gebhart/patrepeval huggingface dataset:
Supplementary Methods, Tables 1 - 9, Figures 1 - 8 from Systematic Functional Characterization of Resistance to PI3K Inhibition in Breast Cancer (2023)

&lt;p&gt;Supplementary Methods, Tables 1 - 9, Figures 1 - 8. Supplementary Table 1. Functional classification for validated genes. Supplementary Table 2. Validated 43 candidate genes' genetic alteration status in the invasive breast cancer (TCGA) database. Supplementary Table 3. Receptor status, mutational status and intrinsic subtypes of breast cancer cell lines used in this study. Supplementary Table 4. GI50 of BYL719 in different breast cancer cell lines with overexpression of PIM isoforms. Supplementary Table 5. PIM1 and AKT phosphorylation sites in PRAS40, BAD, p21 and p27. Supplementary Table 6. PIM gene expression levels in PIK3CA-mutant breast cancer cell lines. Supplementary Table 7. GI50 of BYL719 in the presence of LGH447 (1Î¼M) or DMSO in PIK3CA-mutant breast cancer cell lines. Supplementary Table 8. Signature genes that changed concordantly in patient sample pairs and PIM signature. Supplementary Table 9. Hormonal receptor status by immunohistochemistry (IHC), HER2 status by FISH and IHC of PIM1 amplified or overexpressed breast cancer tumor samples from the invasive breast cancer (TCGA) database. Supplementary Figure 1. Lentiviral infection efficacy quality in the large-scale ORF screen. Supplementary Figure 2. PIM1 confers resistance to breast cancer cell lines with different PIK3CA mutations and various intrinsic subtypes. Supplementary Figure 3. PIM1 confers resistance to inhibitors targeting key components of PI3K pathway. Supplementary Figure 4. PIM1 inhibitors alone have minimal inhibitory effects on T47D cells with or without PIM1 overexpression. Supplementary Figure 5. PIM1 expression abrogates cell-cycle arrest in cells treated with BYL719. Supplementary Figure 6. BYL719 and AZD1208 or LGH447 demonstrated synergy in PIM1 expressing T47D cells. Supplementary Figure 7. PIM activation signature. Supplementary Figure 8. PIM and PI3K pathway genetic mutations showed mutual exclusivity in treatment-naive breast cancers.&lt;/p&gt;
Using transformer parasitics for resonant converters - a review of the calculation of the stray capacitance of transformers (2005)

Parasitic capacitances of conventional transformers can be used as resonant elements in resonant DC-DC converters in order to reduce the overall system size. For predicting the values of the parasitic capacitors without building the transformer different approaches for calculating these capacitances are compared. A systematic summary of the known approaches is given and missing links between the different theories and missing equations are added. Furthermore, a new simple procedure for modelling parasitic capacitances which is based on the known approaches is proposed. The resulting equations are verified by measurements on four different high voltage transformers.
Human Chorionic Gonadotrophin (hCG) as a diagnostic test to differentiate between Parathyroid Carcinoma, Primary Benign Hyperparathyroidism and Secondary Hyperparathyroidism. (2018)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Organization of Ureaplasma urealyticum urease gene cluster and expression in a suppressor strain of Escherichia coli (1996)

Ureaplasma urealyticum is a pathogenic ureolytic mollicute which colonizes the urogenital tracts of humans. A genetic polymorphism between the two biotypes of U. urealyticum at the level of the urease genes was found. The urease gene cluster from a biotype 1 representative of U. urealyticum (serotype I) was cloned and sequenced. Seven genes were found, with ureA, ureB, and ureC encoding the structural subunits and ureE, ureF, ureG, and a truncated ureI) gene encoding accessory proteins. Urease expression was not obtained when the plasmid containing these genes was incorporated into an opal suppressor strain of Escherichia coli, although this enzymatic activity was found in the same E. coli strain transformed with pC6b, a plasmid with previously cloned urease genes from the U. urealyticum T960 strain of biotype 2 (serotype 8). Although there are 12 TGA triplets encoding tryptophan within urease genes, the level of expression obtained was comparable to the levels reported for other bacterial genes expressed in E. coli. Nested deletion experiments allowed us to demonstrate that ureD is necessary for urease activity whereas another open reading frame located downstream is not. The promoter for ureA and possibly other urease genes was identified for both serotypes.
Antenna Aperture Tuning with High-Voltage Bulk-CMOS Switch-Based RF Capacitor (2019)

