gebhart/patrepeval huggingface dataset:
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima (2013)

Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified a large fraction of genes committed to carbohydrate degradation and utilization in the model bacterium Thermotoga maritima. Knowledge of these genes enabled comprehensive reconstruction of biochemical pathways comprising the carbohydrate utilization network. However, transcriptional factors (TFs) and regulatory mechanisms driving this network remained largely unknown. Here, we used an integrated approach based on comparative analysis of genomic and transcriptomic data for the reconstruction of the carbohydrate utilization regulatory networks in 11 Thermotogales genomes. We identified DNA-binding motifs and regulons for 19 orthologous TFs in the Thermotogales. The inferred regulatory network in T. maritima contains 181 genes encoding TFs, sugar catabolic enzymes and ABC-family transporters. In contrast to many previously described bacteria, a transcriptional regulation strategy of Thermotoga does not employ global regulatory factors. The reconstructed regulatory network in T. maritima was validated by gene expression profiling on a panel of mono- and disaccharides and by in vitro DNA-binding assays. The observed upregulation of genes involved in catabolism of pectin, trehalose, cellobiose, arabinose, rhamnose, xylose, glucose, galactose, and ribose showed a strong correlation with the UxaR, TreR, BglR, CelR, AraR, RhaR, XylR, GluR, GalR, and RbsR regulons. Ultimately, this study elucidated the transcriptional regulatory network and mechanisms controlling expression of carbohydrate utilization genes in T. maritima. In addition to improving the functional annotations of associated transporters and catabolic enzymes, this research provides novel insights into the evolution of regulatory networks in Thermotogales.
Association Between Plasma Diacetylspermine and Tumor Spermine Synthase With Outcome in Triple-Negative Breast Cancer (2019)

Metabolomic profiling identified plasma DAS as a predictive marker for TNBC progression and metastasis.
<title>Low-power highly miniaturized image sensor technology</title> (1997)

A second generation image sensor technology has been developed at the NASA Jet Propulsion Laboratory with performance comparable to charge-coupled device (CCDs). This sensor is implemented using the industry-standard complementary metal-oxide semiconductor (CMOS) technology employed for nearly all microprocessors and memory chips and thus takes advantage of the rapid worldwide development of this technology. The CMOS active pixel sensor (APS) maintains the performance of CCDs regarding noise and quantum efficiency and offers unique advantages for ultra low power focal plane operation and integration of supporting electronics such as timing, control, clock, signal chains and analog-to-digital converters. This paper describes the technology for implementing a low power camera-on-a-chip.
Whole-Genome Analyses and Circulating Tumor DNA Approaches in Cancer (2013)

In this interview we discuss advances in whole-genome analyses, as well as novel blood-based assays in development to help diagnose and follow cancer patients through their treatment.
Rate-Splitting Multiple Access for Multi-Antenna Downlink Communication Systems: Spectral and Energy Efficiency Tradeoff (2021)

Rate-splitting (RS) has recently been recognized as a promising physical-layer technique for multi-antenna broadcast channels (BC). Due to its ability to partially decode the interference and partially treat the remaining interference as noise, RS is an enabler for a powerful multiple access, namely rate-splitting multiple access (RSMA), that has been shown to achieve higher spectral efficiency (SE) and energy efficiency (EE) than both space division multiple access (SDMA) and non-orthogonal multiple access (NOMA) in a wide range of user deployments and network loads. As SE maximization and EE maximization are two conflicting objectives in the moderate and high signal-to-noise ratio (SNR) regimes, the study of the tradeoff between the two criteria is of particular interest. In this work, we address the SE-EE tradeoff by studying the joint SE and EE maximization problem of RSMA in multiple input single output (MISO) BC with rate-dependent circuit power consumption at the transmitter. To tackle the challenges coming from multiple objective functions and rate-dependent circuit power consumption, we first propose two models to transform the original problem into two single-objective problems, namely, weighted-sum method and weighted-power method. A low-complexity algorithm with closed-form solution is proposed to solve each single-objective problem in the two-user system. For the generalized <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$K$ </tex-math></inline-formula> -user system, a successive convex approximation (SCA)-based algorithm is then proposed to optimize the precoders of each transformed problem. Numerical results show that our algorithm converges much faster than existing algorithms. In addition, the performance of RSMA is superior to or equal to SDMA and NOMA in terms of SE, EE and their tradeoff.
Switch mode constant current LED Driver with high efficiency, high precision and wide dimming ratio (2013)

