/patrepeval huggingface dataset:
Regulation of sialic acid transport and catabolism in <i>Haemophilus influenzae</i> (2007)

Virulence of nontypeable Haemophilus influenzae (NTHi) is dependent on the decoration of lipooligosaccharide with sialic acid. This sugar must be derived from the host, as NTHi cannot synthesize sialic acids. NTHi can also use sialic acid as a carbon source. The genes encoding the sialic acid transporter and the genes encoding the catabolic activities are localized to two divergently transcribed operons, the siaPT operon and the nan operon respectively. In this study, we identified SiaR as a repressor of sialic acid transport and catabolism in NTHi. Inactivation of siaR resulted in the unregulated expression of the genes in both operons. Unregulated catabolism of sialic acid in the siaR mutant resulted in the reduction of surface sialylation and an increase in serum sensitivity. In addition to SiaR-mediated repression, CRP, the cAMP receptor protein, was shown to activate expression of the siaPT operon but not the nan operon. We describe a model in which SiaR and CRP work to modulate intracellular sialic acid levels. Our results demonstrate the importance of SiaR-mediated regulation to balance the requirement of surface sialylation and the toxic accumulation of intracellular sialic acid.
Acoustic coupling in capacitive microfabricated ultrasonic transducers: modeling and experiments (2005)

In the design of low-frequency transducer arrays for active sonar systems, the acoustic interactions that occur between the transducer elements have received much attention. Because of these interactions, the acoustic loading on each transducer depends on its position in the array, and the radiated acoustic power may vary considerably from one element to another. Capacitive microfabricated ultrasonic transducers (CMUT) are made of a two-dimensional array of metallized micromembranes, all electrically connected in parallel, arid driven into flexural motion by the electrostatic force produced by an applied voltage. The mechanical impedance of these membranes is typically much lower than the acoustic impedance of water. In our investigations of acoustic coupling in CMUTs, interaction effects between the membranes in immersion were observed, similar to those reported in sonar arrays. Because CMUTs have many promising applications in the field of medical ultrasound imaging, understanding of cross-coupling mechanisms and acoustic interaction effects is especially important for reducing cross-talk between array elements, which can produce artifacts and degrade image quality. In this paper, we report a finite-element study of acoustic interactions in CMUTs and experimental results obtained by laser interferometry measurements. The good agreement found between finite element modeling (FEM) results and optical displacement measurements demonstrates that acoustic interactions through the liquid represent a major source of cross coupling in CMUTs.
Circulating tumor cells: A step toward precision medicine in hepatocellular carcinoma (2022)

Serum alpha-fetoprotein and radiologic imaging are the most commonly used tests for early diagnosis and dynamic monitoring of treatment response in hepatocellular carcinoma (HCC). However, the accuracy of these tests is limited, and they may not reflect the underlying biology of the tumor. Thus, developing highly accurate novel HCC biomarkers reflecting tumor biology is a clinically unmet need. Circulating tumor cells (CTCs) have long been proposed as a noninvasive biomarker in clinical oncology. Most CTC assays utilize immunoaffinity-based, size-based, and/or enrichment-free mechanisms followed by immunocytochemical staining to characterize CTCs. The prognostic value of HCC CTC enumeration has been extensively validated. Subsets of CTCs expressing mesenchymal markers are also reported to have clinical significance. In addition, researchers have been devoting their efforts to molecular characterizations of CTCs (e.g. genetics and transcriptomics) as molecular profiling can offer a more accurate readout and provide biological insights. As new molecular profiling techniques, such as digital polymerase chain reaction, are developed to detect minimal amounts of DNA/RNA, several research groups have established HCC CTC digital scoring systems to quantify clinically relevant gene panels. Given the versatility of CTCs to provide intact molecular and functional data that reflects the underlying tumor, CTCs have great potential as a noninvasive biomarker in HCC. Large-scale, prospective studies for HCC CTCs with a standardized protocol are necessary for successful clinical translation.
Nested codebook design for MIMO precoders (2008)

