gebhart/patrepeval huggingface dataset:
Terbinafine Resistance of Trichophyton Clinical Isolates Caused by Specific Point Mutations in the Squalene Epoxidase Gene (2017)

Terbinafine is one of the allylamine antifungal agents whose target is squalene epoxidase (SQLE). This agent has been extensively used in the therapy of dermatophyte infections. The incidence of patients with tinea pedis or unguium tolerant to terbinafine treatment prompted us to screen the terbinafine resistance of all <i>Trichophyton</i> clinical isolates from the laboratory of the Centre Hospitalier Universitaire Vaudois collected over a 3-year period and to identify their mechanism of resistance. Among 2,056 tested isolates, 17 (≈1%) showed reduced terbinafine susceptibility, and all of these were found to harbor <i>SQLE</i> gene alleles with different single point mutations, leading to single amino acid substitutions at one of four positions (Leu<sup>393</sup>, Phe<sup>397</sup>, Phe<sup>415</sup>, and His<sup>440</sup>) of the SQLE protein. Point mutations leading to the corresponding amino acid substitutions were introduced into the endogenous <i>SQLE</i> gene of a terbinafine-sensitive <i>Arthroderma vanbreuseghemii</i> (formerly <i>Trichophyton mentagrophytes</i>) strain. All of the generated <i>A. vanbreuseghemii</i> transformants expressing mutated SQLE proteins exhibited obvious terbinafine-resistant phenotypes compared to the phenotypes of the parent strain and of transformants expressing wild-type SQLE proteins. Nearly identical phenotypes were also observed in <i>A. vanbreuseghemii</i> transformants expressing mutant forms of <i>Trichophyton rubrum</i> SQLE proteins. Considering that the genome size of dermatophytes is about 22 Mb, the frequency of terbinafine-resistant clinical isolates was strikingly high. Increased exposure to antifungal drugs could favor the generation of resistant strains.
Lipid Formulations of Amphotericin B Significantly Improve Outcome in Solid Organ Transplant Recipients with Central Nervous System Cryptococcosis (2009)

Lipid formulations of amphotericin B were independently associated with better outcome and may be considered as the first-line treatment for CNS cryptococcosis in these patients.
ChemInform Abstract: The Synthesis and anti‐HIV Activity of Pyrimidine Dioxolanyl Nucleosides. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Observation of carrier-concentration-dependent reflectionless tunneling in a superconductor–two-dimensional-electron-gas–superconductor structure (1994)

We report on the conductance of a short (100 nm) silicon-based two-dimensional electron gas with superconducting source and drain electrodes. Below 1 K a zero-bias enhanced conductance is observed which depends on the carrier concentration in the electron gas. The data can qualitatively be understood as due to reflectionless tunneling; i.e., quantum-coherent-enhanced Andreev scattering.
Fine Particles of Silicon. I. Crystal Growth of Spherical Particles of Si (1987)

Fine crystals of Si having spherical shapes of less than 200 nm, as well as hybrid particles of Si and β-SiC were prepared by a gas evaporation method using an arc discharge as the heat source. Si particles always contain stacking faults and twins which are categorized as growth faults. All the planar faults in a particle occur in the same orientation (parallel to a [110] direction). The nature of these planar faults was examined in terms of crystal growth using an electron microscope. As a result, it has been concluded that these spherical Si particles are crystallized from liquid droplets which condense from Si vapors.
General and Rapid Pyrimidine Condensation by Addressing the Rate Limiting Aromatization (2014)

The rate limiting aromatization within the condensation approach toward pyrimidines utilizing amidines and activated olefins was addressed to provide for a general and rapid process. A strong solvent effect was elucidated to affect the rate for the initial alkoxide elimination from the intermediate Michael adduct wherein polar aprotic solvents demonstrate an addition controlled aromatization. Spectroscopic studies support a solvent dependent equilibrium between the amidine and alkoxide base wherein the rate for aromatization is optimal when the equilibrium toward the amidine anion was strongly favored.
Development of Direct Carbonate Fuel Cell Systems for Achieving Ultrahigh Efficiency (2011)