A high efficiency hard switching constant current LED driver is presented with high overall efficiency, high current precision, high LED efficacy, flicker-free and wide constant current dimming ratio. The high stable lighting source provides the best solution for office light, reading light and LCD backlight.
Natalizumab Improves the Health Related Quality of Life (HRQOL) in Crohnʼs Disease Patients (2005)

Purpose: Crohn's disease is associated with impaired HRQOL. This analysis investigated HRQOL outcomes during maintenance therapy with natalizumab (a humanized monoclonal IgG4 antibody to α4 integrin) in the ENACT-2 trial where higher rates of sustained response and remission were observed compared with placebo. Methods: Patients who responded to natalizumab induction therapy (n = 339) were randomized to natalizumab 300 mg (n = 168) or placebo infusions (n = 171) given monthly for up to 12 months. HRQOL was measured by the Inflammatory Bowel Disease Questionnaire (IBDQ) and the Short Form-36 (SF-36) at months 0, 3, 6, 9, and 12. Higher scores indicate better HRQOL. A minimally important difference (MID) is defined as 16 pts for Total IBDQ and 5 pts for SF-36 summary scores. Results: The change for all IBDQ scales from ENACT-1 baseline was significantly greater (p < 0.05) in natalizumab-treated patients at all timepoints. Changes in 7 of 10 SF-36 scales were significant by month 3 and all were significant in months 9 and 12. A significantly greater proportion of natalizumab patients achieved MID on the Total IBDQ at months 6–12 and the SF-36 PCS at months 3–12. Mean scores for physical function, social function, role-emotional, and mental health approximated US norms at month 12. Conclusions: Maintenance therapy with natalizumab resulted in significantly improved HRQOL, as evidenced by both disease specific (IBDQ) and general (SF-36) measures.Table: Change From Baseline [Mean (SD)]
Understanding Polymorph Transformations in Core‐Chlorinated Naphthalene Diimides and their Impact on Thin‐Film Transistor Performance (2015)

Though charge transport is sensitive to subtle changes in the packing motifs of molecular semiconductors, research addressing how intermolecular packing influences electrical properties has largely been carried out on single‐crystals, as opposed to the more technologically relevant thin‐film transistors (TFTs). Here, independent and reversible access to the monoclinic and triclinic crystal structures of a core‐chlorinated naphthalene tetracarboxylic diimide (NTCDI‐1) is demonstrated in polycrystalline thin films via post‐deposition annealing. Time‐resolved measurements of these transitions via UV–visible spectroscopy and grazing‐incidence X‐ray diffraction indicate that the polymorphic transformations follow second‐order Avrami kinetics, suggestive of 2D growth after initial nucleation. Thin‐film transistors comprising triclinic NTCDI‐1 consistently outperform those comprising its monoclinic counterpart. This behavior contrasts that of single‐crystal transistors in which devices comprising monoclinic crystals are consistently superior to devices with triclinic crystals. This difference is attributed to more uniform in‐plane charge transport in polycrystalline thin films having the triclinic compared to the monoclinic polymorph. As the mobility of TFTs is a reflection of ensemble‐average charge transport across crystalline grains having different molecular orientations, this study suggests that among different polymorphs of a particular molecular semiconductor, those with smaller in‐plane anisotropy are more beneficial for efficient lateral charge transport in polycrystalline devices.
Observation of $B_{c}^{+} \to J/ψD^{(*)} K^{(*)}$ decays (2016)

A search for the decays Bc+→J/ψD(∗)0K+ and Bc+→J/ψD(∗)+K∗0 is performed with data collected at the LHCb experiment corresponding to an integrated luminosity of 3 fb-1. The decays Bc+→J/ψD0K+ and Bc+→J/ψD∗0K+ are observed for the first time, while first evidence is reported for the Bc+→J/ψD∗+K∗0 and Bc+→J/ψD+K∗0 decays. The branching fractions of these decays are determined relative to the Bc+→J/ψπ+ decay. The Bc+ mass is measured, using the J/ψD0K+ final state, to be 6274.28±1.40(stat)±0.32(syst) MeV/c2. This is the most precise single measurement of the Bc+ mass to date.
Accurate Dopant and Interface Characterization in Oxidized SiC with Refined Non-Contact C-V Technique (2019)