In multi-input, multi-output (MIMO) communication systems, significant throughput gains can be obtained by closed-loop operation, where two aspects of the transmission are adapted to channel conditions: the transmission rank (number of independent spatial layers); and the precoding matrix which maps the spatial layers to the transmit antennas. To facilitate feedback and signaling, the precoding matrix for each rank is often restricted to a finite pre-determined codebook. Prior research has studied the problem of designing the codebook independently for each rank, with the aim of maximizing throughput gains for a given codebook size. In this paper, we propose to jointly design the family of codebooks for various transmission ranks. Our nested codebooks greatly simplify both codebook design and the selection of precoding matrix for a specific channel. In addition, we prove by analysis and simulation results that the complexity reduction is obtained without sacrificing throughput gains. Due to these advantages, the proposed structured codeboook design has been accepted for use in the 3GPP Long Term Evolution (LTE) standard [9].
Photochemically Driven Biomimetic Oxidation of Alkanes and Olefins (1990)

A photochemical reaction for oxidation of hydrocarbons that uses molecular oxygen as the oxidant is described. A reductive photoredox cycle that uses a tin(IV)- or antimony(V)-porphyrin photosensitizer generates the co-reductant equivalents required to activate oxygen. This "artificial" photosynthesis system drives a second catalytic cycle, mimicking the cytochrome P450 reaction, which oxidizes hydrocarbons. An iron(III)- or manganese (III)-porphyrin is used as the hydrocarbon-oxidation catalyst. Methylviologen can be used as a redox relay molecule to provide for electron-transfer from the reduced photosensitizer to the Fe or Mn porphyrin, but appears not to enhance efficiency of the process. The system is long-lived and may be used in time-resolved spectroscopic studies of the photo-initiated reaction to determine reaction rates and intermediates.
Compromised mitochondrial quality control triggers lipin1-related rhabdomyolysis (2021)

<i>LPIN1</i> mutations are responsible for inherited recurrent rhabdomyolysis, a life-threatening condition with no efficient therapeutic intervention. Here, we conduct a bedside-to-bench-and-back investigation to study the pathophysiology of lipin1 deficiency. We find that lipin1-deficient myoblasts exhibit a reduction in phosphatidylinositol-3-phosphate close to autophagosomes and late endosomes that prevents the recruitment of the GTPase Armus, locks Rab7 in the active state, inhibits vesicle clearance by fusion with lysosomes, and alters their positioning and function. Oxidized mitochondrial DNA accumulates in late endosomes, where it activates Toll-like receptor 9 (TLR9) and triggers inflammatory signaling and caspase-dependent myolysis. Hydroxychloroquine blocks TLR9 activation by mitochondrial DNA <i>in vitro</i> and may attenuate flares of rhabdomyolysis in 6 patients treated. We suggest a critical role for defective clearance of oxidized mitochondrial DNA that activates TLR9-restricted inflammation in lipin1-related rhabdomyolysis. Interventions blocking TLR9 activation or inflammation can improve patient care <i>in vivo</i>.
Long Length MgB<sub>2</sub> Conductors for Industrial Applications (2006)

In spite of the relatively short time dedicated to the development of MgB2 conductors since its discovery in 2001, a remarkable progress has been already achieved in terms of critical current density, homogeneity of the conductors and reproducibility of the results over long lengths. Unlike other HTS and LTS materials, MgB2 conductor processing is more open to a number of improvements and modifications that help in making it more attractive for several DC and AC applications. Up to now our work has been focused on the improvement of the production capacity in order to allow for the assembly of large prototype magnets to test the capability of MgB2 to maintain the present level of performance over very long lengths. Long MgB2 tapes of about 1600 m with superconducting and mechanical properties suitable for making low field magnets are already available. Presently we are focusing on the enhancement of the irreversibility field. This would open the possibility of using MgB2 also for high field applications.
A Pilot Study Examining the Performance of Polynomial‐Modeled Ventricular Shock Electrograms for Rhythm Discrimination in Implantable Devices (2006)

Our data demonstrate the feasibility of simple polynomial equations that reproduce the depolarization and repolarization phases of human ventricular shock EGM. The ratio of first-order to zero-order QR coefficient was able to reliably discriminate between SVT and VT while reducing the polynomial model to a first-order system. The results of this pilot trial may serve as the basis for a larger prospective trial implementing a discrimination algorithm for use in low computational power implantable devices.
Tapered rib adiabatic following fiber couplers in etched GaAs materials for monolithic spot-size transformation (1997)