FuelCell Energy, Inc. (FCE) has developed products based on its Direct FuelCell® (DFC®) technology with efficiencies near 50% based on lower heating values of natural gas. DFC is an internally reformed molten carbonate fuel cell, which operates in the 550–700°C range. The combination of the internal reforming of methane and atmospheric pressure and moderately high temperature of operation has resulted in very simple power plant system configurations. Recently, FCE has developed system concepts to further increase the net electric efficiency to beyond 60% efficiency in sub-MW and MW class power plants. One of these system concepts is the arrangement of the fuel cell stacks in series for very high utilization of fuel in the stacks. Although, in principle, the concept of fuel cell stacks in series is very simple, the implementation of the concept in the actual hardware poses challenges requiring innovative solutions. These challenges include concerns with thermomechanical issues, flow and utilization patterns within the fuel cell stacks, and management of the pressure balance between the anode and the cathode. To address these issues, various analytical tools, including system-level modeling and simulation and computational fluid dynamics (CFD), were utilized. FCE has developed a comprehensive fuel cell stack operation simulation model including hydrodynamics, kinetics, electrochemical, and heat transfer mechanisms to investigate and optimize the design for performance as well as endurance. Various system configurations were developed, which included methods for fueling the second tier stacks in the series. System simulation studies using first principle mass and energy conversation laws were performed. Parametric studies were completed. Subsequent to the system modeling results, the fuel cell stack operations were analyzed using the comprehensive stack simulation model. The CFD modeling of the fuel cell stacks was performed in support of the system simulation parametric studies. The results of the CFD modeling provided insight to the thermal and flow profiles of both first and second tier stacks in series. The net outcome of the investigation was the design of the system, which met the goals of ultrahigh efficiency and yet complied with the thermomechanical requirements of the fuel cell stack components. In this paper, FCE will describe various system options for the very high efficiency systems, the issues related to the design, and the practical solutions to overcome the issues.
Corn Tiller Yield Contributions and Ear Development in Low Plant Densities (2021)

Research in modern corn (Zea mays L.) hybrids investigating tiller contributions and ear development at low plant densities is scarce, particularly in water-limited environments. To fill this research gap, a second season of replicated experiments was conducted in 2020 at 7 sites across Kansas (Keats, Buhler, Greensburg, Garden City, Goodland, and two sites in Colby) evaluating two common, tiller-prone corn hybrids (P0805AM and P0657AM) at three target plant density levels (10000, 17000, and 24000 plants/a). Five of the listed sites also considered a tillering factor (tiller removal at development stage V10 [tenth-leaf] or tiller maintenance). Seasonal phenology, partitioned grain yield, harvested ear type characterizations, and environmental conditions were recorded and analyzed to quantify tiller contributions in each site. Results showed that intact tillers had either no effect or were able to boost yields. In the best environments, tillers were able to successfully compensate for losses of 60% in plant density. Five of the seven tested sites produced approximately 50% of total harvested ears as desirable tiller lateral ears in the 10000 plants/a target plant density. The highest percentage of undesirable tiller tassel ear development in the 10000 plants/a density was 13%. Future research will seek to find explanations of the ear type relationships on a deeper level and predict tiller yield contributions considering various environments and ear development outcomes.
30.8 A 3.5mm×3.8mm Crystal-Less MICS Transceiver Featuring Coverages of ±160ppm Carrier Frequency Offset and 4.8-VSWR Antenna Impedance for Insertable Smart Pills (2020)