The non-contact C-V technique has been recently gaining interest as a precise, cost and time effective metrology for wide-bandgap semiconductors. Originally focused on dopant measurement, non-contact C-V has been expanding to encompass wide-bandgap surface and interface characterization, including complex reliability issues critical for the future of power devices. In this work, we report progress achieved using a new direct method for determining the flatband voltage, V FB , and capacitance, C FB . Experimental results are presented for n-type oxidized epitaxial 4-H SiC. They demonstrate the approach and the unique self-consistent measurement producing an entire set of pertinent electrical parameters, including the interface trap density, D it .
Exploring Cryptococcus neoformans capsule structure and assembly with a hydroxylamine-armed fluorescent probe (2020)

Chemical biology is an emerging field that enables the study and manipulation of biological systems with probes whose reactivities provide structural insights. The opportunistic fungal pathogen <i>Cryptococcus neoformans</i> possesses a polysaccharide capsule that is a major virulence factor, but is challenging to study. We report here the synthesis of a hydroxylamine-armed fluorescent probe that reacts with reducing glycans and its application to study the architecture of the <i>C. neoformans</i> capsule under a variety of conditions. The probe signal localized intracellularly and at the cell wall-membrane interface, implying the presence of reducing-end glycans at this location where the capsule is attached to the cell body. In contrast, no fluorescence signal was detected in the capsule body. We observed vesicle-like structures containing the reducing-end probe, both intra- and extracellularly, consistent with the importance of vesicles in capsular assembly. Disrupting the capsule with DMSO, ultrasound, or mechanical shear stress resulted in capsule alterations that affected the binding of the probe, as reducing ends were exposed and cell membrane integrity was compromised. Unlike the polysaccharides in the assembled capsule, isolated exopolysaccharides contained reducing ends. The reactivity of the hydroxylamine-armed fluorescent probe suggests a model for capsule assembly whereby reducing ends localize to the cell wall surface, supporting previous findings suggesting that this is an initiation point for capsular assembly. We propose that chemical biology is a promising approach for studying the <i>C. neoformans</i> capsule and its associated polysaccharides to unravel their roles in fungal virulence.
Bubble translation due to radiation force in SWL (2000)

The clustering of cavitation bubbles may lead to enhanced stone comminution and influence the extent of tissue damage during shock wave lithotripsy (SWL) treatment. Recent research has focused on changing the SWL pulse, or timing between pulses, to intensify or mitigate collapse or localize these clusters. Such research has targeted radial, not translational motion. We investigate whether bubble translation due to radiation force is sufficiently large to influence cluster formation. The translational dynamics of a single spherical bubble were modeled according to the formulation proposed by Watanabe and Kukita [Phys. Fluids 5(11) (1993)]. After radius-time data were obtained using the Gilmore equation, translational motion was calculated by numerical integration of the Watanabe equation. Calculations were performed for a range of bubble sizes (R0=2–20 μm) and pressure rise times (10−9–10−7 s). The results show that, during bubble growth and collapse induced by a single pulse or two pulses with microsecond delays, bubble translations are ∼0.1 mm. Although bubble translation from a single pulse may not have a noticeable effect on bubble distribution, the effect may be cumulative for the 1000+ shots fired during clinical SWL treatment. [Work supported by NIH DK43881, NSF, CRDF, and FIRCA.]
Measurement of theT+TNeutron Spectrum Using the National Ignition Facility (2013)

