gebhart/patrepeval huggingface dataset:
Supplementary Methods from Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer (2023)

&lt;p&gt;Supplemental Methods&lt;/p&gt;
Clinical Evaluation of Gemcitabine in Dogs with Spontaneously Occurring Malignancies (2005)

Abstract We conducted a clinical evaluation of gemcitabine in 19 dogs with spontaneously occurring malignancies. The principal objectives of this study were to characterize toxicity and seek preliminary evidence of antitumor activity of gemcitabine administered every 2 weeks (biweekly) as a 30-minute IV infusion. A total of 64 doses, ranging from 300 mg/m2 to 675 mg/m2, were administered during the initial 8-week evaluation period, and an additional 131 doses were administered during the extended evaluation period. The total cumulative dose for the 10 dogs receiving gemcitabine in the extended evaluation period ranged from 1,500 mg/m2 to 24,300 mg/m2. Clinical evidence of toxicity was minimal. Cumulative myelosuppression was not apparent. Unexplained retinal hemorrhages occurred in 1 dog. No complete or partial remissions were observed during the initial evaluation period; however, objective responses were observed in 2 dogs during the extended evaluation period. Gemcitabine is a promising new chemotherapeutic agent that can be used safely in dogs with cancer. Biweekly administration of doses of 675 mg/m2 IV results in minimal and acceptable toxicity.
Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation (2015)

Electron transfer dissociation (ETD) is a valuable tool for protein sequence analysis, especially for the fragmentation of intact proteins. However, low product ion signal-to-noise often requires some degree of signal averaging to achieve high quality MS/MS spectra of intact proteins. Here we describe a new implementation of ETD on the newest generation of quadrupole-Orbitrap-linear ion trap Tribrid, the Orbitrap Fusion Lumos, for improved product ion signal-to-noise via ETD reactions on larger precursor populations. In this new high precursor capacity ETD implementation, precursor cations are accumulated in the center section of the high pressure cell in the dual pressure linear ion trap prior to charge-sign independent trapping, rather than precursor ion sequestration in only the back section as is done for standard ETD. This new scheme increases the charge capacity of the precursor accumulation event, enabling storage of approximately 3-fold more precursor charges. High capacity ETD boosts the number of matching fragments identified in a single MS/MS event, reducing the need for spectral averaging. These improvements in intra-scan dynamic range via reaction of larger precursor populations, which have been previously demonstrated through custom modified hardware, are now available on a commercial platform, offering considerable benefits for intact protein analysis and top down proteomics. In this work, we characterize the advantages of high precursor capacity ETD through studies with myoglobin and carbonic anhydrase.
Model-based SRAF insertion through pixel-based mask optimization at 32nm and beyond (2008)

SRAF insertion through inverse microlithography methodologies has been explored at length in recent years as one of the most promising approaches to determining the right placements of Model-based SRAF (MBSRAF) for complex two dimensional geometrical configurations for advanced nodes. This work will discuss the latest development of MBSRAF insertion software at Mentor Graphics. The software system operates on the principles of inverse methods of microlithography or pixel inversion. The ability to examine the image of every pixel in the work region as well as the mathematical solution to synthesize the mask shapes as a cost minimization problem make it possible to reliably deal with SRAF insertion for advanced illumination schemes such as quasar, dipole and cross-quad. Pixel inversion involving high transmission attenuated PSM as well as hard PSM will be also discussed. We will also report on the MRC capability to make the pixel inversion mask shapes manufacturable.
Supplementary Table S1 from Functional Gene Expression Analysis Uncovers Phenotypic Switch in Aggressive Uveal Melanomas (2023)

Supplementary Table S1 from Functional Gene Expression Analysis Uncovers Phenotypic Switch in Aggressive Uveal Melanomas
Anaplastic lymphoma kinase inhibitors as anticancer therapeutics: a patent review (2014)

Novel ALK inhibitors continued to be discovered at a fast pace over the covered period, with many distinct chemotypes emerging. Crizotinib received FDA approval in 2011, and six additional ALK inhibitors have entered clinical trials. The focus of ALK research appears to have shifted toward inhibitors that display activity against resistant mutants unearthed in clinical studies with crizotinib.
Topotecan hydrochloride effects on retinal vessels in newborn rats. (2012)

A physiological system, i.e. rodent retina during vessel formation and hierarchical organization, was utilised for assaying antiangiogenic properties of Topotecan, a topoisomerase I inhibitor, capable of inhibiting tumoral growth in animal models of retinoblastoma. In particular we analysed possible differences in effectiveness and side effects among different drug dosages and ways of administration. In the present research only qualitative analyses were undertaken. After preliminary experiments, in which suckling animals subcutaneously treated with Topotecan dosages comprised between 9 and 3 mg/kg underwent high lethality and extremely severe systemic damages, 7 day-old rats were subcutaneously, intravenously or peribulbary injected with a single dose of 1 mg/kg; retinal vessels were visualized in retinal fluorangio-graphies taken 1 and 2 weeks after treatment. The most important and frequent alterations were found to affect radial vessels, which showed non-perfused and/or regionally mislocated segments, together with abnormal branching and enlargements in retinal periphery; persistence of capillary-free periarteriolar regions, non-vascularised regions and spots of extravascular FITC were also detected. Despite the high individual variability the alterations were substantially similar among the different ways of drug administration, while they appeared milder in 21 day-old rats, with respect to younger ones. The extensive vascular remodelling found after Topotecan administration, besides demonstrating the antiangiogenic properties of this chemioterapic drug, confirms the rodent retina as a highly valuable model system for studying angiogenesis modulation.
A vertical cavity light emitting InGaN quantum well heterostructure (1999)