Gastroscopy is a common diagnosis method for gastrointestinal (GI) diseases, but it needs to be performed in hospitals. Existing ingestible pills can collect patients' GI information over a longer period outside of a hospital, and various sensors can be incorporated to collect more information. However, ingestible pills passing through the GI system cannot make long recordings in specific places of interest. New gastroscope research focuses on the use of the biopsy channel of an insertion tube to attach the pill on a specific surface of the GI tract for some time before it detaches itself [1]. One of the most challenging parts of such “insertable” pill design is the volume constraint. The biopsy channels in gastroscopes have a diameter of ~3.5mm (at least 3x less than existing pills), and the length of the non-bendable part should be <; 15mm (Fig 30.8.1). Since the pill is at places covered by up to 15cm of tissue, a wireless system operating in the 402-to-405MHz MICS band is preferable because of lower tissue attenuation compared to higher frequency bands, e.g., 2.4GHz. It also provides a longer communication distance and wider signal bandwidth compared to near-field communication systems [2]. Finally, the interference control in MICS ensures the implants having an interference-free channel. However, the volume constraint poses significant challenge for a MICS transceiver design because external components should be avoided, and it interfaces with an electrically small ( (10) antenna which has high sensitivity to the surrounding environment. A crystal-less transceiver is preferred because the crystal is typically the biggest off-chip component. A mm-scale radio in [3] replaces the crystal with an FBAR but requires a special manufacturing process. A mm-scale crystal-free radio in [4] presented a network-assisted timing synchronization for its Pulse-Position-Modulation(PPM)-based system. However, transceivers operating in MICS must adhere to a carrier stability better than ± 100ppm which mandates carrier synchronization for crystal-free operation, and it is especially critical for FSK/PSK transceivers that are preferred in MICS for their better channel selectivity and interference resilience. Power-oscillator topologies [5] have been widely adopted in recent mm-scale radios owing to their small size and high efficiency. However, the external coil impedance variation due to the direct contact of tissues can influence the carrier stability of the power oscillator, and the power oscillator cannot be reconfigured as an LO for FSKIPSK-based RXs.
Adaptive radio resource assignment for simultaneous services (2004)

An adaptive algorithm for selecting rate matching parameters has been developed to satisfy the operating frame error rate requirements for simultaneous services in 3G Universal Mobile Telecommunications System (UMTS) under Rayleigh fading channels. The results show that the adaptive algorithm can achieve the target error rates for multiplexed services of varying data rates and types, and only requires a few adjustments for convergence.
Responses of Model Cortical Neurons to Temporal Interference Stimulation and Related Transcranial Alternating Current Stimulation Modalities (2022)

Abstract Objective Temporal interference stimulation (TIS) was proposed as a non-invasive, focal, and steerable deep brain stimulation method. However, the mechanisms underlying experimentally-observed suprathreshold TIS effects are unknown, and prior simulation studies had limitations in the representations of the TIS electric field (E-field) and cerebral neurons. We examined the E-field and neural response characteristics for TIS and related transcranial alternating current stimulation modalities. Approach Using the uniform-field approximation, we simulated a range of stimulation parameters in biophysically realistic model cortical neurons, including different orientations, frequencies, amplitude ratios, amplitude modulation, and phase difference of the E-fields, and obtained thresholds for both activation and conduction block. Main results For two E-fields with similar amplitudes (representative of E-field distributions at the target region), TIS generated an amplitude-modulated total E-field. Due to the phase difference of the individual E-fields, the total TIS E-field vector also exhibited rotation where the orientations of the two E-fields were not aligned (generally also at the target region). TIS activation thresholds (75–230 V/m) were similar to those of high-frequency stimulation with or without modulation and/or rotation. For E-field dominated by the high-frequency carrier and with minimal amplitude modulation and/or rotation (typically outside the target region), TIS was less effective at activation and more effective at block. Unlike amplitude-modulated high-frequency stimulation, TIS generated conduction block with some orientations and amplitude ratios of individual E-field at very high amplitudes of the total E-field (&gt;1700 V/m). Significance The complex 3D properties of the TIS E-fields should be accounted for in computational and experimental studies. The mechanisms of suprathreshold cortical TIS appear to involve neural activity block and periodic activation or onset response, consistent with computational studies of peripheral axons. These phenomena occur at E-field strengths too high to be delivered tolerably through scalp electrodes and may inhibit endogenous activity in off-target regions, suggesting limited significance of suprathreshold TIS.
3‐Hydroxybenzene 1,2,4‐Trisphosphate, a Novel Second Messenger Mimic and unusual Substrate for Type‐I myo‐Inositol 1,4,5‐Trisphosphate 5‐Phosphatase: Synthesis and Physicochemistry (2006)