A circuit for tuning the aperture of inverted-F antenna (IFA) utilizing a high-voltage RF-switch-based digitally-tunable capacitor in bulk-CMOS technology is demonstrated. The tuning network consists of the 5-bit switchable capacitor and a parallel inductor which are placed at the high-voltage plane of the radiating element with peak RF voltages of 60 V applied across the circuit. The antenna covers low and middle cellular frequency bands with fine tuning steps, providing return loss at the feed point of above 6 dB for more than 90% of the target frequency range. The measured peak reflected second and third harmonics generated by the tuned antenna when driven by the 34 dBm low-band RF signal are −38 dBm and −56 dBm respectively.
Genetic Characterization of Novel Oral Polio Vaccine Type 2 Viruses During Initial Use Phase Under Emergency Use Listing — Worldwide, March–October 2021 (2022)

The emergence and international spread of neurovirulent circulating vaccine-derived polioviruses (cVDPVs) across multiple countries in Africa and Asia in recent years pose a major challenge to the goal of eradicating all forms of polioviruses. Approximately 90% of all cVDPV outbreaks are caused by the type 2 strain of the Sabin vaccine, an oral live, attenuated vaccine; cVDPV outbreaks typically occur in areas of persistently low immunization coverage (1). A novel type 2 oral poliovirus vaccine (nOPV2), produced by genetic modification of the type 2 Sabin vaccine virus genome (2), was developed and evaluated through phase I and phase II clinical trials during 2017-2019. nOPV2 was demonstrated to be safe and well-tolerated, have noninferior immunogenicity, and have superior genetic stability compared with Sabin monovalent type 2 (as measured by preservation of the primary attenuation site [domain V in the 5' noncoding region] and significantly lower neurovirulence of fecally shed vaccine virus in transgenic mice) (3-5). These findings indicate that nOPV2 could be an important tool in reducing the risk for generating vaccine-derived polioviruses (VDPVs) and the risk for vaccine-associated paralytic poliomyelitis cases. Based on the favorable preclinical and clinical data, and the public health emergency of international concern generated by ongoing endemic wild poliovirus transmission and cVDPV type 2 outbreaks, the World Health Organization authorized nOPV2 for use under the Emergency Use Listing (EUL) pathway in November 2020, allowing for its first use for outbreak response in March 2021 (6). As required by the EUL process, among other EUL obligations, an extensive plan was developed and deployed for obtaining and monitoring nOPV2 isolates detected during acute flaccid paralysis (AFP) surveillance, environmental surveillance, adverse events after immunization surveillance, and targeted surveillance for adverse events of special interest (i.e., prespecified events that have the potential to be causally associated with the vaccine product), during outbreak response, as well as through planned field studies. Under this monitoring framework, data generated from whole-genome sequencing of nOPV2 isolates, alongside other virologic data for isolates from AFP and environmental surveillance systems, are reviewed by the genetic characterization subgroup of an nOPV working group of the Global Polio Eradication Initiative. Global nOPV2 genomic surveillance during March-October 2021 confirmed genetic stability of the primary attenuating site. Sequence data generated through this unprecedented global effort confirm the genetic stability of nOPV2 relative to Sabin 2 and suggest that nOPV2 will be an important tool in the eradication of poliomyelitis. nOPV2 surveillance should continue for the duration of the EUL.
Multipolarized Vector Sensor Antenna Array (2015)

This chapter contains sections titled: 9.1 Introduction, 9.2 UAV Characteristics for Vector Sensor Antenna Integration, 9.3 Vector Sensor Antenna Prototype: Design and Fabrication, 9.4 Measured Radiation Patterns of Vector Sensor Prototypes Installed on a UAV, 9.5 Summary, References
Teaching and Learning Electromagnetics in 2020 (2021)

Electromagnetic theory has been taught for well over a century and has faced many challenges and pressures as approaches, applications, and curricular models have evolved. We consider the issues and challenges that face those who teach EM theory and identify some of the trends and opportunities that lie ahead in EM education.
Reductions of activated carbonyl compounds with chiral-bridged 1,4-dihydropyridines. An investigation of scope and structural effects (1985)

