gebhart/patrepeval huggingface dataset:
Characteristic adsorption ofXeon aSi(111)−(7×7)surface at low temperature (2002)

Site-dependent adsorption structures of Xe atoms on a $\mathrm{Si}(111)\ensuremath{-}7\ifmmode\times\else\texttimes\fi{}7$ surface were studied by scanning tunneling microscopy at 8 K. Xe atoms initially adsorb as dimers on the site between a rest atom and its two neighboring center adatoms, and then near the corner adatom site. Similar structures were formed at both the faulted half (FH) and the unfaulted half (UH) of the $7\ifmmode\times\else\texttimes\fi{}7$ unit. The observed structure is in excellent agreement with that estimated by the rigid ball model, however, site-dependent bias dependence and different stabilities were observed for them, indicating the existence of different interactions between Xe and Si atoms in the $7\ifmmode\times\else\texttimes\fi{}7$ unit despite the stable electronic structure of Xe. Based on the results with thermal desorption spectroscopy, the adsorption energies are estimated to be 200 and 220 meV for FH and UH units, respectively.
Quadruple adaptive observer of the core temperature in cylindrical Li-ion batteries and their health monitoring (2012)

Temperature monitoring is a critical issue for lithium ion batteries. Since only the surface temperature of the battery can be measured, a thermal model is needed to estimate the core temperature, which can be higher and hence more critical. In this paper, an on-line parameter identification scheme is designed for a cylindrical lithium ion battery thermal model, by which the parameters of the thermal model can be identified automatically. An adaptive observer is designed based on the on-line parameterization methodology and the closed loop architecture. A linear battery thermal model is explored first, where the internal resistance is assumed to be constant. The methodology is later extended to address temperature dependent internal resistance with non-uniform forgetting factors. The capability of the methodology to track the long term variation of the internal resistance is beneficial for battery health monitoring.
Failure Defects Observed in Post-Breakdown High-&#x003BA;/Metal Gate Stack Mosfet (2006)

Failure defects associated with breakdown of the HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /TaN/TiN gate stack metal-oxide-semiconductor field effect transistor (MOSFET) are studied. Very fast degradation rate in the gate leakage current is attributed to gate material filament of the breakdown path, leading to various degrees of severity in micro structural damages in the narrow width MOSFET structure. This observation is different from that reported for the poly crystalline-silicon (poly-Si) gate MOSFET. On the other hand, some common failure mechanisms driven by gate dielectric breakdown, such as dielectric-breakdown-induced epitaxy (DBIE) and silicide migration i.e. dielectric-breakdown-induced migration (DBIM), previously observed in poly-Si gate MOSFET are still found in metal gate MOSFET
Poster 60: Fascia Lata for the Prevention of Recurrent Posterior Vaginal Wall Prolapse: Subanalysis of a Randomized, Controlled Trial (2005)

OBJECTIVE: The objective of this study was to evaluate the efficacy of solvent dehydrated cadaveric fascia lata in preventing recurrent posterior vaginal wall prolapse during reconstructive surgery. METHODS: This was a subanalysis of all women enrolled in a prospective, randomized, controlled trial evaluating the impact of a 2 × 4-cm patch of solvent dehydrated cadaveric fascia lata on recurrent prolapse. Women with anterior vaginal wall prolapse to the hymenal ring and beyond were randomized to standard repair with or without a fascial patch in the anterior and posterior compartments. The patch was sutured in place between the plicated endopelvic connective tissue and vaginal epithelium. Subjects were evaluated by the POP-Q system preoperatively and at 2, 6, 12, 52 weeks postoperatively. Patients were also asked to return for follow up beyond 1 year. “Failure” was defined as ICS stage II posterior wall prolapse. Groups were compared using chi-squared or Fisher exact tests. Multiple logistic regression analysis was used to control for potential confounding variables. RESULTS: Of 154 subjects randomized from July 1999 to November 2002, 148 underwent posterior colporrhaphy (75 patch; 73 no patch). One hundred thirty-three subjects (90%) returned for either a 52-week or long-term evaluation. Baseline characteristics, including age, parity, previous reconstructive surgery, concomitant surgeries, and preoperative prolapse stage, were not significantly different between the 2 study groups. Thirteen of 75 subjects (17%) and 12 of 73 controls (16%) experienced recurrent stage II or greater posterior wall prolapse (P=0.772). Rates of postoperative dyspareunia (13% vs 11%), constipation (32% vs 35%), and fecal incontinence (8% vs 10%) were not significantly different between the 2 study groups. CONCLUSION: The use of solvent dehydrated fascia lata as a barrier during posterior colporrhaphy does not appear to decrease the rate of recurrent rectocele. Although grafts in the posterior compartment are being used with increasing frequency, comparative trials demonstrating improved anatomic or symptomatic outcomes are still needed.
Kisspeptin Is Essential for the Full Preovulatory LH Surge and Stimulates GnRH Release from the Isolated Ovine Median Eminence (2011)