A method is described for fabricating a vertical cavity light emitting structure for nitride semiconductors. The process involves the separation of a InGaN/GaN/AlGaN quantum well heterostructure from its sapphire substrate an its enclosure by a pair of high reflectivity, low loss dielectric mirrors to define the optical resonator. We have demonstrated a cavity Q factor exceeding 600 in initial experiments, suggesting that the approach can be useful for blue and near ultraviolet resonant cavity light emitting diodes and vertical cavity lasers.
Supplementary Table 1 from Patients with Biallelic BRCA1/2 Inactivation Respond to Olaparib Treatment Across Histologic Tumor Types (2023)

&lt;p&gt;Supplementary Table 1&lt;/p&gt;
Synthesis and Structure−Activity Relationships of 8-(Pyrid-3-yl)pyrazolo[1,5-a]-1,3,5-triazines: Potent, Orally Bioavailable Corticotropin Releasing Factor Receptor-1 (CRF1) Antagonists (2009)

This report describes the syntheses and structure-activity relationships of 8-(substituted pyridyl)pyrazolo[1,5-a]-1,3,5-triazine corticotropin releasing factor receptor-1 (CRF(1)) receptor antagonists. These CRF(1) receptor antagonists may be potential anxiolytic or antidepressant drugs. This research resulted in the discovery of compound 13-15, which is a potent, selective CRF(1) antagonist (hCRF(1) IC(50) = 6.1 +/- 0.6 nM) with weak affinity for the CRF-binding protein and biogenic amine receptors. This compound also has a good pharmacokinetic profile in dogs. Analogue 13-15 is orally effective in two rat models of anxiety: the defensive withdrawal (situational anxiety) model and the elevated plus maze test. Analogue 13-15 has been advanced to clinical trials.
Modulation Formats For 100Gb/s Coherent Optical Systems (2009)

A set of modulation formats for 100Gb/s optical transmission are compared based on OSNR tolerance, equalization complexity, and A/D requirements. Propagation penalty as a function of dispersion compensation is studied for a chosen candidate.
Wild-Grown and Cultivated Glechoma hederacea L.: Chemical Composition and Potential for Cultivation in Organic Farming Conditions (2022)

<i>Glechoma hederacea</i> L. is a medicinal plant that is known in traditional medicine for its anti-inflammatory, antibacterial, antiviral, and anticancer properties. This study evaluated the potential for commercial production of <i>G. hederacea</i> and compared the chemical composition and activity of 70% ethanol extracts and steam-distilled essential oils from wild-grown and cultivated <i>G. hederacea</i> collected in different harvesting periods. The main compounds identified in the 70% ethanol extracts were phenolic acids (chlorogenic and rosmarinic acids) and flavonoid O-glycosides. The essential oil varied in the three accessions in the range of 0.32-2.98 mL/kg<sup>-1</sup> of dry weight. The extracts possessed potent antioxidant and anti-inflammatory properties in LPS-treated bone-marrow-derived macrophages. The results of flow cytometry show that extracts from different vegetation periods reduced the conversion of macrophages to the proinflammatory phenotype M1. The chemical composition varied the most with the different harvesting periods, and the most suitable periods were the flowering and vegetative phases for the polyphenolic compounds and essential oils, respectively. <i>G. hederacea</i> can be successfully grown under organic farming conditions, and cultivation does not significantly affect the chemical composition and biological activity compared to wild-grown plants.
Supplementary Figure 7 from EMD 1214063 and EMD 1204831 Constitute a New Class of Potent and Highly Selective c-Met Inhibitors (2023)

&lt;p&gt;PDF file - 54K, Dose-dependent induction of caspase-3 cleavage by EMD 1204831. Mice bearing established (100-200mm3) Hs746T tumors received a single dose of 3, 10, 30, and 100 mg/kg of EMD 1204831. The effects on caspase-3 activation were determined by Western blot analyses, using an antibody (clone 5A1E) specifically recognizing the large fragment (17/19 kDa) of activated caspase-3 resulting from cleavage adjacent to Asp 175. This antibody does not recognize full-length caspase-3 or other cleaved caspases. Treatment with EMD 1204831 resulted in a transient increase in cleaved caspase-3 that peaked at 24 h and declined at 48 h. Data are representative of three separate experiments.&lt;/p&gt;
Network in the Air (2019)