A series of chiral bridged macrocyclic 1,4-dihydropyridines has been prepared, and the potential of these compounds for enantioselective reductions has been examined. A typical synthesis begins with pyridine-3-5-dicarboxylic acid (9, W = OH), which is coupled with (S)-valine to produce ultimately the bis-coupled product 10 (X = OH). This is converted to the bis(cesium carboxylate) and is allowed to react in dimethylformamide (DMF) solution at 10-2 to 5 × 10-3 M concentration with 1,5-dibromo-3-oxapentane. The macrocycle 11a (R = CH(CH3)2) is obtained in 48% yield. Subsequent methylation with CH3I/Mg(ClO4)2·1.5H2O leads to the pyridinium perchlorate, which is reduced to 1,4-dihydropyridine with Na2S2O4. In this manner, 28 different chiral bridged macrocyclic 1,4-dihydropyridines (7) have been synthesized by starting from valine, alanine, phenylglycine, phenylalanine, and proline. Various bridges of different compositions, lengths, and shapes have been incorporated. All these bridged compounds in a nonprotic solvent like CH3CN in the presence of a stoichiometric amount of Mg(ClO4)2·1.5H2O reduce activated carbonyl compounds to the corresponding alcohols; the corresponding pyridinium salt is formed. The most studied example is the reduction of ethyl phenylglyoxylate to ethyl mandelate. If the amino acids have the S configuration, the ethyl mandelate produced will have the S configuration. The enantiomeric excesses vary between 36% and 90% and decrease with increasing bridge length of the macrocycle from a maximum for a bridge with a length of five atoms (either pentamethylene or 3-oxapentyl). An explanation for these results is offered. It is assumed that the reactive species is a complex of bridged 1,4-dihydropyridine, Mg2+, and carbonyl component. Although Mg2+ does not bind strongly to the macrocycles (log Ks 2-3 depending on the compound), this cation apparently has the ability to organize the macrocycles, even when they can assume several conformations of widely differing shape, into a common geometry which leads to reduction. The cation has the ability in fact to redistribute the conformational populations. These conclusions are supported by 13C NMR studies of complexation as well as circular dichroism (CD) studies, which are reported separately.
Thin Film Si Bottom Cells for Tandem Device Structures: Final Technical Report, 15 December 2003 - 15 October 2007 (2008)

GIT and IEC developed thin-film Si bottom cell and showed that deposition of top cell in tandem device did not reduce bottom cell performance.
Amblyopia: a tale of two approaches (1995)

Our understanding of the physiological basis for amblyopia in humans has undergone dramatic changes over the past two decades. The first such change occurred when we were first able to record from single neurones in different parts of the visual pathway and develop neural models of the anomaly. The second came from psychophysical investigations and evaluations of these animal models. Our understanding has progressed from one focused on the properties of single cortical cells to an appreciation of the anomalous behaviour of cellular networks.
Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems (2022)

From individual cells to whole organisms, O<sub>2</sub> transport unfolds across micrometer- to millimeter-length scales and can change within milliseconds in response to fluid flows and organismal behavior. The spatiotemporal complexity of these processes makes the accurate assessment of O<sub>2</sub> dynamics via currently available methods difficult or unreliable. Here, we present "sensPIV," a method to simultaneously measure O<sub>2</sub> concentrations and flow fields. By tracking O<sub>2</sub>-sensitive microparticles in flow using imaging technologies that allow for instantaneous referencing, we measured O<sub>2</sub> transport within (1) microfluidic devices, (2) sinking model aggregates, and (3) complex colony-forming corals. Through the use of sensPIV, we find that corals use ciliary movement to link zones of photosynthetic O<sub>2</sub> production to zones of O<sub>2</sub> consumption. SensPIV can potentially be extendable to study flow-organism interactions across many life-science and engineering applications.
Preparation and Characterization of a Novel Swellable and Floating Gastroretentive Drug Delivery System (sfGRDDS) for Enhanced Oral Bioavailability of Nilotinib (2020)