Kisspeptins are the product of the Kiss1 gene and potently stimulate GnRH secretion. In sheep, Kiss1 mRNA-expressing cells are found in the arcuate nucleus (ARC) and dorsal-lateral preoptic area and both appear to mediate the positive feedback effect of estradiol to generate the preovulatory GnRH/LH surge. To determine the role of kisspeptin in transmitting estrogen-positive feedback in the hypothalamus, we administered the kisspeptin antagonist p-271 to ewes subjected to an estradiol benzoate-induced LH surge. Kisspeptin antagonist treatment significantly attenuated these LH surges. We further examined the response to kisspeptin treatment prior to the LH surge. Kisspeptin significantly stimulated GnRH secretion into the hypophysial portal system, but the response to kisspeptin was similar in luteal and late-follicular phase ewes. Kiss1r mRNA expression in GnRH neurons was also similar across the estrous cycle. To examine alternative pathways for kisspeptin stimulation of GnRH neurons, we examined the origin of kisspeptin neuronal fibers in the external zone of the median eminence (ME) using neuronal tracing and immunohistochemical techniques. ARC populations of kisspeptin neurons project fibers to the ME. Finally, we showed kisspeptin stimulates GnRH release from ovine ME-cultured explants. This suggests direct kisspeptin to GnRH terminal-to-terminal communication within the ME. Overall, these data indicate an essential role for kisspeptin in receiving stimulatory estrogen signals and generating the full positive feedback GnRH/LH surge. Kisspeptin neurons of the ARC project to the external zone of the ME and kisspeptin acts upon the GnRH fibers at this level.
Blue and green laser diodes for large laser display (2013)

Watt-class AlInGaN blue and green laser diodes (LDs) on c face GaN substrate are fabricated. The optical output powers of blue LDs and green LDs were 3.75 W and 1.01 W, and the wall plug efficiencies were 38.5% and 14.1%, respectively. The lifetimes were estimated to be over 30,000 and 15,000 hours at a case temperature of 50°C.
Position Sensorless Control Method in Low Speed Region for Permanent Magnet Synchronous Motors Using the Neutral Point Voltage of Stator Windings (2015)

In this paper, we propose a new sensorless control method using the neutral point voltage of stator windings. Each inductance of the three phase coils of the permanent magnet synchronous motor (PMSM) is slightly changed by the rotor magnet flux. As a result, the neutral point voltage also changes depending on the rotor position. According to this principle, the rotor position can be estimated by detecting the neutral point voltage, even in the zero speed region. We implement this technique and show the experimental results.
Contrast‐to‐noise ratio in functional MRI of relative cerebral blood volume with sprodiamide injection (1997)

The purpose of this study was to investigate the dependence of contrast-to-noise ratio (CNR) on the dose and rate of sprodiamide injection in magnetic resonance relative cerebral blood volume (rCBV) imaging. rCBV maps for 35 normal volunteers were constructed from dynamic MR image sets acquired with echo-planar spin-echo imaging after intravenous injection of sprodiamide. Doses of .1, .2, and .3 mmol/kg, at rates of 2 ml/second and 5 ml/second, were tested. CNRs and blood/volume ratios of gray to white matter were computed. CNR depended on dose (P < .0001) but was independent of injection rate (P < .69). rCBV ratios of gray to white matter were dose independent (P < .38) and rate independent (P < .97). The dependence of CNR on dose, but not injection rate, has practical implications in optimal protocol design. The independence of gray/white ratios supports the theory underlying the generation of rCBV maps.
Spin-Torque-Triggered Magnetization Reversal in Magnetic Tunnel Junctions with Perpendicular Shape Anisotropy (2021)

