gebhart/patrepeval huggingface dataset:
Local delivery of a zoledronate solution improves osseointegration of titanium implants in a rat distal femur model (2018)

This study aimed to determine whether locally applied anti-resorptive agents acetazolamide or zoledronic acid would improve mechanical stability in implant osseointegration when applied as a solution within the medullary canal. Thirty-three rats received titanium-implants bilaterally in their intramedullary femoral canals. Prior to implantation, animals received 0.1 ml saline, 1 mM acetazolamide solution, or 0.7 mM zoledronic acid solution directly into the medullary cavity. The control group only received saline within the medullary canal while the treatment groups only received the respective treatment to which they were randomized. Animals were allowed to heal 4 weeks, at which time they were euthanized and femurs isolated for mechanical and radiographic evaluation. Push-out force to failure increased 152% in the zoledronic acid group relative to the control. There was no significant difference in push-out force with acetazolamide relative to control. Also, zoledronic acid increased metaphyseal bone volume fraction 46% and increased metaphyseal bone-implant contact 58% relative to the control. Recent research exploring local injection of medications to improve implant osseointegration and minimize systemic-effects has failed to quantitatively evaluate implant fixation strength on non-hydroxyapatite coated implants or implants without previous bone compaction. This study demonstrated that a simple injection of zoledronic acid into the medullary canal, rather than coatings or commercial gels, can increase fixation strength of an uncoated titanium-implant. Our findings indicate simple injection of zoledronic acid in saline solution has the potential for improving fixation of uncemented joint implants. Clinical Significance: Intramedullary injection of local bisphosphonate solutions could be implemented to improve osseointegration in cementless arthroplasty. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:3294-3298, 2018.
Giardia intestinalis thymidine kinase is a high-affinity enzyme crucial for DNA synthesis and an exploitable target for drug discovery (2022)

Giardiasis is a diarrheal disease caused by the unicellular parasite Giardia intestinalis, for which metronidazole is the main treatment option. The parasite is dependent on exogenous deoxyribonucleosides for DNA replication and thus is also potentially vulnerable to deoxyribonucleoside analogs. Here, we characterized the G. intestinalis thymidine kinase, a divergent member of the thymidine kinase 1 family that consists of two weakly homologous parts within one polypeptide. We found that the recombinantly expressed enzyme is monomeric, with 100-fold higher catalytic efficiency for thymidine compared to its second-best substrate, deoxyuridine, and is furthermore subject to feedback inhibition by dTTP. This efficient substrate discrimination is in line with the lack of thymidylate synthase and dUTPase in the parasite, which makes deoxy-UMP a dead-end product that is potentially harmful if converted to deoxy-UTP. We also found that the antiretroviral drug azidothymidine (AZT) was an equally good substrate as thymidine and was active against WT as well as metronidazole-resistant G. intestinalis trophozoites. This drug inhibited DNA synthesis in the parasite and efficiently decreased cyst production in vitro, which suggests that it could reduce infectivity. AZT also showed a good effect in G. intestinalis-infected gerbils, reducing both the number of trophozoites in the small intestine and the number of viable cysts in the stool. Taken together, these results suggest that the absolute dependency of the parasite on thymidine kinase for its DNA synthesis can be exploited by AZT, which has promise as a future medication effective against metronidazole-refractory giardiasis.
An adaptive dead-zone inverse controller for systems with sandwiched dead-zones (2001)

This paper addresses adaptive control of sandwich nonlinear systems having an unknown sandwiched deadzone between the linear dynamic blocks, as illustrated by a hydraulic valve system. An adaptive hybrid control scheme for control of such sandwiched dead-zone systems is developed. The proposed control scheme employs an inner-loop discrete-time feedback design and an outer-loop continuous-time feedback design, combined with an adaptive dead-zone inverse to cancel the dead-zone effect for improving output tracking. Tracking performance of the closed-loop control system is analyzed. Simulation results are used to illustrate the effectiveness of the proposed adaptive dead-zone inverse controller.
Roadmap of ultrafast x-ray atomic and molecular physics (2018)

X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (10 20 W cm -2 ) of x-rays at wavelengths down to 1 ngstrom, and HHG provides unprecedented time resolution (50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of 280 eV (44 ngstroms) and the bond length in methane of 1 ngstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and ngstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at ngstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since its discovery roughly 30 years ago, showcasing experiments in AMO physics and other applications. Here we capture the perspectives of 17 leading groups and organize the contributions into four categories: ultrafast molecular dynamics, multidimensional x-ray spectroscopies; high-intensity x-ray phenomena; attosecond x-ray science.
A logical approach to renal stone removal (1984)

