gebhart/patrepeval huggingface dataset:
Resistance to methotrexate due to gene amplification in a patient with acute leukemia. (1984)

A patient is described with acute myelocytic leukemia refractory to conventional therapy, who also became highly resistant to methotrexate (MTX) after repeated courses of this drug. Leukemia cells from this patient were found to contain an elevated level of dihydrofolate reductase (DHFR) activity, with no change in the affinity of the enzyme for MTX. A sensitive "dot blot" assay revealed a fourfold increase in the gene copy number of DHFR. Southern blot analysis with a human DHFR cDNA probe confirmed this increase in the gene copy number, and demonstrated a similar restriction pattern with Eco R1, Hind III, and Pst 1 as seen with a highly amplified human leukemia cell line, K562. Additional DHFR fragments were detected, not seen in the K562 blot, suggesting the presence of pseudogenes, or a result of gene rearrangements occurring as part of the amplification process. Resistance to MTX in this patient was therefore ascribed to gene amplification and overproduction of DHFR.
Mutations in pmrB Confer Cross-Resistance between the LptD Inhibitor POL7080 and Colistin in Pseudomonas aeruginosa (2019)

Pseudomonas aeruginosa is a major bacterial pathogen associated with a rising prevalence of antibiotic resistance. We evaluated the resistance mechanisms of P. aeruginosa against POL7080, a species-specific, first-in-class antibiotic in clinical trials that targets the lipopolysaccharide transport protein LptD. We isolated a series of POL7080-resistant strains with mutations in the two-component sensor gene pmrB. Transcriptomic and confocal microscopy studies support a resistance mechanism shared with colistin, involving lipopolysaccharide modifications that mitigate antibiotic cell surface binding.
Acoustically enhanced bubble growth at low frequencies and its implications for human diver and marine mammal safety (1994)

Computations are made of the conditions necessary to obtain bubble growth by rectified diffusion under a variety of conditions associated with low-frequency sound propagation in the ocean. The complex issue of microbubble nuclei stabilization is treated by assuming either a sufficient level of supersaturation to stabilize the initial bubble size, or by examining a microbubble nucleus with zero surface tension. The bubble growth rates and thresholds are obtained for a range of SPLs (re: 1 μPa) from 150–220 dB, for initial bubble radii from 1–10 μm, and for levels of the dissolved gas concentration from 100% to 223% of saturation. It was determined that for the range of conditions examined, it was necessary to utilize three different formulations of the equations for bubble growth. The results of these calculations and assumptions indicate that for SPLs in excess of 210 dB, significant bubble growth can be expected to occur, and divers and marine mammals exposed to these conditions could be at risk. For SPLs below about 190 dB, however, significant bubble growth is unexpected. [Work supported in part by NSMRL.]
Influence of CD4+CD25+ Regulatory T Cells on Low/High-Avidity CD4+ T Cells following Peptide Vaccination (2006)

We have recently reported that NY-ESO-1-specific naive CD4+ T cell precursors exist in most individuals but are suppressed by CD4+CD25+ regulatory T cells (Tregs), while memory CD4+ T cell effectors against NY-ESO-1 are found only in cancer patients with spontaneous Ab responses to NY-ESO-1. In this study, we have analyzed mechanisms of CD4+ T cell induction following peptide vaccination in relation to susceptibility to Tregs. Specific HLA-DP4-restricted CD4+ T cell responses were elicited after vaccination with NY-ESO-1(157-170) peptide (emulsified in IFA) in patients with NY-ESO-1-expressing epithelial ovarian cancer. These vaccine-induced CD4+ T cells were detectable from effector/memory populations without requirement for in vitro CD4+CD25+ T cell depletion. However, they were only able to recognize NY-ESO-1(157-170) peptide but not naturally processed NY-ESO-1 protein and had much lower avidity compared with NY-ESO-1-specific pre-existing naive CD4+CD25- T cell precursors or spontaneously induced CD4+ T cell effectors of cancer patients with NY-ESO-1 Ab. We propose that vaccination with NY-ESO-1(157-170) peptide recruits low-avidity T cells with low sensitivity to Tregs and fails to modulate the suppressive effect of Tregs on high-avidity NY-ESO-1-specific T cell precursors.
17O NMR investigation of acetyl and formylthiophenes, furans and pyrroles (1988)

