gebhart/patrepeval huggingface dataset:
Effects of indium concentration on the electronic structures of Be acceptors confined inInxGa1−xAs/Al0.3Ga0.7Asquantum-well structures (2000)

Electronic structures of acceptors confined at the center of ${\mathrm{In}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}{\mathrm{A}\mathrm{s}/\mathrm{A}\mathrm{l}}_{0.3}{\mathrm{Ga}}_{0.7}\mathrm{As}$ quantum wells are studied experimentally and theoretically. The aim of this investigation is to explore the effects of biaxial deformation potential on acceptors confined in quantum-well structures. Satellite peaks related to $2S$ and $2P$ of the confined acceptors have been observed in selective photoluminescence spectra. The deduced energy separations between the acceptor heavy holelike ground-state and different excited-states are compared with the theoretical calculated results. The impurity states are calculated using a four-band effective-mass theory, in which the valence-band mixing as well as the mismatch of the band parameters and the dielectric constants between well and barrier materials have been taken into account. An excellent agreement between experimental and theoretical data was found.
Alignment of Self-Assembled Hierarchical Microstructure in Liquid Crystalline Diblock Copolymers Using High Magnetic Fields (2004)

Large area microdomain alignment in a ferroelectric liquid crystalline diblock copolymer (LCBCP) poly(styrene)-block-poly(isoprene-LC), (PS−PILC), incorporating a biphenyl 3-nitro-4-alkoxy-benzoate LC mesogenic group and a non-LC block hexagonally packed cylinder microstructure, was successfully accomplished by application of a magnetic field at elevated temperatures. Small- and medium-angle X-ray scattering demonstrated that the PS cylinders in the LC matrix orient over large areas with their long axes perpendicular to the applied magnetic field. Correspondingly, the smectic layers of the LC mesophase in the matrix are also perpendicular to the field as the anchoring of the mesogens at the intermaterial dividing surface (IMDS) between the cylindrical microdomains and the matrix is planar (homogeneous) in this material. A negative diamagnetic anisotropy for the LC mesogens is inferred from the data. A lamellar sample was also studied and found to exhibit no preferred microstructural orientation when subjected to the magnetic field. This result is consistent with the orientational state degeneracy of planar anchoring of mesogens at the flat lamellar IMDS and closely parallels our prior results obtained by orientation of nonferroelectric LCBCPs using oscillatory shear.
NEUTRAL MECHANICAL ALIGNMENT: APPRECIATING THE BOUNDARIES (2015)

Most discussions of alignment after TKA focus on defining “malalignment”; the prefix mal- is derived from Latin and refers to bad, abnormal or defective and thus by definition malalignment is bad, abnormal or defective alignment. No one then wants a “malaligned” knee. The intellectually curious, however, might switch the focus to the other end of the spectrum and ask what does an ideally aligned knee look like in 2015? Is there really one simple target value for alignment in all patients undergoing TKA? Is that target broad (zero +/−3 degrees mechanical axis) or is it a narrow target in which a penalty, in regard to durability or function, is incurred as soon as you deviate even 1 degree? Is that ideal target the same if we are evaluating the functional performance of the TKA versus the durability of the TKA or could there be 2 different targets, one that maximises function and one that maximises durability? Is that target adequately described by a single 2-dimensional value (varus/valgus alignment in the frontal plane) as measured on a static radiograph? Is that value the same if the patient has a fixed pelvic obliquity, a varus thrust in the contralateral knee or an abnormal foot progression angle? It is revealing to ask “do we understand TKA alignment better in 2015 than in 1979…?” Maybe not. We allowed ourselves over the past 2 decades to be intellectually complacent in regard to questions of ideal alignment after TKA. The constraints on accuracy imposed by our standard total knee instruments and the constraints on assessment imposed by 2-dimensional radiographs made broad, simple targets like a mechanical axis +/− 3 degrees reasonable starting points yet we have not further worked to verify if we can do better. It is naive to think that the complex motion at the knee occurring in 6-dimensions over time can be reduced to a single static target value like a neutral mechanical axis and have strong predictive value in regard to the success or failure of an individual TKA. We assessed 399 knees of 3 different modern cemented designs at 15 years and found that factors other than alignment were more important than alignment in determining the 15-year survival. Until more precise alignment targets can be identified for individual patients or sub-groups of patients then a neutral mechanical axis remains a reasonable surgical goal. However, the traditional description of TKA alignment as a dichotomous variable (aligned versus malaligned) defined around the broad, generic target value of 0 +/− 3 degrees relative to the mechanical axis is of little practical value in predicting the durability or function of modern TKA.
BRAF Inhibition: Bridge or Boost to T-cell Therapy? (2019)