On the basis of experience with over 350 percutaneous stone extractions, a logical approach assuring a high success rate and minimizing complications is described. The importance of the position of the kidney in the body, the caliceal anatomy, the renal arterial anatomy, and the instrumentation used on puncture site selection are discussed. Strategies for removal of caliceal, pelvic, ureteral, and staghorn calculi, rationale, and treatment of complications are also described.
Workflow and data management in InConcert (2002)

InConcert is an object-oriented client-server workflow management system. An overview is provided of the functionality of InConcert and how it is implemented on an underlying relational database management system. Data management issues in supporting distributed workflow are briefly reviewed.
Longitudinal evaluation of clustering of chronic sinonasal and related symptoms using exploratory factor analysis (2018)

Although the current approaches to symptom characterization in CRS imply a single underlying latent construct, our results suggest that there are at least 3 latent constructs relevant to CRS. Further studies are needed to evaluate whether these clusters have identifiable underlying pathobiologies.
TU‐G‐134‐03: MR‐Only‐Based Generation of Electron Density Maps and Digitally Reconstructed Radiographs of the Pelvis (2013)

Purpose: To generate electron density (ED) maps and digitally reconstructed radiographs (DRRs) of the pelvis based only on magnetic resonance imaging (MRI). Methods: A conventional 3D fast‐field dual‐echo sequence was used to acquire image data of 8 healthy subjects with a Philips 3.0T Ingenia TX system in approximately 1:50 min scan time per volunteer. Dixon reconstruction of the nearly out‐of‐phase (echo 1) and in‐phase images (echo 2) allowed for water and fat classification. A bone‐enhanced image was generated by automatically thresholding the noise level of the in‐phase image with subsequent background removal. ED maps were then produced by assigning known bulk electron densities to the classified bone and tissue fractions. A bone probability atlas derived from CT data was registered to the ED map in order to filter out misclassified voxels. Finally, DRRs were reconstructed from bone‐enhanced images as well as from ED maps. Results: The proposed MRI sequence with subsequent Dixon reconstruction and probabilistic filtering makes it possible to classify cortical bone, soft tissue and adipose tissue in the pelvis and yields ED maps and corresponding DRRs. Bowel content was misclassified as cortical bone or air and compromised the segmentation in some slices as well as in the DRRs. Automatic probabilistic atlas filtering can significantly reduce artifacts induced by bowel content without affecting pelvic bone structures markedly. In total, the artifact/bone fraction dropped from 1.7 before filtering to 0.2 after filtering. The average reduction of artifact volume is 87%, and the average bone preservation is 99%. Remaining artifacts are spatially close to the true bone in areas of positive bone probability. Conclusion: This study demonstrated the feasibility of generating realistic ED maps of the pelvis by using MRI only. The method has the potential to become an essential component of emerging applications such as MR‐only‐based radiation therapy planning. All authors have the following relevant financial interest or relationship to disclose with regard to the subject matter of this presentation: Company name: Philips Research; Type of relationship: Employee
Carbon-13 nuclear magnetic resonance studies of the redox reactions of aurothiomalates with selenocyanate in aqueous solution (1995)

The interactions of SCN– and SeCN– with aurothiomalate [Au(tm)]n in aqueous solution were studied by 13C NMR spectroscopy. The [Au(tm)]n is further polymerized in the presence of SCN–, however, SeCN– binds to [Au(tm)]n forming monomeric [Au(SeCN)(tm)]–. This complex initially disproportionates to give [Au(SeCN)2]– and [Au(tm)2]–. The [Au(SeCN)2]– eventually decomposed to give [Au(CN)2]– and metallic selenium. The free tm– released from [Au(tm)]n is oxidized to the thiomalic disulfide (tm)2. When the bis complex [Au(tm)2]– reacted with SeCN– it did not form [Au(SeCN)(tm)]–, but instead gave (tm)2, [Au(CN)2]– and Se22–.
Characterization of foam flowing in a granular medium in the presence of oil by small angle neutron scattering (2020)

We present an experimental study of foam-flow characterization inside a 3D granular medium packed in a cell. The foam is formed by coinjecting a surfactant solution and gas inside a cell filled with silica grains. The porous medium is initially saturated with dodecane and water before the gas-surfactant coinjection. To simplify the interpretation of the measurements, a contrast matching methodology has been applied in order to obtain a two phase system regarding the scattering length density values. The combination of transmission and incoherent scattering allows us to estimate the volume fractions of each phase, whereas the coherent scattering is used to estimate the surface to volume ratio S/V related to water-oil and water-gas interfaces. Considering the evolution of S/V ratio, volume fractions and pressure difference, we infer some mechanisms of foam generation and transportation as well as oil removal.
Fun with Microarrays Part III: Integration and the End of Microarrays as We Know Them (2008)