Abstract The 17 O nmr chemical shifts of 20 acetyl and formylthoiphenes, furans, and pyrroles are reported. The chemical shifts qualitatively correlate with the electronic character of the heterocyclic rings. The effect of steric factors are noted for the 17 O chemical shifts of alkyl substituted acetylthiophenes and for N ‐methylpyr‐roles.
Chip design for thin-film deep ultraviolet LEDs fabricated by laser lift-off of the sapphire substrate (2017)

We report on a chip design which allows the laser lift-off (LLO) of the sapphire substrate sustaining the epitaxial film of flip-chip mounted deep ultraviolet light emitting diodes. A nanosecond pulsed excimer laser with a wavelength of 248 nm was used for the LLO. A mechanically stable chip design was found to be the key to prevent crack formation in the epitaxial layers and material chipping during the LLO process. Stabilization was achieved by introducing a Ti/Au leveling layer that mechanically supports the fragile epitaxial film. The electrical and optical characterization of devices before and after the LLO process shows that the device performance did not degrade by the LLO.
Experimental Demonstration of Vanadium Dioxide Phase Change Thin Film Based Tunable Spiral Inductors (2020)

In this paper, a tunable spiral inductor integrated with vanadium dioxide (VO 2 ) thin film on coplanar waveguide (CPW) transmission line is proposed. The tunable inductance is achieved by using the reversible, thermally controlled VO 2 thin film. VO 2 is one of metal to insulator phase transition (MIT) materials, which can be a potential solution for reconfigurable RF/microwave wireless communication systems. The VO 2 based tunable inductors were fabricated on the sapphire substrate. A model is used to study the fingerprints of MIT and verify the nature of transition in the film. The scattering parameter measurements are taken in the frequency range from 10 MHz to 8 GHz with 801 points. The equivalent circuits have been used to characterize the behavior of tunable inductors and extract the equivalent component values, which show excellent matching to the measured S parameters. The measured results have shown an inductance tunability of 35.24% (3.856 nH−2.498 nH) at 4 GHz.
The potential of carbocyclic nucleosides for the treatment of AIDS: synthesis of carbocyclic 6′-fluoro-2′,3′-dideoxythymidine (1991)

The carbocyclic nucleoside 4 and the corresponding triphosphate 5 were prepared from cyclopent-2-enylmethanol 6 in 8 and 10 steps respectively. The key step in the synthesis is the reaction of the azido alcohol 9 with diethylaminosulphur trifluoride: participation of the azido group led to the formation of the isomeric fluorides 10 and 11(ratio ca. 2:1). The triphosphate 5 was found to be a poor inhibitor of HIV-coded reverse transcriptase.
Versatile Transfer of an Ultralong and Seamless Nanowire Array Crystallized at High Temperature for Use in High-Performance Flexible Devices (2017)

Nanowire (NW) transfer technology has provided promising strategies to realize future flexible materials and electronics. Using this technology, geometrically controlled, high-quality NW arrays can now be obtained easily on various flexible substrates with high throughput. However, it is still challenging to extend this technology to a wide range of high-performance device applications because its limited temperature tolerance precludes the use of high-temperature annealing, which is essential for NW crystallization and functionalization. A pulsed laser technique has been developed to anneal NWs in the presence of a flexible substrate; however, the induced temperature is not high enough to improve the properties of materials such as ceramics and semiconductors. Here, we present a versatile nanotransfer method that is applicable to NWs that require high-temperature annealing. To successfully anneal NWs during their transfer, the developed fabrication method involves sequential removal of a nanoscale sacrificial layer. Using this method, we first produce an ultralong, perfectly aligned polycrystalline barium titanate (BaTiO<sub>3</sub>) NW array that is heat treated at 700 °C on a flexible polyethylene terephthalate (PET) substrate. This high-quality piezoelectric NW array on a flexible substrate is used as a flexible nanogenerator that generates current and voltage 37 and 10 times higher, respectively, than those of a nanogenerator made of noncrystallized BaTiO<sub>3</sub> NWs.
Tuning growth from clusters to continuous ultrathin films: Experiments and molecular dynamics simulations of Pd plasma sputter deposition (2002)