Recently, the concept of perpendicular shape anisotropy spin-transfer-torque magnetic random-access memory (PSA STT MRAM) was proposed to enhance the thermal stability factor, $\mathrm{\ensuremath{\Delta}}$, of the storage layer through its shape anisotropy, thus enabling the downsizing scalability of conventional STT MRAM beyond sub-20-nm technological nodes. However, this is expected to negatively impact the writing current and switching time, calling for the search for the best compromise. Here, we report a micromagnetic study of the STT-driven magnetization reversal of sub-20-nm PSA STT MRAM cells, with a particular emphasis on the technologically relevant case of $\mathrm{\ensuremath{\Delta}}\ensuremath{\simeq}80$, thus providing guidelines for their practical design. For an aspect ratio ($\ensuremath{\eta}$) of the storage layer of $\ensuremath{\eta}\ensuremath{\le}1$, magnetization reversal obeys a macrospinlike mechanism, while for $\ensuremath{\eta}&gt;1$ a noncoherent reversal is observed, which is characterized by buckling or nucleation of a transverse domain wall at the ferromagnet-insulator interface, which then propagates along the vertical axis. Decreasing the lateral size while maintaining a constant value of $\mathrm{\ensuremath{\Delta}}$ implies a larger height, which is found to lead to an increase of the switching voltage. In all cases, the inverse of the switching time scales linearly with the applied voltage.
The future of child and adolescent clinical psychopharmacology: A systematic review of phase 2, 3, or 4 randomized controlled trials of pharmacologic agents without regulatory approval or for unapproved indications (2023)

We aimed to identify promising novel medications for child and adolescent mental health problems. We systematically searched https://clinicaltrials.gov/ and https://www.clinicaltrialsregister.eu/ (from 01/01/2010-08/23/2022) for phase 2 or 3 randomized controlled trials (RCTs) of medications without regulatory approval in the US, Europe or Asia, including also RCTs of dietary interventions/probiotics. Additionally, we searched phase 4 RCTs of agents targeting unlicensed indications for children/adolescents with mental health disorders. We retrieved 234 ongoing or completed RCTs, including 26 (11%) with positive findings on ≥ 1 primary outcome, 43 (18%) with negative/unavailable results on every primary outcome, and 165 (70%) without publicly available statistical results. The only two compounds with evidence of significant effects that were replicated in ≥ 1 additional RCT without any negative RCTs were dasotraline for attention-deficit/hyperactivity disorder, and carbetocin for hyperphagia in Prader-Willi syndrome. Among other strategies, targeting specific symptom dimensions in samples stratified based on clinical characteristics or established biomarkers may increase chances of success in future development programmes.
Development of IsoTaG, a Chemical Glycoproteomics Technique for Profiling Intact N- and O-Glycopeptides from Whole Cell Proteomes (2017)

Protein glycosylation can have an enormous variety of biological consequences, reflecting the molecular diversity encoded in glycan structures. This same structural diversity has imposed major challenges on the development of methods to study the intact glycoproteome. We recently introduced a method termed isotope-targeted glycoproteomics (IsoTaG), which utilizes isotope recoding to characterize azidosugar-labeled glycopeptides bearing fully intact glycans. Here, we describe the broad application of the method to analyze glycoproteomes from a collection of tissue-diverse cell lines. The effort was enabled by a new high-fidelity pattern-searching and glycopeptide validation algorithm termed IsoStamp v2.0, as well as by novel stable isotope probes. Application of the IsoTaG platform to 15 cell lines metabolically labeled with Ac<sub>4</sub>GalNAz or Ac<sub>4</sub>ManNAz revealed 1375 N- and 2159 O-glycopeptides, variously modified with 74 discrete glycan structures. Glycopeptide-bound glycans observed by IsoTaG were found to be comparable to released N-glycans identified by permethylation analysis. IsoTaG is therefore positioned to enhance structural understanding of the glycoproteome.
Targeted Learning of The Probability of Success of An In Vitro Fertilization Program Controlling for Time-dependent Confounders (2012)