Microarray experiments are an important method for the high-throughput investigation of biological phenomenon. A wide variety of techniques and algorithms exist for analyzing and extracting information from microarrays. This is the last of a series of reviews outlining the technological, computational, and experimental aspects of microarray experiments. This part focuses on cutting-edge applications of microarrays, with examples from drug discovery, evolutionary biology, and polymorphism analysis. A discussion of the future of array-based research is also given. Overall, microarray technologies are rapidly reaching maturation, and the focus is on their clever application to address previously intractable biological problems.
ChemInform Abstract: Total Synthesis of (.+‐.)‐Cylindricines A (I) and B (II). (2000)

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.
Effect of Cobicistat on Tenofovir Disoproxil Fumarate (TDF): What Is True for TAF May Also Be True for TDF (2017)

Coadministration with COBI resulted in significantly higher tenofovir concentrations and higher TDF discontinuation compared with other antiretroviral regimens. Accordingly, the possibility that the lack of proper dose adjustment for TDF when given with COBI might have biased the safety comparisons with tenofovir alafenamide during registrative trials cannot be ruled out.
Inverse-designed Nonlinear Nanophotonic Structures: Enhanced Frequency Conversion at the Nano Scale (2016)

We describe a large-scale computational approach based on topology optimization that enables automatic discovery of novel nonlinear photonic structures. As examples, we design complex cavity and fiber geometries that can achieve high-efficiency nonlinear frequency conversion.
Dynamic wavelength conversion of an optical pulse traveling in a 2D photonic crystal waveguide (2007)

We report on a first successful wavelength conversion of a signal pulse traveling in a two-dimensional photonic crystal waveguide via dynamic refractive index change by a control pulse.
Charge transport enhancement in supramolecular oligothiophene assemblies using Pt(ii) centers as a guide (2019)

The self-assembly properties of a series of square planar Pt(<sc>ii</sc>) complexes have been related to their charge transport properties, finding higher mobility values in the complexes placing the Pt centers in closer proximity.
Hybrid Silicon Evanescent Amplifiers (2006)

The structure and design of a hybrid silicon evanescent amplifier, incorporating III-V offset quantum wells bonded on a silicon waveguide, is proposed and discussed.
Barrier to Migration of the Silicon Self-Interstitial (1984)

The first total-energy calculations of barriers to interstitial migration have been used to study silicon self-interstitial migration. Migration occurs through the low-electron-density path. Relaxation was found to be important in determining the barrier for both ${\mathrm{Si}}^{(0)}$ and ${\mathrm{Si}}^{(++)}$. Electron-assisted migration has been demonstrated. ${\mathrm{Si}}^{(++)}$ was found to have lower energy at the tetrahedral site while ${\mathrm{Si}}^{(0)}$ has lower energy at the hexagonal site.
GHz flip chip interconnect experiments (2004)

The flip chip is recognized as the most reliable chip interconnect method and renders an extremely high production yield at very low cost. Furthermore, flip chip gives extraordinary electrical performance, which is vital at GHz frequencies. The flip-chip interconnect is based on three fundamental elements, bumps on a die, chip carrier and the method of joining a die to a carrier. These elements are interdependent, thus important to consider each in order to select the optimal flip-chip system for a specific application. The tentative use of an encapsulant is another consideration. Most obviously, the gold pad and conductor metallurgy of GaAs chips bring the need for alternate bumping methods. Two different joining schemes tentatively suitable for GaAs chip pad metallurgies were tested based on thermocompression joining. Bumps were applied to the chip carrier, a thin film substrate and were either plated gold cylinders or gold ball bond studs. Cross-sections, shear tests, and X-ray imaging were used to determine the joint quality.
Survey of High Risk Donor Utilization Practices in Canadian Transplant Programs. (2014)

Introduction: The use of high risk donors (HRDs) has the potential to significantly increase the donor pool. However, transplant practitioners may be reluctant to use such donors due to the increased risk of HIV and HCV transmission. As part of the Canadian National Transplant Research Program (CNTRP), we conducted a survey of Canadian transplant programs to assess practice patterns for HRD utilization. Methods: A 26 question survey was administered to the medical and surgical program lead of each organ transplant program in Canada by one-on-one telephone or in-person interview. Questions addressed knowledge of HRD criteria, recipient factors for HRDs, and viral nucleic acid testing (NAT). Responses were compared using Chisquared for Fisher's exact tests as appropriate. Results: Of the 40 surveys, 23 (57.5%) were completed. Responders represented 18 kidney, 6 liver, 6 heart, and 1 lung transplant program. Eight pediatric programs were represented. 60.9% of programs had a formal policy on HRDs. However, 21.7% of programs had never used a HRD for transplantation. The primary disincentives for the use of HRD included harm to patient (77.2%) or having a transmission reflect poorly on the transplant program (71.2%). Respondents were most likely to use HRD organs for heart and lung transplants (vs. kidney or liver). Almost all programs counselled patients regarding HRD at the time of organ offer; however, only 39.1% of patients discussed HRDs with their patients at the time of listing. Viral NAT significantly increased the likelihood of using a HRD over serologic testing alone (for IVDU 8.7% to 64.6%; p<0.0001; for MSM 26.1% to 82.6%; p=0.0003). However, NAT was available in a timely fashion for only 43.6% of programs. 56.5% respondents stated that a standardized consent form would significantly increase their utilization of HRDs. The majority of respondents would use a HCV positive donor for a HCV+ recipient. However, 52.6% of respondents would not use a HIV+ donor for a HIV+ recipient. Most (60.9%) felt that HRD use would increase in the next 5 years. Conclusions: This survey demonstrates significant practice variation in the use of HRDs. The results suggest utilization could be optimized by measures such as standardized informed consent and more universal availability of NAT.
Linearizing wideband wireless transmitters using memory effect separation based linearization techniques (2009)