Design details and demonstration data are presented for an (Al,Ga)As monolithic tapered rib waveguide achieving modal spot-size transformation. The tapered rib adiabatic following fiber coupler structure (TRAFFIC) achieves two-dimensional (2-D) expansion of the output optical mode of single-transverse-mode semiconductor waveguide modulators and lasers using a one-dimensional (1-D) taper between noncritical initial and final taper widths which are compatible with optical lithographic techniques. Measurements are presented of total mode expansion losses between /spl sim/1.5-2.0 dB and semiconductor to single-mode-fiber waveguide coupling losses of /spl sim/0.5-1.0 dB for doped pin optical-modulator-type waveguides using the TRAFFIC waveguide. A semiconductor laser with a TRAFFIC tapered-rib mode-expansion section and measured coupling loss between the laser output and single-mode fiber of only 0.9 dB is described. Finally, a TRAFFIC Spot-size transformer for undoped waveguide modulators with total mode expansion losses of 1.84 dB and excellent modal behavior at 1.32-/spl mu/m wavelength is presented. The TRAFFiC structure is particularly well suited for integration with both active and passive etched rib waveguide devices. Fabrication is relatively simple, requiring only patterning and etching of the tapered waveguide and uniform-width outer mesa waveguide without any epitaxial regrowth.
Development of a new fiber optic probe for fluorophore quantification in tissues (1998)

A new type of fiber optic probe can measure fluorescence intensities from tissues which is insensitive to changes in the background pigment concentration, and may be calibrated to be insensitive to scattering coefficient changes.
MgO(111) Nanosheets with Unusual Surface Activity (2007)

MgO(111) nanosheets can be prepared via a facile wet chemical process. The MgO(111) nanosheets possessing the exposed (111) plane as a main surface have a thickness typically between 3 and 5 nm. Study of MgO(111) nanosheets by in situ diffuse reflectance Fourier transform (DRIFT) spectroscopy suggests that hydroxyl groups, oxygen vacancies, and surface oxygen anions exist on the surface and the (111) surface may be stabilized by hydroxyl groups. DRIFTS and temperature-programmed desorption (TPD) studies of CO2 adsorption reveal that there are large amounts of medium basic sites which can be attributed to the high concentration of surface O2- Lewis basic sites. DRIFTS and temperature-programmed reaction studies (TPRS) of methanol have demonstrated that, in contrast to commercial MgO, MgO(111) nanosheets are highly reactive toward the decomposition of methanol. Methanol can be decomposed and the surface CO species formed can be oxidized readily at low temperature by the high concentration of oxygen anions on the surface of MgO(111) nanosheets, which demonstrates that these nanosheets have potential application in fuel cells and methanol-based alternative energy technologies.
Dental pulp of the third molar: a new source of pluripotent-like stem cells (2012)

Summary Dental pulp is particularly interesting in regenerative medicine because of the accessibility and differentiation potential of the tissue. Dental pulp has an early developmental origin with multi-lineage differentiation potential as a result of its development during childhood and adolescence. However, no study has previously identified the presence of stem cell populations with embryonic-like phenotypes in human dental pulp from the third molar. In the present work, we describe a new population of dental pulp pluripotent-like stem cells (DPPSCs) that were isolated by culture in medium containing LIF, EGF and PDGF. These cells are SSEA4 + , OCT3/4 + , NANOG + , SOX2 + , LIN28 + , CD13 + , CD105 + , CD34 − , CD45 − , CD90 + , CD29 + , CD73 + , STRO1 + and CD146 − , and they show genetic stability in vitro based on genomic analysis with a newly described CGH technique. Interestingly, DPPSCs were able to form both embryoid-body-like structures (EBs) in vitro and teratoma-like structures that contained tissues derived from all three embryonic germ layers when injected in nude mice. We examined the capacity of DPPSCs to differentiate in vitro into tissues that have similar characteristics to mesoderm, endoderm and ectoderm layers in both 2D and 3D cultures. We performed a comparative RT-PCR analysis of GATA4 , GATA6 , MIXL1 , NANOG , OCT3/4 , SOX1 and SOX2 to determine the degree of similarity between DPPSCs, EBs and human induced pluripotent stem cells (hIPSCs). Our analysis revealed that DPPSCs, hIPSC and EBs have the same gene expression profile. Because DPPSCs can be derived from healthy human molars from patients of different sexes and ages, they represent an easily accessible source of stem cells, which opens a range of new possibilities for regenerative medicine.
Long coherence length for cw photolytic atomic iodine lasers at 1315 μm (1991)