Plasma sputter deposition experiments and simple molecular dynamics calculations are performed for highlighting the effects of plasma ions and kinetic energy of palladium atoms on the morphology of thin films. A transition between cluster and continuous film growth is observed. It is attributed to the kinetic energy of the depositing sputtered palladium atoms and to high binding energy trapping sites resulting from the effects of ions incident on the surface during deposition. These high binding energy trapping sites act as additional nucleation centres that are allowed to be visited by the diffusing Pd atoms.
Improvement of lipid stability in oat products by alkaline wet-processing conditions (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImprovement of lipid stability in oat products by alkaline wet-processing conditionsKirsi. Liukkonen, Anu. Kaukovirta-Norja, and Simo. LaaksoCite this: J. Agric. Food Chem. 1992, 40, 10, 1972–1976Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://pubs.acs.org/doi/10.1021/jf00022a048https://doi.org/10.1021/jf00022a048research-articleACS PublicationsRequest reuse permissionsArticle Views83Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
High-throughput micromachining of steel and ceramics with solid state UV laser (2000)

Performance limits of 10 kHz, 15 nsec-pulse diode-pumped solid- state laser in microdrilling of metals and ceramics were studied. Average drilling rates approaching 1 cm/sec with micrometer-range accuracy of micro-holes are achievable in steel and ceramic samples up to 1 mm thick. We found that shielding effects of plasma plume can be minimized by proper selection of laser intensity. In samples 1 mm and thicker, using third harmonic output allows drilling of high aspect ratio holes at almost an order of magnitude higher ablation rates as compared to IR laser output.
Ab initio study of structures and binding energies for anion-water complexes (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAb initio study of structures and binding energies for anion-water complexesJiali. Gao, Debra S. Garner, and William L. JorgensenCite this: J. Am. Chem. Soc. 1986, 108, 16, 4784–4790Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/ja00276a016https://doi.org/10.1021/ja00276a016research-articleACS PublicationsRequest reuse permissionsArticle Views385Altmetric-Citations121LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Infrared biosensors based on graphene plasmonics: modeling (2013)

We propose a biosensor by exploiting localized plasmons in graphene and biomolecule adsorption on it. Numerical simulations demonstrate that the sensitivity of such a device can achieve a high value of up to 1697 nm/RIU (refractive index unit) when the wavelength shift at the plasmon resonance is detected. The transparent substrate supporting graphene can be chosen potentially from a wide range of materials including insulators, semiconductors, polymers, and gels. The plasmon resonance wavelength can be tuned with electrostatic doping and/or structure modulation of graphene. Furthermore, the device works in a wide angle range of incident light since the transverse magnetic (TM) polarization is independent of incident angles.
Relationship between diabetic retinopathy, diabetic macular oedema and erectile dysfunction in type 2 diabetics (2013)

The presence and severity of diabetic retinopathy but not diabetic macular oedema are independently associated with self-reported erectile dysfunction.
Synthesis and Development of Gadomer: A Dendritic MRI Contrast Agent (2005)