Infertility is a global public health issue and various treatments are available. In vitro fertilization (IVF) is an increasingly common treatment method, but accurately assessing the success of IVF programs has proven challenging since they consist of multiple cycles. We present a double robust semiparametric method that incorporates machine learning to estimate the probability of success (i.e., delivery resulting from embryo transfer) of a program of at most four IVF cycles in the French Devenir Apr`es Interruption de la FIV (DAIFI) study and several simulation studies, controlling for time-dependent confounders. We find that the probability of success in the DAIFI study is 50% (95% confidence interval [0.48, 0.53]), therefore approximately half of future participants in a program of at most four IVF cycles can expect a delivery resulting from embryo transfer.
168. Efficacy of the Novel gwt1 Inhibitor APX2039 in a Rabbit Model of cryptococcus Meningitis (2020)

Abstract Background Cryptococcal meningitis (CM), caused primarily by Cryptococcus neoformans, is uniformly fatal if not treated. Treatment options are limited especially in resource-poor geographical regions, and mortality rates remain high despite current therapies. New oral treatment options are needed that demonstrate rapid reductions in CFU in CSF and brain tissue. APX2039 is a novel inhibitor of the fungal Gwt1 enzyme, which catalyzes an early step in glycosylphosphatidyl inositol (GPI) anchor biosynthesis. It is highly active against both C. neoformans and C. gattii and has previously demonstrated significant efficacy in a mouse delayed-treatment model of CM. CSF Fungal Burden in Rabbits Methods Male New Zealand White rabbits were inoculated with C. neoformans H99 (1.4 ×106 CFU) directly into the cisterna magna. Rabbits were immunosuppressed with cortisone acetate at 7.5 mg/kg (i.m.), starting on Day -1 relative to inoculation and then administered drug daily throughout the 14-day experimental period. Treatment was initiated on Day 2 postinfection and continued through Day 14 consisting of: 50 mg/kg APX2039 PO (BID), 80 mg/kg fluconazole (FLU) PO (QD), c) 1 mg/kg amphotericin B deoxycholate (AMB) IV (QD); and vehicle control. CSF was removed via an intracisternal tap on Days 2, 7, 10 and 14 post-infection and CFU/ml was assessed. Animals were sacrificed on Day 14 and CFU/g brain tissue was assessed. Results APX2039 demonstrated rapid reduction in CFU in both CSF and brain tissue. The range in CFU values in rabbit CSF is shown (Figure). Reductions in CFU were statistically different from the control group for all treatment groups. APX2039 was also different from both FLU and AMB and resulted in sterilization in CSF by Day 10. Brain harvested on Day 14 demonstrated a reduction in CFU/g tissue vs control of 1.8 log10 and 3.4 log10 for FLU and AMB, respectively, while a &amp;gt; 6 log10 reduction (tissue sterilization) was observed for APX2039. Conclusion APX2039 demonstrated potent efficacy in a rabbit model of CM. The more rapid clearance in CSF than either AMB or FLU, as well as &amp;gt; 6 log10 reduction in brain CFU highlights the unique properties of this drug, warranting further investigation of this molecule for the treatment of CM. Disclosures Karen J. Shaw, PhD, Amplyx (Consultant)Forge Therapeutics (Consultant) Charles D. Giamberardino, Jr., MR, Box (Shareholder) John R. Perfect, MD, amplyx (Grant/Research Support)astellas (Grant/Research Support)astellas (Grant/Research Support)
Sequential Copper-Catalyzed Vinylation/Cyclization:  An Efficient Synthesis of Functionalized Oxazoles (2007)

A modular and practical synthesis of highly substituted oxazoles has been developed. The transformation consists of a sequential copper-catalyzed amidation of vinyl halides followed by cyclization promoted by iodine. A wide variety of functionalized oxazoles and polyazoles can be obtained in a selective manner from simple and easily accessible precursors.
Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1 (1998)

hnRNP A1 regulates alternative splicing by antagonizing SR proteins. It consists of two closely related, tandem RNA-recognition motifs (RRMs), followed by a glycine-rich domain. Analysis of variant proteins with duplications, deletions, or swaps of the RRMs showed that although both RRMs are required for alternative splicing function, each RRM plays distinct roles, and their relative position is important. Surprisingly, RRM2 but not RRM1 could support this function when duplicated, despite their very similar structure. Specific RNA binding and annealing are not sufficient for hnRNP A1 alternative splicing function. These observations, together with phylogenetic and structural data, suggest that the two RRMs are quasi-symmetric but functionally nonequivalent modules that evolved as components of a single bipartite domain.
Somatic Mutation Screening: Identification of Individuals Harboring K-ras Mutations With the Use of Plasma DNA (2000)