The concept of treatment-refractory disease has evolved as checkpoint modulation has changed the therapeutic landscape for patients with metastatic melanoma. Developing meaningful salvage strategies will involve the exploration of combination therapies and new immunotherapeutics, including adoptive transfer of tumor-infiltrating lymphocytes or other T-cell-based therapy.<i>See related article by Atay et al., p. 2783</i>.
Age-related decline in physical activity: generalization to nonhumans (2000)

The question of whether the age-related decline in physical activity reported in humans has a biological basis is addressed by reviewing gerontological studies that have used nonhuman subjects. From at least three separate arguments, this review provides strong support for a biological basis of this phenomenon. First, age-related decline in activity measured in many different ways is observed across a wide range of nonhuman species. Second, the activity decline appears predictive of lifespan. Increased levels of activity predict longevity, and increasing activity through exercise increases median lifespan. Third, activity declines appear related to altered neurotransmission involving the central dopamine system. Reduced dopamine release or loss of dopamine receptors appears to underlie age-related activity decline, and interventions that enhance dopamine function can increase activity levels in aged animals.
The Branch Point Metabolite for Pyocyanine Biosynthesis in Pseudomonas aeruginosa (1972)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Saturation characteristics of fast photodetectors (1999)

Saturation of photodetectors is measured in the time domain using optical pulses of different duration and in the frequency domain using amplitude-modulated optical carriers. In the time domain, saturation is characterized by a reduction in peak photocurrent and growth of a pulse tail indicating that significant carrier velocity reduction is occurring as the opposing space-charge field persists. In the frequency domain, saturation is characterized by a reduction in response to a sinusoidal signal. The time-domain saturation measurements are shown to result in substantially larger 1-dB compression currents than frequency-domain measurements for the same photodiode. Transient space-charge calculations and a spectral analysis based on Gaussian pulses are shown to help to explain the apparent differences and to correlate the measured results from the time and frequency domains.
1139: Risk Adjusted Analysis of Positive Surgical Margins Following Laparoscopic and Retropubic Radical Prostatectomy (2006)

You have accessJournal of UrologyDiscussed Poster, Tuesday, May 23, 2006, 9:00 am - 12:00 pm1 Apr 20061139: Risk Adjusted Analysis of Positive Surgical Margins Following Laparoscopic and Retropubic Radical Prostatectomy Karim Touijer, Kentaro Kuroiwa, James A. Eastham, Andrew J. Vickers, Victor E. Reuter, Peter T. Scardino, and Bertrand Guillonneau Karim TouijerKarim Touijer More articles by this author , Kentaro KuroiwaKentaro Kuroiwa More articles by this author , James A. EasthamJames A. Eastham More articles by this author , Andrew J. VickersAndrew J. Vickers More articles by this author , Victor E. ReuterVictor E. Reuter More articles by this author , Peter T. ScardinoPeter T. Scardino More articles by this author , and Bertrand GuillonneauBertrand Guillonneau More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)33364-0AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1139: Risk Adjusted Analysis of Positive Surgical Margins Following Laparoscopic and Retropubic Radical Prostatectomy." The Journal of Urology, 175(4S), p. 366 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 175Issue 4SApril 2006Page: 366 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Karim Touijer More articles by this author Kentaro Kuroiwa More articles by this author James A. Eastham More articles by this author Andrew J. Vickers More articles by this author Victor E. Reuter More articles by this author Peter T. Scardino More articles by this author Bertrand Guillonneau More articles by this author Expand All Advertisement PDF DownloadLoading ...
Histone Modifications and DNA Double-Strand Break Repair after Exposure to Ionizing Radiations (2013)