Neutron time-of-flight spectra from inertial confinement fusion experiments with tritium-filled targets have been measured at the National Ignition Facility. These spectra represent a significant improvement in energy resolution and statistics over previous measurements, and afford the first definitive observation of a peak resulting from sequential decay through the ground state of (5)He at low reaction energies E(c.m.) 100 </~ keV. To describe the spectrum, we have developed an R-matrix model that accounts for interferences from fermion symmetry and intermediate states, and show these effects to be non-negligible. We also find the spectrum can be described by sequential decay through ℓ=1 states in (5)He, which differs from previous interpretations.
Effect of shape and nano-segregation in Δ2-isoxazoline and isoxazole on the mesogenic behavior of 1,3-bis-isophthalimines (2022)

Bis-1,3-isophthalimines flanked by two side 3-aryl-5-perfluoroalkylisoxazoline or 3-aryl-5-perfluoroalkylisoxazol arms were produced and liquid crystal properties were analysed. Monotropic smectic A mesophase was found for bis-1,3-isophthalimines containing the 3-aryl-5-perfluorooctylisoxazoline (8b). Thermal behaviour was analysed and discussed by DSC, POM, DFT calculations, cohesive energy density (CED), Hildebrand solubility parameters and molecular-shape features. Notably, for long side arm perfluorooctyl 8b, the reduced value of CED is partially compensated by molecular shape of the molecules in the condensed state favouring the SmA mesophase formation.
Optimizing infusion scheduling through lean methods and data science. (2016)

e18240 Background: Mid-day peaks in chair utilization commonly result in long waiting times for patients and a surge in pharmacy and nursing workload. The size of the solution space is enormous – a 35-chair infusion center operating 12 hours per day with appointments scheduled at 10 minute intervals throughout the day has 3.3 * 10^106 possible configurations. It is therefore impossible to “find” an optimal solution using the traditional approaches of scheduling by chair or by nurse. Methods: We have applied an optimization algorithm, based on the lean principle of level loading demand (Heijunka). The algorithm captures center-specific parameters such as the operating hours, nurse staffing/schedule and patient volume/acuity as constraints. It then analyzes the expected duration of each appointment and “shuffles the appointment deck” by sequencing the start time of appointments in the order that would level load the infusion chairs throughout the day. The final output is a “fingerprint” template unique for each hour of each day given the specific operating parameters of the infusion center. This template works within the existing scheduling system so that schedulers do not experience any change in their workflow. Results: The solution has been stable for approximately a year with positive results (Table). Conclusions: Level loading chair utilization improves both the patient experience as well as the financial performance of the infusion center. The patient experience is improved by creating more appointment slots and by reducing wait times especially in the middle of the day. Financial performance is improved by reducing overtime dollars and by completing more treatments within the existing fixed cost structure. Improvements in infusion center performance. Metric Baseline (Q4 FY 13) Current (Q1 FY 16) Improvement (%) Number of treatments 54,000 (in 2013) 65,000 (in 2015) 20.4% increase Median Wait time 14:36 minutes 10:00 minutes 31.5% reduction % patients with a wait time under 15 minutes 51% 66% 29.4% improvement Emergency Callback (ECB) per pay period N/A N/A 81.6% reduction Unit cost of service N/A N/A 17% reduction Nurse satisfaction N/A N/A 25 percentile point improvement
Partial breast radiotherapy after breast-conserving surgery (2020)

Techniques for accelerated partial breast irradiation focus on the tumor bed and a zone of surrounding tissue of variable depth, and rates of local control to date appear comparable to whole breast irradiation for matched and appropriately selected patients. A commentary accompanying the first results of the TARGeted Intraoperative radioTherapy-A trial claimed partial breast irradiation to be a new standard of care for suitably selected patients. Published trials have confirmed that rates of local control lie within pre-defined non-inferiority margins. Historically, lumpectomy followed by whole breast irradiation has been the foundation of breast-conservation therapy and provides an acceptable alternative to mastectomy in the management of early-stage breast cancer. One meta-analysis systemically examined 24 studies involving 1933 patients undergoing oncoplastic surgery and external beam whole breast irradiation. It was concluded that improved communication between disciplines could allow for better tumor bed identification and reduced treatment volumes.
Effect of Quantum Barrier Thickness in the Multiple-Quantum-Well Active Region of GaInN/GaN Light-Emitting Diodes (2013)

