gebhart/patrepeval huggingface dataset:
Design and performance of a high resolution electrospray ion source for a magnetic sector mass spectrometer with a heated capillary inlet (1995)

The design and performance of an electrospray ion source for a high resolution magnetic sector mass spectrometer that utilizes a heated capillary has been presented. Low pressure, high sensitivity, stable electrospray, low flow rates, and low electronic noise were important factors in achieving high resolution electrospray mass spectrometry. A unit mass resolution has been achieved for biomolecules with MW > 12,000, and an accuracy of 1.4 ppm has been achieved for the average molecular weight of bovine insulin.
A pilot study of AMP-224, a PD-L2 Fc fusion protein, in combination with stereotactic body radiation therapy (SBRT) in patients with metastatic colorectal cancer. (2016)

560 Background: AMP-224, a PD-L2 Fc fusion protein, binds to PD-1, an inhibitory receptor that is present on the cell surface of exhausted, activated, effector, and memory T cells. AMP-224 has a unique mechanism of action in that it binds specifically to PD-1 HI T cells (chronically stimulated / exhausted T cells) but not PD-1 LO cells which represent the normal activated T cell population. Preclinical studies have documented an increase in antitumor immunity following radiation therapy (RT), but also tumor PD-L1 expression as an escape mechanism. The aim of the study is to evaluate whether inhibition of PD-1/PDL-1 axis could improve anti-tumor immunity effects of RT. Methods: Patients with histologically confirmed metastatic colorectal cancer to liver were treated with SBRT to a site of liver metastasis at 8Gy in a single fraction (DL1) or 8Gy in 3 daily fractions (DL2). All patients received AMP-224 10mg/kg IV beginning Day 1 after SBRT preceded by cyclophosphamide 200mg/m2 (D0). Primary objective was to determine the safety and feasibility of AMP-224 in combination with stereotactic body radiation therapy (SBRT) to metastatic hepatic metastasis in patients with advanced colorectal cancer. Mandatory pre- and post-treatment biopsies were attempted on all patients. Results: N = 17 patients with refractory metastatic CRC were enrolled. N = 2 pts were unevaluable. 6pts were treated at DL1 (8Gy x 1fraction SBRT, AMP-224 10mg/kg q2-weekly) and 9pts were treated at DL2 (8Gy x 3fractions SBRT, AMP-224 10mg/kg q2-weekly) No DLT was encountered. The most common toxicity was fatigue (G1/2) in all patients in DL2. N = 3 patients experienced G2 infusion reaction which responded to standard interventions. 5/15 pts did not complete treatment due to rapid PD. No objective responses have been seen, although N = 6 pts remain on study. Pre- and post-tumor biopsies were performed on 7 of first 11 pts. Conclusions: AMP-224 in combination with SBRT to site of colorectal hepatic metastases is safe and feasible. Preliminarily no objective responses have been seen. Full clinical and correlative data including post-therapeutic radiated and non-radiated tumor biopsies will be presented. Clinical trial information: NCT02298946.
Bacterial flagella explore microscale hummocks and hollows to increase adhesion (2013)

Biofilms, surface-bound communities of microbes, are economically and medically important due to their pathogenic and obstructive properties. Among the numerous strategies to prevent bacterial adhesion and subsequent biofilm formation, surface topography was recently proposed as a highly nonspecific method that does not rely on small-molecule antibacterial compounds, which promote resistance. Here, we provide a detailed investigation of how the introduction of submicrometer crevices to a surface affects attachment of Escherichia coli. These crevices reduce substrate surface area available to the cell body but increase overall surface area. We have found that, during the first 2 h, adhesion to topographic surfaces is significantly reduced compared with flat controls, but this behavior abruptly reverses to significantly increased adhesion at longer exposures. We show that this reversal coincides with bacterially induced wetting transitions and that flagellar filaments aid in adhesion to these wetted topographic surfaces. We demonstrate that flagella are able to reach into crevices, access additional surface area, and produce a dense, fibrous network. Mutants lacking flagella show comparatively reduced adhesion. By varying substrate crevice sizes, we determine the conditions under which having flagella is most advantageous for adhesion. These findings strongly indicate that, in addition to their role in swimming motility, flagella are involved in attachment and can furthermore act as structural elements, enabling bacteria to overcome unfavorable surface topographies. This work contributes insights for the future design of antifouling surfaces and for improved understanding of bacterial behavior in native, structured environments.
P$^{3}$DCT—Partial-Power Pre-Regulated DC Transformer (2018)