Ionizing radiation exposure induces highly lethal DNA double-strand breaks (DSBs) in all phases of the cell cycle. After DSBs are detected by the cellular machinery, these breaks are repaired by either of two mechanisms: (1) nonhomologous end joining (NHEJ), which re-ligates the broken ends of the DNA and (2) homologous recombination (HR), that makes use of an undamaged identical DNA sequence as a template to maintain the fidelity of DNA repair. DNA DSB repair must occur within the context of the natural cellular DNA structure. Among the major factors influencing DNA organization are specific histone and nonhistone proteins that form chromatin. The overall chromatin structure regulates DNA damage responses since chromatin status can impede DNA damage site access by repair proteins. During the process of DNA DSB repair, several chromatin alterations are required to sense damage and facilitate accessibility of the repair machinery. The DNA DSB response is also facilitated by hierarchical signaling networks that orchestrate chromatin structural changes that may coordinate cell-cycle checkpoints involving multiple enzymatic activities to repair broken DNA ends. During DNA damage sensing and repair, histones undergo posttranslational modifications (PTMs) including phosphorylation, acetylation, methylation and ubiquitylation. Such histone modifications represent a histone code that directs the recruitment of proteins involved in DNA damage sensing and repair processes. In this review, we summarize histone modifications that occur during DNA DSB repair processes.
758. Towards Gene Knock out Therapy for AIDS/HIV: Targeted Disruption of CCR5 Using Engineered Zinc Finger Protein Nucleases (ZFNs) (2006)

HIV entry into target cells requires binding of the envelope protein GP120 to the CD4 co-receptors CCR5 or CXCR4. Loss of these HIV co-receptors is therefore attractive as a potential therapy for HIV patients, yet no current methods permit the efficient therapeutic disruption of a chosen gene in the human genome. To this end, we have developed designed zinc-finger protein nucleases (ZFNs) to target predetermined sequences within the CCR5 gene. Once these ZFNs create a double strand break (DSB) in the targeted DNA, natural DNA repair pathways, including Non-Homologous End Joining (NHEJ), subsequently repair the DSB. Importantly, however, NHEJ is error prone and thus can result in permanent disruption of the targeted gene. Designed ZFNs that recognize coding sequences within the CCR5 gene were generated and their DNA-binding and cleavage properties were determined in vitro. Vectors encoding the validated ZFNs were introduced into human cells for in vivo assessment of function. ZFNs targeted to the CCR5 co-receptor efficiently cleaved their expected DNA target sites, leading to high efficiency target gene disruption (>5%) in transiently transfected cells even in the absence of selective pressure. These results have been confirmed in relevant primary cell types (monocytes, CD4+ T cells, CD34+ hematopoietic precursors). We also demonstrated that PM-1 and GHOST cells modified by the CCR5-ZFNs became resistant to HIV infection. Challenge assays using T cells pre-treated with these ZFNs are in progress, although it is well established that a patients cells carrying a deletion within the CCR5 gene are resistant to infection despite repeated exposure to R5-tropic virus. Moreover, the frequency of gene disruption observed supports its examination as a possible method for the therapeutic modification of isolated patient cells to generate HIV resistant T cells or hematopoietic precursors. Full-time employee of Sangamo BioSciences.
CD40/CD40 Ligand Signaling in Mouse Cerebral Microvasculature After Focal Ischemia/Reperfusion (2005)

Our findings indicate that CD40/CD40L signaling contributes to inflammatory and prothrombogenic responses and brain infarction induced by MCAO and reperfusion. The CD40/CD40L dyad may play a significant pathogenic role in the acute phase of ischemic stroke.
Server I/O networks past, present, and future (2003)