A novel dendritic contrast agent for magnetic resonanceimaging (MRI) has been synthesized. Gadomer consists of 24 macrocyclic gadolinium chelates covalently linked to a dendritic L-lysine skeleton. Due to its high molecular weight (17.5 kDa) the compound has excellent blood pool properties and remains in the intravascular space for a prolonged period of time after i.v. administration without relevant extravasation. This is the first dendritic gadolinium-based contrast agent to have entered clinical trials. The drug proved to be safe and its pharmacological/toxicological profile as well as the imaging properties are excellent. The development of a reproducible and robust synthesis led to the preparation of several multi kgbatches for tox studies and clinical trials.
A One-dimensional Finite Element Method for Simulation-based Medical Planning for Cardiovascular Disease (2002)

We have previously described a new approach to planning treatments for cardiovascular disease, Simulation-Based Medical Planning, whereby a physician utilizes computational tools to construct and evaluate a combined anatomic/physiologic model to predict the outcome of alternative treatment plans for an individual patient. Current systems for Simulation-Based Medical Planning utilize finite element methods to solve the time-dependent, three-dimensional equations governing blood flow and provide detailed data on blood flow distribution, pressure gradients and locations of flow recirculation, low wall shear stress and high particle residence. However, these methods are computationally expensive and often require hours of time on parallel computers. This level of computation is necessary for obtaining detailed information about blood flow, but likely is unnecessary for obtaining information about mean flow rates and pressure losses. We describe, herein, a space-time finite element method for solving the one-dimensional equations of blood flow. This method is applied to compute flow rate and pressure in a single segment model, a bifurcation, an idealized model of the abdominal aorta, in three alternate treatment plans for a case of aorto-iliac occlusive disease and in a vascular bypass graft. All of these solutions were obtained in less than 5 min of computation time on a personal computer.
Halogenation of the N‐Terminus Tyrosine 10 Promotes Supramolecular Stabilization of the Amyloid‐β Sequence 7–12 (2020)

Here, we demonstrate that introduction of halogen atoms at the tyrosine 10 phenol ring of the DSGYEV sequence derived from the flexible amyloid-β <i>N</i>-terminus, promotes its self-assembly in the solid state. In particular, we report the crystal structures of two halogen-modified sequences, which we found to be stabilized in the solid state by halogen-mediated interactions. The structural study is corroborated by Non-Covalent Interaction (NCI) analysis. Our results prove that selective halogenation of an amino acid enhances the supramolecular organization of otherwise unstructured biologically-relevant sequences. This method may develop as a general strategy for stabilizing highly polymorphic peptide regions.
Multimolecular Process in a Packed‐Bed Immobilized Enzyme Reactor: Numerical Simulation and Back‐Mixing Effects (1990)

In a previous report, we presented a new analytical model describing the performance of a packed-bed catalytic unit, where the reaction between two cosubstrates is catalyzed by an enzyme immobilized on a porous carrier. The model explicitly takes into account the changes in concentrations of both cosubstrates along the reactor, as well as the hydrodynamic regimen (i.e., back-mixing) prevailing in the packed bed. In the present report, and on the basis of the procedures developed, we present a detailed analysis of the performance of the reactor. With numerical simulations, the effects of internal diffusion limitations, the depth of the pores, the substrates' concentration in the feed, and kinetic parameters are evaluated. Particular attention is also given here to the back-mixing effects prevailing in the reactor. An experimental procedure for assessing their extent is described.
Phase II Trial of Combination of Bortezomib and Rituximab in Relapsed and/or Refractory Waldenstrom Macroglobulinemia (2008)