In this paper, a new approach to regulate the output voltage of a resonant, constant voltage transfer ratio 380 V/48 V isolated dc-dc converter is presented. Rather than applying variable frequency control to the resonant converter, which would result in reactive power processing and a more complicated electromagnetic compatibility filter design, the converter remains in its optimal operating point all time and an additional partial-power (PP) processing auxiliary converter is used to tightly regulate the output voltage. The PP converter, supplied through a tertiary winding of the resonant converter's transformer, regulates the output by adding or subtracting voltage from the dc input and has only a marginal impact on the overall efficiency of the dc-dc converter. The principal of operation is explained in detail including Sankey diagrams to illustrate the power processing of the converter and a feedback control system is proposed to tightly regulate the 48 V output voltage. A hardware demonstrator rated at 1.5 kW is implemented to cope with input voltage variations between 340 and 420 V and experimental results are provided showing that the output voltage can be kept within ±1% of the nominal 48 V even under harsh input voltage and load transients. The realized dc-dc converter with PP pre-regulation features an overall efficiency of 97.7% at rated power and a power density of 8.6 kWdm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> (141w/ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> in).
Large-scale electromagnetic design optimization of PM machines over a target operating cycle (2015)

A novel automated design algorithm for application-based optimization of permanent magnet (PM) machines is presented in this paper. The proposed algorithm features precise performance evaluation of the potentially heavily saturated machines at high-energy-throughput operating zones using finite element (FE) techniques. First, the energy consumption function associated with the machine's operating cycle is efficiently modeled by a number of representative load points using a k-means clustering algorithm. Subsequently, a new approach is developed to assess the performance of the machine at each representative load point with proper control to conform to practical operational constraints imposed by voltage and current limits of the motor-drive system. The developed algorithm is applicable to the optimization of any configuration of PM and synchronous reluctance motors over any conceivable operating cycle. Its effectiveness is demonstrated by optimizing the well-established reference/benchmark design represented by the 2004 Toyota Prius IPM motor configuration over a compound operating cycle consisting of common US driving schedules.
Stereospecific Oxidative Demetallation of Highly Functionalized CpCo(1,3-Diene) Complexes: An Experimental and Computational Study (2015)

Three diastereomers of a highly functionalized tetrasubstituted cyclopentadienylcobalt–diene complex, (Cp)Co[η<sup>4</sup>-CH(CO<sub>2</sub>Et)=C(SO<sub>2</sub>Ph)C(SiMe<sub>3</sub>)=CH(CO<sub>2</sub>Et)] (<b>4</b>-<i>ZE</i>, <b>4</b>-<i>EZ</i>, <b>4</b>-<i>ZZ</i>; Cp = C<sub>5</sub>H<sub>5</sub>), undergo oxidative demetallation by ceric ammonium ­nitrate (CAN) to give the corresponding metal-free dienes, CH(CO<sub>2</sub>Et)=C(SO<sub>2</sub>Ph)C(SiMe<sub>3</sub>)=CH(CO<sub>2</sub>Et) (<b>5</b>-<i>ZE</i>, <b>5</b>-<i>EZ</i>, <b>5</b>-<i>ZZ</i>), with retention of configuration. The oxidation of <b>4</b>-<i>ZE</i> by iodine occurs with a different stereoselectivity than that observed with CAN, to provide the fourth diastereomer <b>5</b>-<i>EE</i> in high yield. B97D/Def2-TZVPP(CH<sub>2</sub>Cl<sub>2</sub>) calculations predict the diene free-energy ordering as: <b>5</b>-<i>EE</i> < <b>5</b>-<i>ZE</i> < <b>5</b>-<i>EZ</i> < <b>5</b>-<i>ZZ</i>.
Titelbild: “We Create Chemistry for a Sustainable Future”: Chemie schafft nachhaltige Lösungen für eine wachsende Weltbevölkerung / Chemie neu erfinden (Angew. Chem. 11/2015) (2015)