Enterprise and technical customers place a diverse set of requirements on server I/O networks. In the past, no single network type has been able to satisfy all of these requirements. As a result several fabric types evolved and several interconnects emerged to satisfy a subset of the requirements. Recently several technologies have emerged that enable a single interconnect to be used as more than one fabric type. This paper will describe the requirements customers place on server I/O networks; the various fabric types and interconnects that have been used to satisfy those requirements; the technologies that are enabling network convergence; and how these new technologies are being deployed on various network families.
Waveform and Beamforming Design for Intelligent Reflecting Surface Aided Wireless Power Transfer: Single-User and Multi-User Solutions (2022)

In this paper, we study the waveform and passive beamforming design for intelligent reflecting surface (IRS)-aided wireless power transfer (WPT). Generalized multi-user and low complexity single-user algorithms are demonstrated based on alternating optimization (AO) framework to maximize the weighted sum output direct current (DC), subject to the transmit power constraints and passive beamforming modulus constraints. The input signal waveform and IRS passive beamforming phase shifts are jointly designed as a function of users’ individual frequency-selective channel state information (CSI). The energy harvester nonlinearity is explored and two IRS deployment schemes, namely frequency selective IRS (FS-IRS) and frequency flat IRS (FF-IRS), are modeled and analyzed. This paper highlights the fact that IRS can provide an extra passive beamforming gain on output DC power over conventional WPT designs and significantly influence the waveform design by leveraging the benefit of passive beamforming, frequency diversity and energy harvester nonlinearity. Even though FF-IRS exhibits lower output DC than the ideal FS-IRS, it still achieves substantially increased DC power over conventional WPT designs. Performance evaluations confirm the significant benefits of a joint waveform and passive beamforming design accounting for the energy harvester nonlinearity to boost the performance of single-user and multi-user WPT systems.
Membrane-Protein Interactions Contribute to Efficient 27-Hydroxylation of Cholesterol by Mitochondrial Cytochrome P450 27A1 (2002)

Mitochondrial cytochrome P450 27A1 (P450 27A1) catalyzes 27-hydroxylation of cholesterol, the first step in the alternative bile acid biosynthetic pathway. Although several crystal structures of P450s are known, no structural information is available for the mammalian, membrane-bound enzymes involved in the removal of cholesterol from the body. We prepared a three-dimensional model of P450 27A1 based on the structure of P450 BM-3. Conservative and non-conservative mutations were introduced at hydrophobic and positively charged residues in the putative F-G loop and the adjacent helix G (positions 219-237). Subcellular distribution of the mutant P450s expressed in Escherichia coli was used as a measure of membrane-protein interactions. Conservative substitutions of residues located on the surface, according to our model, L219V, L219I, Y220F, F223Y, L224I, R229K, V231L, F234Y, K236R, and R237K, weakened the association of the mutant P450s with the membrane and led to the appearance of up to 21% of P450 27A1 in the bacterial cytosol. It is likely that the mutated side chains are involved in binding to membrane phospholipids. Substitutions in the F-G loop did not significantly affect the K(m) value for cholesterol hydroxylation. However, non-conservative mutants, L219N, Y220A, Y220S, F223A, K226R, and R229A, had significantly impaired catalytic properties, indicating strict requirements for the size and polarity of the side chains at these positions for the catalysis. The results provide insight into the membrane topology of mitochondrial P450s and indicate the importance of membrane-protein interactions in the efficiency of reactions catalyzed by P450 27A1.
Pharmacokinetics of fluorobenzyl polyethylene glycol conjugated tetraiodothyroacetic acid (NP751), a novel anticancer thyrointegrin αvβ3 antagonist (2022)