Wideband wireless transmitters will exhibit strong memory effects which heavily compromise the linearization performance of traditional memoryless predistorters. In this paper, the nonlinear behaviors of a wideband wireless transmitter are analyzed. According to the nonlinearity analysis, a novel memory effect separation based linearization technique is presented to linearize the wideband wireless transmitter. The novel predistorter is constructed with a static memoryless nonlinear block followed by a dynamic nonlinear block with memory. The static memoryless nonlinear block is utilized to pre-compensate the memoryless nonlinearity, whereas the dynamic nonlinear block is deployed to eliminate the memory effects. The validation results, carried out on a transmitter prototype for WCDMA systems, reveal that the proposed predistortion technique outperforms the traditional Hammerstein predistortion linearization scheme in suppressing the memory effects.
100 Gb/s DQPSK field trial: Live video transmission over an operating LambdaXtreme® network (2010)

Successful transmission of live (real time) video traffic is demonstrated using a prototype 100 Gb/s single-polarization differential quadrature phase shift keying (DQPSK) transmitter and receiver over an in-service 504 km link of the LambdaXtreme® optical transport platform. Teaming with Verizon Business, we demonstrate the feasibility of upgrading an existing, live traffic bearing network to 100 Gb/s per wavelength without any changes to the current hardware or software. The 107 Gb/s signal is added at a reconfigurable optical add/drop multiplexer (ROADM) at a network node in Tampa, Florida, and dropped at a ROADM in Miami, Florida, where both live video and pseudorandom test sequences are received. In addition, we discuss the steps leading up to this field trial that included several important precursor laboratory experiments. We detail the generation, detection, coding, and long-haul transmission of single-polarization DQPSK at a line rate of 53.5 Gbaud to support a net information bit rate of 100 Gb/s. é 2010 Alcatel-Lucent.
Independence of normal phenotypic properties and cell surface receptor mobility in variant cell lines (1978)

We report the use of three classes of variants from the long-established, malignantly transformed LM cell line to demonstrate that the apparent mobility of cell surface receptors need not be dependent on the expression of the transformed phenotype in vitro.
Data from Systematic Kinome shRNA Screening Identifies CDK11 (PITSLRE) Kinase Expression Is Critical for Osteosarcoma Cell Growth and Proliferation (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Identification of new targeted therapies is critical to improving the survival rate of patients with osteosarcoma. The goal of this study is to identify kinase based potential therapeutic target in osteosarcomas.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We used a lentiviral-based shRNA kinase library to screen for kinases which play a role in osteosarcoma cell survival. The cell proliferation assay was used to evaluate cell growth and survival. siRNA assays were applied to confirm the observed phenotypic changes resulting from the loss of kinase gene expression. CDK11 (PITSLRE) was identified as essential for the survival of osteosarcoma cells, and its expression was confirmed by Western blot analysis and immunohistochemistry. Overall patient survival was correlated with the CDK11 expression and its prognosis. The role of CDK11 expression in sustaining osteosarcoma growth was further evaluated in an osteosarcoma xenograft model &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Osteosarcoma cells display high levels of CDK11 expression. CDK11 expression knocked down by either lentiviral shRNA or siRNA inhibit cell growth and induce apoptosis in osteosarcoma cells. Immunohistochemical analysis showed that patients with osteosarcoma with high CDK11 tumor expression levels were associated with significantly shorter survival than patients with osteosarcoma with low level of tumor CDK11 expression. Systemic &lt;i&gt;in vivo&lt;/i&gt; administration of &lt;i&gt;in vivo&lt;/i&gt; ready siRNA of CDK11 reduced the tumor growth in an osteosarcoma subcutaneous xenograft model.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We show that CDK11 signaling is essential in osteosarcoma cell growth and survival, further elucidating the regulatory mechanisms controlling the expression of CDK11 and ultimately develop a CDK11 inhibitor that may provide therapeutic benefit against osteosarcoma. &lt;i&gt;Clin Cancer Res; 18(17); 4580–8. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;