Die Badische Anilin- & Sodafabrik – die BASF – wurde am 6. April 1865 von Friedrich Engelhorn in Mannheim gegründet und wird damit in diesem Jahr 150 Jahre alt. Das vorliegende Heft bietet anlässlich dieses besonderen Firmenjubiläums eine Sammlung von Aufsätzen und Essays, die sich mit Beiträgen der Chemie zu den Themen Energie, Ernährung und städtisches Leben befassen. Woher wird die Energie in Zukunft kommen, die wir brauchen? Wie können genug Nahrung und sauberes Wasser für alle Menschen bereit gestellt werden? Wie werden die Städte der Zukunft aussehen? Passend dazu sind auf dem Titelbild einige Highlights aus der breiten Produktpalette der BASF herausgestellt: Kathodenmaterialien für Lithium-Ionen-Batterien (oben), Membranen für sauberes Wasser (unten) sowie Xemium®, ein neuer fungizider Wirkstoff. Dieses Heft begleitet drei BASF-Jubiläumssymposien in Ludwigshafen (9./10. März), Chicago (23./24. Juni) und Shanghai (10./11. November), bei denen Autoren dieses Heftes vortragen. Es wird eingeleitet von einem Essay von A. Kreimeyer et al. auf S. 3220 ff. über die Geschichte und aktuelle Position der Forschung der BASF, worauf ein Essay von G. M. Whitesides auf S. 3238 ff. folgt, in dem er zu einem Umdenken in der chemischen Forschung aufruft. Alle zwanzig Essays und Aufsätze dieses Heftes demonstrieren die enorme Bedeutung chemischer Forschung – sie muss und wird zur Hebung des durchschnittlichen Lebensstandards einer wachsenden Weltbevölkerung beitragen. Die Redaktion der Angewandten Chemie gratuliert der BASF zu ihrem Jubiläum.
An ATM routing and concentration chip for a scalable multicast ATM switch (1997)

We have proposed a new architecture for building a scalable multicast ATM switch from a few tens to a few thousands of input/output ports. The switch, called the Abacus switch, employs input and output buffering schemes. Cell replication, cell routing, and output contention resolution are all performed in a distributed way so that the switch can be scaled up to a large size. The Abacus switch adopts a novel algorithm to resolve the contention of both multicast and unicast cells destined for the same output port (or output module). The switch can also handle multiple priority traffic by routing cells according to their priority levels. This paper describes a key ASIC chip for building the Abacus switch. The chip, called the ATM routing and concentration (ARC) chip, contains a two-dimensional array (3/spl times/32) of switch elements that are arranged in a cross-bar structure. It provides the flexibility of configuring the chip into different group sizes to accommodate different ATM switch sizes. The ARC chip has been designed and fabricated using 0.8-/spl mu/m CMOS technology and tested to operate correctly at 240 MHz, Although the ARC chip was designed to handle the line rate at OC-3 (155 Mb/s), the Abacus switch can accommodate a much higher line rate at OC-12 (622 Mb/s) or OC-48 (2.5 Gb/s) by using a bit-sliced technique or distributing cells in a cyclic order to different inputs of the ARC chip. When the latter scheme is used, the cell sequence is retained at the output of the Abacus switch.
Treatment of Type 2 Diabetes by Adenoviral-Mediated Overexpression of the Glucokinase Regulatory Protein (2001)

The enzyme glucokinase (GK) plays a central role in glucose homeostasis. Hepatic GK activity is acutely controlled by the action of the GK regulatory protein (GKRP). In vitro evidence suggests that GKRP reversibly binds to GK and inhibits its activity; however, less is known about the in vivo function of GKRP. To further explore the physiological role of GKRP in vivo, we used an E1/E2a/E3-deficient adenoviral vector containing the cDNA encoding human GKRP (Av3hGKRP). High fat diet-induced diabetic mice were administered Av3hGKRP or a control vector lacking a transgene (Av3Null). Surprisingly, the Av3hGKRP-treated mice showed a significant improvement in glucose tolerance and had lower fasting blood glucose levels than Av3Null-treated mice. A coincident decrease in insulin levels indicated that the Av3hGKRP-treated mice had sharply improved insulin sensitivity. These mice also exhibited lower leptin levels, reduced body weight, and decreased liver GK activity. In vitro experiments indicated that GKRP was able to increase both GK protein and enzymatic activity levels, suggesting that another role for GKRP is to stabilize and/or protect GK. These data are the first to indicate the ability of GKRP to treat type 2 diabetes and therefore have significant implications for future therapies of this disease.
Potential for Virus Endogenization in Humans through Testicular Germ Cell Infection: the Case of HIV (2020)