Regarding compliance and minimization of side effects of nilotinib therapy, there is a medical need to have a gastroretentive drug delivery system (GRDDS) to enhance the oral bioavailability that is able to administer an optimal dose in a quaque die (QD) or daily manner. In this study, the influence on a swelling and floating (<i>sf</i>) GRDDS composed of a polymeric excipient (HPMC 90SH 100K, HEC 250HHX, or PEO 7000K) and Kollidon<sup>®</sup> SR was examined. Results demonstrated that PEO 7000K/Kollidon SR (P/K) at a 7/3 ratio was determined to be a basic GRDDS formulation with optimal swelling and floating abilities. MCC PH102 or HPC<sub>sssl,SFP</sub> was further added at a 50% content to this basic formulation to increase the tablet hardness and release all of the drug within 24 h. Also, the caplet form and capsule form containing the same formulation demonstrated higher hardness for the former and enhanced floating ability for the latter. A pharmacokinetic study on rabbits with pH values in stomach and intestine similar to human confirmed that the enhanced oral bioavailability ranged from 2.65-8.39-fold with respect to Tasigna, a commercially available form of nilotinib. In conclusion, the multiple of enhancement of the oral bioavailability of nilotinib with <i>sf</i>GRDDS could offer a pharmacokinetic profile with therapeutic effectiveness for the QD administration of a reasonable dose of nilotinib, thereby increasing compliance and minimizing side effects.
Plasma-enhanced atomic layer deposited indium oxide film using a novel dimethylbutylamino-trimethylindium precursor for thin film transistors (2021)

In this study, plasma-enhanced atomic layer deposited indium oxide (InOx) films were analyzed using a new [dimethylbutylamino]trimethylindium (DATI) liquid precursor and Ar/O2 plasma. The growth property using the DATI precursor, such as growth per cycle, is relatively higher (≥1.0 Å/cycle) than other precursors even in low deposition temperatures (100–250 °C). In addition, impurities (C and N) in the thin films were below the XPS detection limit. Because the number of oxygen vacancies that generate carriers in the InOx thin films increased with the deposition temperature, the carrier concentration (2.7 × 1018–1.4 × 1019 cm−3) and Hall mobility (0.3–1.1 cm2/V s) of the InOx thin film were increased. InOx channel based staggered bottom gate structure thin film transistors (TFTs) were fabricated, and their switching performance were studied. Because the InOx films were deposited with high purity, the electrical properties of TFTs show superior switching performance in terms of saturation mobility (17.5 cm2/V s) and Ion/Ioff ratio (2.9 × 109). Consequently, InOx films deposited with DATI have the potential to be widely used in indium oxide semiconductors, especially backplane TFTs.
High-dose chemotherapy and stem-cell rescue for salvage therapy for relapsed malignant mixed ovarian germ cell tumor: A case report (2017)

High-dose chemotherapy with stem cell transplant is a viable salvage therapy for patients with platinum-resistant germ cell tumors.
A robot suit with hardware-based safety devices: Transient response analysis of a velocity-based safety device (2015)

We have developed a rehabilitation robot suit with two hardware-based safety devices - the "velocity-based safety device" and the "torque-based safety device". The robot suit assists a patient's knee joint. The torque-based safety device stops the robot suit if it detects an unexpected high joint torque. Similarly, the velocity-based safety device stops the robot suit if it detects an unexpected high joint angular velocity. The safety devices work even when the computer breaks down, because they consist of only passive mechanical components without actuators, controllers, or batteries. However, we have never analyzed the transient response of the velocity-based safety device. In order to design the velocity-based safety device efficiently, we need to analyze the transient response. In this paper, we firstly review the robot suit equipped with the safety devices. Secondly, we analyze the transient response of the velocity-based safety device. Thirdly, we simulate the transient response of a new velocity-based safety device in order to demonstrate the usefulness of the transient response analysis. Finally, we present experimental results to verify the effectiveness of the transient response analysis.
Design and Operational Analysis of a Green Data Center (2017)

Data centers are at the heart of the IT-driven economy. Power consumption of a single data center can range from tens to a hundred megawatts, and operational costs can run into millions of dollars a month. Data center operators incorporate careful design and optimizations to reduce large-scale data centers energy consumption. Because data center design and operations are a source of competitive advantage, insight into modern data centers is scarce. This article describes the design and analysis of a state-of-the-art green university data center, and provides several insights into its operational and efficiency characteristics.
The Kinetics of the Reaction C2H5 • + HI → C2H6 + I• over an Extended Temperature Range (213–623 K): Experiment and Modeling (2015)