With a low-power cw photolytic atomic iodine laser operating at 1.315 microm, coherence lengths greater than 220 m have been observed. These results are to our knowledge the first coherent length measurements of any type of atomic iodine laser. A Michelson interferometer was used to demonstrate this long-coherence-length property. In addition, Fabry-Perot interferometric measurements provided a laser frequency linewidth (Deltaf < 1.0 MHz) consistent with this long-coherence-length observation. Such a large coherence length should be common to all homogeneously broadened, photolytic atomic iodine lasers.
Measuring the distortion of speech by a facemask (2022)

Most prior research focuses on the reduced amplitude of speech caused by facemasks. This paper argues that the interaction between the acoustic properties of a facemask and the acoustic properties of the vocal tract contributes to speech distortion by changing the formants of the voice. Speech distortion of a number of masks was tested by measuring the increase in damping of the first formant. Results suggest that masks dampen the first formant and that increasing the distance between the mask wall and mouth can reduce this distortion. These findings contribute to the research studying the impact of masks on speech.
Process for preparing polyimide adhesives (1975)

High bonding strengths are obtained for metals and fiber-reinforced organic resin composites with no significant loss in thermo-oxidative stability of the adhesive resin.
Universal evaluations and expressions of measuring uncertainty for rotating-element spectroscopic ellipsometers (2015)

We obtain the universal evaluations and expressions of measuring uncertainty for all types of rotating-element spectroscopic ellipsometers. We introduce a general data-reduction process to represent the universal analytic functions of the combined standard uncertainties of the ellipsometric sample parameters. To solve the incompleteness of the analytic expressions, we formulate the estimated covariance for the Fourier coefficient means extracted from the radiant flux waveform using a new Fourier analysis. Our approach can be used for optimization of measurement conditions, instrumentation, simulation, standardization, laboratory accreditation, and metrology.
Facile Fabrication of Scalable, Hierarchically Structured Polymer/Carbon Architectures for Bioelectrodes (2012)

This research introduces a method for fabrication of conductive electrode materials with hierarchical structure from porous polymer/carbon composite materials. We describe the fabrication of (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) scaffolds doped with carbon materials that provide a conductive three-dimensional architecture that was demonstrated for application in microbial fuel cell (MFC) anodes. Composite electrodes from PHBV were fabricated to defined dimensions by solvent casting and particulate leaching of a size-specific porogen (in this case, sucrose). The cellular biocompatibility of the resulting composite material facilitated effective immobilization of a defined preparation of Shewanella oneidensis DSP-10 as a model microbial catalyst. Bacterial cells were immobilized via chemical vapor deposition (CVD) of silica to create an engineered biofilm that exhibits efficient bioelectrocatalysis of a simple-carbon fuel in a MFC. The functionalized PHBV electrodes demonstrate stable and reproducible anodic open circuit potentials of -320 ± 20 mV (vs Ag/AgCl) with lactate as the electron donor. Maximum power densities achieved by the hierarchically structured electrodes (~5 mW cm(3)) were significantly higher than previously observed for graphite-felt electrodes. The methodology for fabrication of scalable electrode materials may be amenable to other bioelectrochemical applications, such as enzyme fuel cells and biosensors, and could easily be adapted to various design concepts.
Tumour suppressor microRNAs contribute to drug resistance in malignant pleural mesothelioma by targeting anti-apoptotic pathways (2019)