Viruses have colonized the germ line of our ancestors on several occasions during evolution, leading to the integration in the human genome of viral sequences from over 30 retroviral groups and a few nonretroviruses. Among the recently emerged viruses infecting humans, several target the testis (e.g., human immunodeficiency virus [HIV], Zika virus, and Ebola virus). Here, we aimed to investigate whether human testicular germ cells (TGCs) can support integration by HIV, a contemporary retrovirus that started to spread in the human population during the last century. We report that albeit alternative receptors enabled HIV-1 binding to TGCs, HIV virions failed to infect TGCs <i>in vitro</i> Nevertheless, exposure of TGCs to infected lymphocytes, naturally present in the testis from HIV<sup>+</sup> men, led to HIV-1 entry, integration, and early protein expression. Similarly, cell-associated infection or bypassing viral entry led to HIV-1 integration in a spermatogonial cell line. Using DNAscope, HIV-1 and simian immunodeficiency virus (SIV) DNA were detected within a few TGCs in the testis from one infected patient, one rhesus macaque, and one African green monkey <i>in vivo</i> Molecular landscape analysis revealed that early TGCs were enriched in HIV early cofactors up to integration and had overall low antiviral defenses compared with testicular macrophages and Sertoli cells. In conclusion, our study reveals that TGCs can support the entry and integration of HIV upon cell-associated infection. This could represent a way for this contemporary virus to integrate into our germ line and become endogenous in the future, as happened during human evolution for a number of viruses.<b>IMPORTANCE</b> Viruses have colonized the host germ line on many occasions during evolution to eventually become endogenous. Here, we aimed at investigating whether human testicular germ cells (TGCs) can support such viral invasion by studying HIV interactions with TGCs <i>in vitro</i> Our results indicate that isolated primary TGCs express alternative HIV-1 receptors, allowing virion binding but not entry. However, HIV-1 entered and integrated into TGCs upon cell-associated infection and produced low levels of viral proteins. <i>In vivo</i>, HIV-1 and SIV DNA was detected in a few TGCs. Molecular landscape analysis showed that TGCs have overall weak antiviral defenses. Altogether, our results indicate that human TGCs can support HIV-1 early replication, including integration, suggesting potential for endogenization in future generations.
A HIGH FREQUENCY OF MICROSATELLITE ALTERATIONS CHARACTERIZES HIV ASSOCIATED LUNG CARCINOMAS (1998)

96 Background: HIV infection has been associated with an increasing incidence of malignancy. Several non-AIDS-defining cancers are reported in increasing incidence in HIV-infected individuals, including lung cancer. HIV infected individuals have a 6.5 fold increased incidence of primary lung carcinoma compared to the general population. We investigated the molecular changes present HIV associated lung cancers and compared them with those present in HIV indeterminate subjects (sporadic tumors). Methods: We investigated the frequency of loss of heterozygosity (LOH) and microsatellite alteration (MA) present in 11 lung carcinomas from HIV seropositive individuals and compared them to the findings from 35 sporadic lung carcinomas arising in HIV indeterminate subjects. After careful microdissection of the tumors, extracted DNA was analyzed by PCR for LOH and MAs at eight chromosomal regions frequently deleted in lung cancer using 16 polymorphic microsatellite markers. Eighteen non-small cell lung carcinoma cell lines from sporadic cases were used to determine the effect of tumor stage on the incidence of MAs. Analyses for the presence of HIV and human papillomavirus sequences were also performed. Results: Our major findings were as follows: a) The overall frequency of LOH at all chromosomal regions tested and the frequencies at most of the individual regions were similar in the two groups; b) The frequency of MAs present in the HIV associated tumors (0.18) was six-fold higher than in sporadic tumors (0.03) (p = 0.0004). At least one MA was present in 10 (91%) of 11 HIV associated tumors versus 17 (48%) of 35 sporadic tumors (p = 0.0163); c) Molecular changes were independent of tumor stage and gender; and, d) Viral sequences were not detected in the HIV associated lung carcinomas. Conclusion: MAs, a reflection of the presence of widespread genomic instability, occur at greatly increased frequency in HIV associated lung carcinomas. Although the mechanism underlying the development of increased MAs is unknown, it may play a crucial role in the development of many HIV associated tumors.
Look-up table-based simulation of scintillation detectors in computed tomography (2008)