Abstract The present study reports temperature dependent rate constants k 1 for the title reaction across the temperature range 213 to 293 K obtained in a Knudsen flow reactor equipped with an external free radical source based on the reaction C 2 H 5 I + H • → C 2 H 5 • + HI and single VUV-photon ionization mass spectrometry using Lyman- α radiation of 10.2 eV. Combined with previously obtained high-temperature data of k 1 in the range 298–623 K using the identical experimental equipment and based on the kinetics of C 2 H 5 • disappearance with increasing HI concentration we arrive at the following temperature dependence best described by a three-parameter fit to the combined data set: k 1 = (1.89 ± 1.19)10 −13 ( T /298) 2.92±0.51 exp ((3570 ± 1500)/ RT ), R = 8.314 J mol – 1 K – 1 in the range 213–623 K. The present results confirm the general properties of kinetic data obtained either in static or Knudsen flow reactors and do nothing to reconcile the significant body of data obtained in laminar flow reactors using photolytic free radical generation and suitable free radical precursors. The resulting rate constant for wall-catalyzed disappearance of ethyl radical across the full temperature range is discussed. Highly correlated ab initio quantum chemistry methods and canonical transition state theory were applied for the reaction energy profiles and rate constants. Geometry optimizations of reactants, products, molecular complexes, and transition states are determined at the CCSD/cc-pVDZ level of theory. Subsequent single-point energy calculations employed the DK-CCSD(T)/ANO-RCC level. Further improvement of electronic energies has been achieved by applying spin-orbit coupling corrections towards full configuration interaction and hindered rotation analysis of vibrational contributions. The resulting theoretical rate constants in the temperature range 213–623 K lie in the range E-11–E-12 cm 3 molecule – 1 s – 1 , however experiments and theoretical modelling seem at great odds with each other.
Absence of seroconversion of HIV-1 antibody in seroreactive individuals (1993)

To the Editor. —The recent article by Roy et al1describes an impressive retrospective study quantifying the error rate of human immunodeficiency virus (HIV) serum antibody testing a large cohort of military personnel. The main conclusion of the article is that true (ie, loss of confirmed HIV seropositivity not resulting from clearance of passively acquired maternal antibodies) does not occur, and that in fact, most (if not all) cases of apparent seroreversion represent errors of attribution or testing. We feel that it is important not to overinterpret these results or necessarily to extend the conclusion to other nonmilitary populations. More than 2.5 million individuals were tested this study, and 4911 were confirmed HIV-seropositive. Only six individuals (excluding 31 transiently seropositive infants) received at least two positive tests followed by a negative test and met the authors' definition of potential seroreverters. It would have been useful to
Image-based plant modeling (2006)

In this paper, we propose a semi-automatic technique for modeling plants directly from images. Our image-based approach has the distinct advantage that the resulting model inherits the realistic shape and complexity of a real plant. We designed our modeling system to be interactive, automating the process of shape recovery while relying on the user to provide simple hints on segmentation. Segmentation is performed in both image and 3D spaces, allowing the user to easily visualize its effect immediately. Using the segmented image and 3D data, the geometry of each leaf is then automatically recovered from the multiple views by fitting a deformable leaf model. Our system also allows the user to easily reconstruct branches in a similar manner. We show realistic reconstructions of a variety of plants, and demonstrate examples of plant editing. Copyright © 2006 by the Association for Computing Machinery, Inc.
An inherently-robust 300&#x00B0;C MEMS temperature sensor for wireless health monitoring of ball and rolling element bearings (2009)

Presented is an inherently-robust wireless capacitive MEMS temperature sensor capable of operating to 300°C. The heart of the sensor is an array of bimorph (metal-dielectric) cantilevers whose deflections are sensed by an array of appropriately placed electrodes. The key advantages of this configuration are the following. First, its dielectric layer is SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thermally-grown at 1,100°C as opposed to conventional low-temperature PECVD or sputtered films. Second, the lack of a sensing surface directly beneath the movable structures renders stiction nearly impossible. Third, the fringing-field sensing results in constant sensitivity throughout the entire temperature range. Fourth, the employed passive approach is immune to high-temperature reliability issues faced by active devices. Furthermore, the fabrication yield is over 99%, even in an academic cleanroom (Birck Nanotechnology Center at Purdue University). When configured with an inductor and wirelessly interrogated, the measured resonant frequency has a linear shift from 206 MHz at room temperature to 199 MHz at 300°C.