Plasma DNA assays for the detection of mutations in K-ras codon 12 may provide a feasible method to screen populations for somatic mutations frequently found in neoplasms. The clinical utility of using this test in screening populations requires further study.
Effect of Inflow Cannula Tip Design on Potential Parameters of Blood Compatibility and Thrombosis (2014)

During ventricular assist device support, a cannula acts as a bridge between the native cardiovascular system and a foreign mechanical device. Cannula tip design strongly affects the function of the cannula and its potential for blood trauma. In this study, the flow fields of five different tip geometries within the ventricle were evaluated using stereo particle image velocimetry. Inflow cannulae with conventional tip geometries (blunt, blunt with four side ports, beveled with three side ports, and cage) and a custom-designed crown tip were interposed between a mixed-flow rotary blood pump and a compressible, translucent silicone left ventricle. The contractile function of the failing ventricle and hemodynamics were reproduced in a mock circulation loop. The rotary blood pump was interfaced with the ventricle and aorta and used to fully support the failing ventricle. Among these five tip geometries, high-shear volume ( γ ˙ ≥ 2778 / s , potential parameter of platelet activation) was found to be the greatest in the blunt tip. The cage tip was observed to have the highest low-shear volume and recirculation volume ( γ ˙ ≤ 100 / s and Vz > 0, respectively; potential parameters of thrombus formation). The crown tip, together with conventional tip geometries with side ports (blunt with four side ports and beveled with three side ports) showed no significant difference in either high-shear volume or low-shear volume. However, recirculation volume was reduced significantly in the crown tip. Despite limited generalizability to clinical situations, these transient-state measurements supported the potential mitigation of complications by changing the design of conventional cannula tip geometries.
Critique of charge collection efficiencies calculated through small perturbation measurements of dye sensitized solar cells (2013)

Through experiment and simulation, we critically examine the conventional method of extracting the charge collection efficiency, ηc, of dye-sensitized solar cells (DSSCs). We demonstrate that the collection efficiency extracted by measuring transient decay rates at short circuit deviates considerably from the true value as ηc decreases. This discrepancy arises from two sources of error: first, transient voltage decay rates are especially sensitive to perturbation size near short circuit, and second, the decay rates are influenced by transient equilibration between trapped and free charge during the measurement. Only if the collection efficiency is high (&amp;gt;90%) do the true and measured values coincide well. This finding finally elucidates the disparity between steady-state and transient measurements of the collection efficiency; the former is more accurate for devices with a low ηc, and the latter for devices with a high ηc. For the first time, we present a fully nondimensional model of the DSSC, allowing us to fit device parameters without extensive material knowledge. The resulting simulations and fitting of solid-state dye sensitized solar cells additionally enable us to quantify the inaccuracy of small perturbation measurements of the collection efficiency when ηc is below 90%.
High-power fiber amplifier using a depressed-clad Yb-doped LMA fiber with low photodarkening (2010)

A 225-&mu;J polarization maintaining ytterbium-doped large-mode-area multiclad fiber was designed and fabricated with an effective mode area of 450 &mu;m<sup>2</sup> and a photodarkening maximum excess loss of ~1 dB/m at 1064 nm. The fiber index profile is based on a depressed-clad to obtain a diffraction-limited output. Optimization for low photodarkening and high conversion efficiency while maintaining a good control on the core's refractive index profile has been achieved by adjusting the ytterbium/phosphorus/aluminum concentrations in the fiber core. Concentration ratios of phosphorus/aluminum from 0.12 to 1.25 were experimentally investigated in terms of photodarkening rate and excess loss. Within this range, the photodarkening excess loss was observed to decrease by a factor of 8. The large-mode-area fiber was used in a 10-ns pulse amplifier at 1064 nm with a repetition rate of 100 kHz and 0.5-nm bandwidth. The diffraction-limited output has a measured M<sup>2</sup> value of 1.04 when the fiber is coiled to a diameter of 12 cm. The fiber amplifier slope efficiency is 70% with a polarization extinction ratio greater than 23 dB. It is shown how the phosphorus/aluminum ratio reduces photodarkening, and how a depressed-clad design improves higher-order mode filtering for reliable, efficient, and compact ytterbium-doped fiber amplifiers.