3-Hydroxybenzene 1,2,4-trisphosphate 4 is a new myo-inositol 1,4,5-trisphosphate analogue based on the core structure of benzene 1,2,4-trisphosphate 2 with an additional hydroxyl group at position-3, and is the first noninositol based compound to be a substrate for inositol 1,4,5-trisphosphate 5-phosphatase. In physicochemical studies on 2, when three equivalents of protons were added, the (31)P NMR spectrum displayed monophasic behaviour in which phosphate-1 and phosphate-2 behaved independently in most of the studied pH range. For compound 4, phosphate-2 and phosphate-4 interacted with the 3-OH group, which does not titrate at physiological pH, displaying complex biphasic behaviour which demonstrated co-operativity between these groups. Phosphate-1 and phosphate-2 strongly interacted with each other and phosphate-4 experienced repulsion because of the interaction of the 3-OH group. Benzene 1,2,4-trisphosphate 2 is resistant to inositol 1,4,5-trisphosphate type I 5-phosphatase catalysed dephosphorylation. However, surprisingly, 3-hydroxybenzene 1,2,4-trisphosphate 4 was dephosphorylated by this 5-phosphatase to give the symmetrical 2,3-dihydroxybenzene 1,4-bisphosphate 16. The extra hydroxyl group is shown to form a hydrogen bond with the vicinal phosphate groups at -15 degrees C, and (1)H NMR titration of the ring and hydroxyl protons in 4 shows the OH proton to be strongly stabilized as soon as the phosphate groups are deprotonated. The effect of the phenolic 3-OH group in compound 4 confirms a critical role for the 6-OH group of the natural messenger in the dephosphorylation mechanism that persists even in radically modified analogues.
Confirmation of the OVOL2 Promoter Mutation c.-307T>C in Posterior Polymorphous Corneal Dystrophy 1 (2017)

Previously identified as the cause of PPCD1, the OVOL2 promoter variant c.-307T>C was herein identified in the original family that established the PPCD1 locus. However, the failure to identify presumed pathogenic coding or non-coding OVOL2 or ZEB1 variants, or CNV involving the PPCD1 and PPCD3 loci in 26 other PPCD probands suggests that other genetic loci may be involved in the pathogenesis of PPCD.
Inside Cover: A Membrane‐Free Neutral pH Formate Fuel Cell Enabled by a Selective Nickel Sulfide Oxygen Reduction Catalyst (Angew. Chem. Int. Ed. 26/2017) (2017)

A membrane-free fuel cell relies on the selectivity of catalysts at both the anode and the cathode. In their Communication on page 7496 ff., Y. Surendranath et al. show that the sulfide N3S2 selectively catalyzes the oxygen reduction reaction (ORR) in the presence of a high concentration of formate. Paired with the known formate oxidation catalyst Pd/C, the selective ORR catalyst Ni3S2 enables the construction of a membrane-free formate fuel cell that operates at neutral pH and outperforms the Pt–Pd device.
Computerized administration of health-related quality of life instruments compared to interviewer administration may reduce sample size requirements in clinical research: a pilot randomized controlled trial among rheumatology patients. (2008)

The reduced variability in 3 of 5 instruments and good acceptance of computerized HRQoL assessment, if confirmed in larger studies, may lead to smaller sample size requirements, with potential reductions in cost and recruitment time for clinical trials and cohort studies.
Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments (2013)

Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6-week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts ('shuffling') in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs <10-km apart can exhibit substantial differences in their physiological response to thermal stress, which could impact their population dynamics under climate change.
Evidence for nonlocality and the crossover from nonlocal to local behavior near the critical temperature in superconducting metals (2003)

We have performed high precision measurements of the temperature dependence of the magnetic penetration depth $\ensuremath{\lambda}(T)$ in pure aluminum and cadmium samples. These superconductors and most of the other superconducting metals are predicted to be in the nonlocal limit of electrodynamics. However, most previous experimental works on $\ensuremath{\lambda}(T)$ in Al reported large deviations from the expected nonlocal behavior. Here we present experimental data which agree remarkably well with theory, giving very strong evidence that nonlocal superconductivity indeed occurs in both Al and Cd. More strikingly, the cadmium data are consistent with the existence of the crossover from nonlocal to local behavior predicted to occur in all superconductors near ${T}_{c}.$
Physical Models of Boron Diffusion in Ultrathin Gate Oxides (1997)

Based on a network defect model for the diffusion of B in we propose that B diffuses via a peroxy linkage defect whose concentration in the oxide changes under different processing conditions. We show that as the gate oxide is scaled below 80 Å in thickness, additional chemical processes act to increase B diffusivity and decrease its activation energy, both as a function of the distance from the interface. For a 15 Å oxide, the B diffusivity at 900°C would increase by a factor of 24 relative to diffusion in a 100 Å oxide. The role of nitridation of to create a barrier to B diffusion is modeled by assuming the N atoms compete with B for occupation of diffusion‐defect sites. The model predicts that nitridation is ineffective in stopping B penetration when implants are used to dope the polysilicon gate and similarly for B implants when the gate oxide thickness decreases below approximately 30 to 40 Å.
Stage‐specific excretory–secretory small heat shock proteins from the parasitic nematode Strongyloides ratti– putative links to host’s intestinal mucosal defense system (2011)

In a search for molecules involved in the interaction between intestinal nematodes and mammalian mucosal host cells, we performed MS to identify excretory-secretory proteins from Strongyloides ratti. In the excretory-secretory proteins of the parasitic female stage, we detected, in addition to other peptides, peptides homologous with the Caenorhabditis elegans heat shock protein (HSP)-17, named Sra-HSP-17.1 (∼ 19 kDa) and Sra-HSP-17.2 (∼ 18 kDa), with 49% amino acid identity. The full-length cDNAs (483 bp and 474 bp, respectively) were identified, and the genomic organization was analyzed. To allow further characterization, the proteins were recombinantly expressed and purified. Profiling of transcription by quantitative real-time-PCR and of protein by ELISA in various developmental stages revealed parasitic female-specific expression. Sequence analyses of both the DNA and amino acid sequences showed that the two proteins share a conserved α-crystallin domain and variable N-terminals. The Sra-HSP-17s showed the highest homology with the deduced small HSP sequence of the human pathogen Strongyloides stercoralis. We observed strong immunogenicity of both proteins, leading to strong IgG responses following infection of rats. Flow cytometric analysis indicated the binding of Sra-HSP-17s to the monocyte-macrophage lineage but not to peripheral lymphocytes or neutrophils. A rat intestinal epithelial cell line showed dose-dependent binding to Sra-HSP-17.1, but not to Sra-HSP-17.2. Exposed monocytes released interleukin-10 but not tumor necrosis factor-α in response to Sra-HSP-17s, suggesting the possible involvement of secreted female proteins in host immune responses.
A ZVS approach for AC/DC converter with PFC (2004)

Other than integrating the PFC and the DC/DC converter, this approach resorts to the conventional two stage design with constant operating frequency and ZVS for all switches. A small switch is added between the PFC and asymmetric half bridge DC/DC converter to produce a four switch AC/DC converter with PFC. A 91% efficiency 12 V 10 A universal off line AC/DC adapter is built to demonstrate its merits.