<b>Aim:</b> Aberrant microRNA expression is a common event in cancer drug resistance, however its involvement in malignant pleural mesothelioma (MPM) drug resistance is largely unexplored. We aimed to investigate the contribution of microRNAs to the resistance to drugs commonly used in the treatment of MPM. <b>Methods:</b> Drug resistant MPM cell lines were generated by treatment with cisplatin, gemcitabine or vinorelbine. Expression of microRNAs was quantified using RT-qPCR. Apoptosis and drug sensitivity assays were carried out following transfection with microRNA mimics or BCL2 siRNAs combined with drugs. <b>Results:</b> Expression of miR-15a, miR-16 and miR-34a was downregulated in MPM cells with acquired drug resistance. Transfection with miR-15a or miR-16 mimics reversed the resistance to cisplatin, gemcitabine or vinorelbine, whereas miR-34a reversed cisplatin and vinorelbine resistance only. Similarly, in parental cell lines, miR-15a or miR-16 mimics sensitised cells to all drugs, whereas miR-34a increased response to cisplatin and vinorelbine. Increased microRNA expression increased drug-induced apoptosis and caused BCL2 mRNA and protein reduction. RNAi-mediated knockdown of BCL2 partly recapitulated the increase in drug sensitivity in cisplatin and vinorelbine treated cells. <b>Conclusion:</b> Drug-resistant MPM cell lines exhibited reduced expression of tumour suppressor microRNAs. Increasing tumour suppressor of microRNA expression sensitised both drug resistant and parental cell lines to chemotherapeutic agents, in part through targeting of BCL2. Taken together, these data suggest that miR-15a, miR-16 and miR-34a are involved in the acquired and intrinsic drug resistance phenotype of MPM cells.
Home is where the (fast) internet is (2010)

Internet traffic to homes is surging, driven by the demand for rich content and the proliferation of home networks. This creates a huge problem for ISPs since residential customers expect the certainty of a fixed bill while ISPs do not want to upgrade backhaul equipment frequently in the absence of extra revenue streams. We consider simple variants on existing flat-rate schemes that will enable homes to self-select a portion of their peak hours traffic and move it to non-peak hours to benefit from offered incentives. We present a well-defined formulation of the problem and characterize its computational complexity. We show that a simple fractional algorithm achieves the optimal traffic reallocation and is realizable with small modifications to existing infrastructure. The fractional model also captures the reality that homes may be willing to move a fraction of their delay-tolerant traffic in response to appropriate incentives. Using trace-driven simulations based on well-accepted utility models and actual backbone traffic from a large ISP, we demonstrate that our incentive scheme can substantially lower peak congestion while still satisfying the increased demand of home networks.
Learning phrase-based head transduction models for translation of spoken utterances (1998)

We describe a method for automatically learning headtransducer models of translation from examples consisting of transcribed spoken utterances and their translations. The method proceeds by first searching for a hierarchical alignment (specifically a synchronized dependency tree) of each training example. The alignments produced are optimal with respect to a cost function that takes into account co-occurrence statistics and the recursive decomposition of the example into aligned substrings. A probabilistic head-transducer model is then constructed from the alignments. We report results of applying the method to English-to-Spanish translation in the domain of air travel information and Englishto-Japanese translation in the domain of telephone operator assistance. We also report on a variation on this modelconstruction method in which multi-word pairings are used in the computation of the hierarchical alignments and head transducer models.
Intertrack Interference Cancellation for Shingled Magnetic Recording (2011)

The intertrack interference in squeezed tracks of a magnetic hard disk drive is investigated based on captured waveforms. Specifically, extracted intertrack interference impulses and statistics are presented as a function of track squeeze and read offset. The bit-error-rate improvement of intertrack interference cancellation is shown based on simulations with captured drive waveforms. Architecture and implementation aspects for hard disk drives with intertrack interference cancellation are described.
Improved Methods for Correlating Transforms in Multiple Description Coding Systems (2006)

Multiple descriptions have been widely investigated as a quality of service technology for the delivery of multimedia information over lossy channels. This paper presents generalized methods for transform based multiple descriptions that do not introduce additional distortion to the transformed information. Previous noiseless methods place restrictions on how the information may be quantized prior to correlation. Typically, the information must be quantized with quasi-uniform quantizers which all have the same quantization step size. This paper expands these methods so that the information may be quantized with any quantizer, and different parts of the information may be quantized with different quantization step sizes. For specific correlating transforms, we propose a computationally efficient correlation transform that makes use of the Hadamard matrix