We have recently reported on the development of fb-PMT (NP751), a conjugate of the thyroid hormone metabolite tetraiodothyroacetic acid (tetrac) and monodisperse polyethylene glycol 36. It exhibited high affinity for thyrointegrin α<sub>v</sub>β<sub>3</sub> receptor and potent anti-angiogenic and anticancer activity <i>in vivo</i>. The objective of the current study is to determine the pharmacokinetics (PK) of fb-PMT in experimental animals, such as mice, rats, and monkeys. NP751 was quantified using a propylene diamine-modified tetraiodothyroacetic acid (DAT) as an internal standard. The limit of quantification (LOQ) for fb-PMT was 1.5 ng/μL and the recovery efficiency was 93.9% with the developed method. The peak plasma concentration (Cmax) and the area under the curve (AUC) results at different doses in mice, rats and monkeys suggest that pharmacokinetics of NP751 is dose-dependent within the dose ranges administered. Results indicate that NP751 has comparable PK parameters that provides enough exposure as a molecularly tumor targeted molecule in multiple species and is a promising anticancer therapeutic.
The value of natural products to future pharmaceutical discovery (2007)

Natural products have provided considerable value to the pharmaceutical industry over the past half century. In particular, the therapeutic areas of infectious diseases and oncology have benefited from numerous drug classes derived from natural product sources. Unfortunately, pharmaceutical companies have significantly decreased activities in natural product discovery during the past several years. Biotechnology companies working in the fields of combinatorial biosynthesis, genetic engineering and metagenomic approaches to identify novel natural product lead molecules have had limited success. Despite what appears to be a slow death of natural product discovery research, many new and interesting molecules with biological activity have been published in the past few years. If natural product materials continue to be tested for desirable therapeutic activities, we believe that significant progress in identifying new antibiotics, oncology therapeutics and other useful medicines will be made.
Maximal Bandwidth of an Archimedean Spiral Antenna Above a Reflector (2014)

In this letter, the maximal achievable bandwidth of an Archimedean spiral antenna above a reflector is investigated. This bandwidth is defined by the frequency range where the gain in the broadside direction is higher than the case without a reflector. To determine this theoretical bandwidth, we propose an analysis consisting in replacing the Archimedean spiral antenna by a bidirectional elliptical plane-waves source above an infinite reflector. Thanks to this approximation, it is possible to evaluate this bandwidth with a simple analytical expression, which is defined by constructive interferences between two plane waves. The maximal bandwidth obtained from this formula is equal to 5:1 for a metallic reflector. Simulations and measurements are then presented in order to confirm this result.
Benchmark Datasets Task 2 Report: Use Case Development and Prioritization Results June 2019 (2019)

The Benchmark Datasets project is a four-year effort to collect and curate building operational and environmental data, with the goal of addressing data gaps that have prevented stakeholders from achieving greater levels of energy efficiency and load flexibility. The effort is led by the U.S. Department of Energy (DOE) Building Technologies Office (BTO) with performers from National Renewable Energy Laboratory (NREL), Lawrence Berkeley National Laboratory (LBNL), Oak Ridge National Laboratory (ORNL), and Pacific Northwest National Laboratory (PNNL). Task 2 of the FY19 project involved identifying and prioritizing use cases that would benefit from targeted data collection and curation. NREL led this task with support from LBNL, ORNL, and PNNL. This report, which was submitted as an internal document to DOE in June 2019, summarizes the method used by the Task 2 team to select high-priority use cases and data needs that formed the focus of the remainder of the project. The high-priority use cases continue to inform subsequent efforts to down-select candidate data sources and engage potential partners.
Optimized Wavelength Selection and Normalization in Spectral Near Infrared Tomography (2010)

Multi-spectral near infrared tomographic imaging has the potential to provide information about patho-physiological function of soft tissue. However, the specific choice of wavelengths used is crucial for the accurate separation of such parameters. Determination of a set of optimized bands of wavelengths is presented and tested using experimental data. The optimization method achieves images as accurate as using the full spectrum, but improves cross talk between parameters. A Jacobian normalization technique is presented which takes into account the varying magnitude of different optical parameters creating a more uniform update within a spectral image reconstruction model.