The dependence of the polarization-induced electric field in GaInN/GaN multiple-quantum-well light-emitting diodes (LEDs) on the GaN quantum barrier (QB) thickness is investigated. Electrostatic arguments and simulations predict that a thin QB thickness reduces the electric field in the quantum wells (QWs) and also improves the LED efficiency. We experimentally demonstrate that the QW electric field decreases with decreasing QB thickness. The lower electric field results in a better overlap of electron and hole wave functions and better carrier confinement in the QWs. A reduced efficiency droop and enhanced internal quantum efficiency is demonstrated for GaInN/GaN LEDs when the QB thickness is reduced from 24.5 to 9.1 nm.
Efficient frequency doubling of a femtosecond pulse with simultaneous group-velocity matching and quasi phase matching in periodically poled, MgO-doped lithium niobate (2003)

We demonstrate efficient frequency doubling of 95-fs pulses with a small temporal broadening in a 10-mm-long, periodically poled, 5-mol % MgO-doped lithium niobate crystal. Simultaneous group-velocity matching and quasi phase matching were achieved by the off-diagonal nonlinear optical coefficient d32 at telecommunications range.
Tumor necrosis factor α plays a central role in immune-mediated clearance of adenoviral vectors (1997)

Adenovirus (Ad) gene transfer vectors are rapidly cleared from infected hepatocytes in mice. To determine which effector mechanisms are responsible for elimination of the Ad vectors, we infected mice that were genetically compromised in immune effector pathways [perforin, Fas, or tumor necrosis factor alpha (TNF-alpha)] with the Ad vector, Ad5-chloramphenicol acetyl transferase (CAT). Mice were sacrificed at 7-60 days postinfection, and the levels of CAT expression in the liver determined by a quantitative enzymatic assay. When the livers of infected mice were harvested 28 days postinfection, the levels of CAT expression revealed that the effectors most important for the elimination of the Ad vector were TNF-alpha > Fas > perforin. TNF-alpha did not have a curative effect on infected hepatocytes, as the administration of TNF-alpha to infected severe combined immunodeficient mice or to infected cultures in vitro had no specific effect on virus persistence. However, TNF-alpha-deficient mice demonstrated a striking reduction in the leukocytic infiltration early on in the infection, suggesting that TNF-alpha deficiency resulted in impaired recruitment of inflammatory cells to the site of inflammation. In addition, the TNF-deficient mice had a significantly reduced humoral immune response to virus infection. These results demonstrate a dominant role of TNF-alpha in elimination of Ad gene transfer vectors. This result is particularly important because viral proteins that disable TNF-alpha function have been removed from most Ad vectors, rendering them highly susceptible to TNF-alpha-mediated elimination.
Identification and quantitation of intracellular retinol and retinoic acid binding proteins in cultured cells. - eScholarship (1984)

Although the mechanism whereby vitamin A mediates normal cell differentiation and inhibits tumor cell proliferation is unknown, intracellular receptor-like proteins for retinol and retinoic acid have been implicated in the molecular action of vitamin A. We have assayed these two binding proteins, cellular retinol binding protein (protein R) and cellular retinoic acid binding protein (protein RA), in the cytosolic fraction of various normal and tumor cells via sucrose density gradient centrifugation and saturation analysis. Employing charcoal separation of bound and free tritiated retinoid, the saturation analysis yields an approximate Kd for ligand binding and an estimate of the number of protein R and protein RA molecules per cell. Unique protein R and protein RA macromolecules sedimenting at 2 S with Kd values of 7-42 nM are detected in murine cells (1 degree epidermal, 3T6 fibroblasts and melanoma) and human neuroblastoma cells. Concentrations of the intracellular binding proteins range from 55 000 to 3 000 000 copies per cell. When one cell line (C-127 mouse mammary) is transformed by bovine papilloma virus, protein RA levels increase from undetectable to 193 000 copies per cell. Assessment of growth inhibition by 10(-6) M retinol or retinoic acid in the culture medium reveals that there exists a partial, but not absolute, correlation between the presence of protein R or protein RA and the antiproliferative effect of the particular retinoid in the tested cell lines. We conclude that the 2 S intracellular binding proteins for the retinoids are present in most vitamin A responsive cells, but may not be essential for biologic actions of the vitamin such as growth inhibition in monolayer culture.