The design of a CT detector requires a precise detector model, since building prototypes for many different proposed detector geometries is too costly. We introduce a look-up table-based simulation of scintillation detectors on X-ray photon level. It uses energy-resolved sinograms of incoming X-ray intensities as input data and generates photon counts for each channel and reading. The effects of X-ray- and optical cross-talk, temporal cross-talk between readings, Poisson noise and electronics effects are covered. The photon interaction data as well as optical cross-talk distribution are provided in the form of detector specific look-up tables. Unlike standard Monte-Carlo simulations of X-ray interaction processes, our approach is capable of simulating whole sinograms in a reasonable amount of time and still offers a very high precision of the detector model. This way the influence of detector effects can be investigated in the reconstructed image data. The simulation is verified against data measured with a CT scanner and data from a fully single photon-based Monte-Carlo simulation in terms of image modulation transfer function (MTF) and detector noise power spectrum (NPS).
Architectural transitions in Vibrio cholerae biofilms at single-cell resolution (2016)

Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development.
ChemInform Abstract: A New Synthesis of Alkyl‐N,N‐dinitramines by Direct Nitration of Isocyanates. (1991)

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.
Interfacial solid-state reaction at thermally oxidized In1−xGaxAsyP1−y alloys (1988)

The interfacial reaction between thermally oxidized In1−xGaxAsyP1−y and an In1−xGaxAsyP1−y epilayer was studied using Raman and x-ray photoelectron spectroscopy (XPS) analyses. In Raman spectra, it was found that the appearance of the phonon modes, i.e., the first-order longitudinal (LO) and transverse-optical (TO) modes for crystalline arsenic, was due to the In1−xGaxAsyP1−y -oxide interfacial reaction. The XPS analyses showed that this reaction corresponded to the GaAs-oxide interfacial reaction, i.e., As2O3+2GaAs→Ga2O3+4As. Furthermore, the reaction depends on the composition y of In1−xGaxAsyP1−y, which may be due to the enhancement in the initial transient reaction by thermal damage of In1−xGaxAsyP1−y occurring at the interface.
Control of a Modular Multilevel Converter With Reduced Internal Data Exchange (2016)

Modular multilevel converters (MMC) are penetrating due to their superior performances. Due to the modular structure of the converter, communication platform has to be established between the submodules (SMs) and a central controller unit (CCU). When the communication platform is designed for such an application, several key parameters have to be considered such as high-speed data transfer with low propagation delay, data integrity, and ability for accurate synchronization. In order to minimize the data flow in the MMC, a hierarchical control is proposed where a CCU calculates an identical reference for all the SMs, while the modulation and capacitor voltage balancing is performed in the controller from the SM. Thus, at each sampling instance, only four bytes references are sent by the central controller to the controllers from the SM, while one or two bytes are received from SMs. Furthermore, the control algorithm is validated through experiments.
Quasi-periodicity to period-doubling of parallel-input/parallel-output boost dc-dc converter (2007)

This work describes the bifurcation behavior of a modular peak current-mode controlled (CMC) dc-dc boost converter from quasi-periodicity to period-doubling. The parallel-input/parallel-output converter consists of two identical boost circuits and operates in the continuous-current conduction mode. A nonlinear mapping in closed form is derived and bifurcation diagrams are generated using MATLAB. Results are verified using the circuit analysis package PSPICE.