Abstract INTRODUCTION: Previous studies have demonstrated the clinical activity of bortezomib as a single agent in patients with Waldenstrom Macroglobulinemia (WM). We performed preclinical studies that demonstrated synergistic activity of bortezomib with the anti-CD20 antibody rituximab in WM cell lines and patient samples. This phase II study aimed to determine safety and activity of weekly bortezomib in combination with rituximab in patients with relapsed/refractory WM. METHODS: Patients who had at least one previous therapy for WM and who had relapsed or refractory disease were eligible. NCI CTCAE v3.0 was used for toxicity assessment. All patients received bortezomib IV weekly at 1.6mg/m2 on days 1, 8, 15, q 28 days × 6 cycles, and rituximab 375 mg/m2 at days 1, 8, 15, 22, on cycles 1 and 4. RESULTS: 37 pts (26 men and 11 women, median age 62 years, range 42 – 73) have been treated to date. All of them had symptomatic disease and required therapy. The median number of lines of prior treatment was 3 (range 1 – 5) including prior bortezomib and prior rituximab in some of those patients. Prior therapy included rituximab, nucleoside analogues (fludarabine and 2-CDA), combination chemotherapy (e.g CHOP, CVP), chloramucil, and bortezomib. The median IgM at baseline was 3540 mg/dL (range 700– 10,800). The median follow up is 10 months (range 1 – 24 months). Thirty pts are currently evaluable for response after completing at least 2 cycles of therapy using IgM monoclonal protein. Complete remission occurred in 1 (3%), partial remission in 16 (53%), and minimal response in 10 (33%). Progressive disease occurred in 1 (3%) and stable disease occurred in 2 (7%). Most patients achieved response rapidly within 3 months of therapy (2–7 months). Rituximab flare occurred only in 6 patients (20%). The median duration of response has not been reached (3–24+ months). Patients tolerated therapy well without significant toxicities: grade 3 peripheral neuropathy occurred in only 1 patient at cycle 6, and completely resolved within one month after stopping therapy. Other grade 3 and 4 toxicities included neutropenia in 3 patients, and anemia and hyponatremia in 1 patient, and thrombocytopenia in 1 patient. Grade 5 pneumonia and viral infection occurred in 1 patient who was within the first cycle of therapy and the family changed his status to comfort care, and the patient passed away within one week. Attributable toxicities otherwise proved manageable with appropriate supportive care and the combination was generally well tolerated. CONCLUSIONS: The combination of weekly bortezomib and rituximab has been well tolerated and demonstrates encouraging activity, with CR+ PR + MR in 90% of evaluable patients with relapsed WM. No significant peripheral neuropathy has been observed to date with this regimen. Studies using this combination in newly diagnosed patients are ongoing.
Expression of BAG-1 and BcL-2 Proteins Before and After Neoadjuvant Chemotherapy of Locally Advanced Breast Cancer (2004)

It has been suggested that expression of anti-apoptotic proteins such as Bcl-2 or BAG-1 may confer cellular resistance to chemotherapy. A corollary of this hypothesis is that expression of these proteins may predict clinical response to treatment and that Bcl-2- or BAG-1-positive cells may selectively be enriched in postchemotherapy tissue specimens. The goal of this exploratory pilot study was to assess these two predictions by using immunohistochemistry in 29 paired pre- and postchemotherapy breast tissue specimens obtained from patients who underwent preoperative doxorubicin-based chemotherapy. All breast cancers expressed BAG-1 protein, and, in individual tumors, 40-100% of neoplastic cells stained positive for this protein. Homogenous cytoplasmic staining was typically observed, though neoplastic cells also showed nuclear staining in many specimens. We found no correlation between prechemotherapy expression of BAG-1 and subsequent pathological response to cytotoxic therapy. Paired pre- and posttreatment specimens showed similar levels of BAG-1 expression when residual tumor could be assessed. Bcl-2 was expressed in 55% of cancers and was localized to the cytoplasm. Absence of Bcl-2 expression in prechemotherapy specimens was associated with more frequent complete pathological response (58% vs. 20%; p = 0.04). However, similar to BAG-1, no difference between pre- and posttherapy expression of Bcl-2 was observed in neoplastic cells in paired tissue specimens. These observations suggest that BAG-1 contributes an important cellular function to breast epithelial cells, which is reflected by its ubiquitous expression in these tissues. However, it does not appear to determine response to doxorubicin-based chemotherapy. In contrast, lack of Bcl-2 expression was associated with a higher probability of complete pathological response to doxorubicin-based chemotherapy.