Today, on-board passengers request Internet-based services, such as video streaming, Voice over IP, etc., at low cost. Many of those services have stringent QoS requirements, e.g., low end-to-end delay. To offer these services efficiently, some problems need to be solved jointly: placement of services (i.e., Virtual Machines (VMs)), at Datacenters (DCs) on the ground, assigning airplanes to services on DCs, and the routing from the flight to the associated VM considering the dynamic position of the flights over time. Further, dynamic VM migrations can be employed for guaranteeing the QoS requirements and/or improving resource utilization. In this work, we introduce and evaluate two heuristic solutions to jointly determine VM placement, routing, and migration decisions for flying airplanes with the objective of minimizing total operational costs. The first results indicate that while reducing the runtime from hours to seconds, the heuristics are able to achieve near-optimal solutions.
Evaluating Soft Contact Lens Quality: A Manufacturerʼs Perspective (1988)

This study was designed to compare quality control between six aphakic contact lens brands. The methodology eliminates the sampling and experimental variables of previous studies. The lenses were all purchased new at +13.00 D power, with the same number of lenses and distribution of manufacturing batch/lots per brand. We measured or assessed 120 study lenses (20 per brand) for diameter, front sagittal height, power and image quality, center thickness, surface and edge quality, and edge design. The base curve radius was calculated accurately using lens cross-sectioning techniques. The reproducibility of measured lens parameters (precision) and conformance to label claims (accuracy) were tabulated separately and the lens brands were ranked and grouped statistically. The tabulated results are represented graphically in one spread sheet where selected American National Standards Institute (ANSI) tolerances were used as a standard to which all lens brands were compared. Lens brands coded as Brand A and Brand B rated the highest using our criterion for ranking overall quality control.
Measurement of Activity Coefficients at Infinite Dilution in Ionic Liquids Using the Dilutor Technique (2002)

Activity coefficients at infinite dilution have been measured with the dilutor technique for 20 solutes (alkanes, alkenes, cyclic hydrocarbons, aromatic hydrocarbons, ketones, alcohols, and water) in the ionic liquids 1-methyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, and 1-ethyl-3-methylimidazolium ethylsulfate. The measurements were carried out in the temperature range between 293.15 K and 333.15 K. The selectivities at infinite dilution ( = / ) for the separation of aliphatics from aromatics and n-hexane from 1-hexene are presented and discussed. From the results it can be concluded that the ionic liquids investigated show different advantages compared to those of the entrainers actually used for the separation of aliphatic from aromatic hydrocarbons by extractive distillation or extraction.
ChemInform Abstract: Improved Synthesis of Vinylimidazoles. (1988)

Abstract 1‐Tritylimidazole‐4‐carboxaldehyde (I) reacts with the phosphonium bromides (II) or the phosphonates (IV) to produce the 4‐vinylimidazoles (III).
Detection of miR-92a and miR-21 in stool samples as potential screening biomarkers for colorectal cancer and polyps (2011)

Stool miRNA are useful for screening CRC and polyps.
Interaction between Human Serum Albumin and the Felbamate Metabolites 4-Hydroxy-5-phenyl-[1,3]oxazinan-2-one and 2-Phenylpropenal (2002)

Felbamate is an anti-epileptic drug associated with hepatotoxicity and aplastic anemia. These toxicities are believed to be mediated by the formation of the reactive species 2-phenylpropenal. 4-Hydroxy-5-phenyl-[1,3]oxazinan-2-one is a metabolic precursor for 2-phenylpropenal. 4-Hydroxy-5-phenyl-[1,3]oxazinan-2-one exists in equilibrium with 3-oxo-2-phenylpropyl carbamate, which can undergo beta-elimination to form 2-phenylpropenal. The work presented here investigates the interaction between 4-hydroxy-5-phenyl-[1,3]oxazinan-2-one and human serum albumin (HSA). HSA (40 mg/mL) was found to decrease the half-life of 4-hydroxy-5-phenyl-[1,3]oxazinan-2-one from 4.57 +/- 0.44 h to 1.07 +/- 0.10 h at pH 7.4. This decrease in the half-life of 4-hydroxy-5-phenyl-[1,3]oxazinan-2-one was due to increased beta-elimination of 3-oxo-2-phenylpropyl carbamate, presumably through HSA-mediated general base catalysis. The k(cat) for HSA-catalyzed decomposition of 4-hydroxy-5-phenyl-[1,3]oxazinan-2-one was determined to be 12.04 min(-)(1) M(-)(1). Competitive binding assays using warfarin and ibuprofen showed that HSA-catalyzed decomposition of 4-hydroxy-5-phenyl-[1,3]oxazinan-2-one is dependent on the subdomain IIA binding site of HSA. LC/MS/MS analyses of trypsin digests of HSA incubations with either 4-hydroxy-5-phenyl-[1,3]oxazinan-2-one or 2-phenylpropenal identified HSA-2-phenylpropenal adducts formed specifically at residues His-242 and His-247. These HSA-2-phenylpropenal adducts were found to be slowly reversible, with a decrease in alkylation of 74.0 +/- 0.6% after extensive dialysis. Interestingly, only the bis-adduct (His-242 and His-247) could be identified after dialysis. These results demonstrate the first direct example of 2-phenylpropenal conjugation to a human protein in vitro and suggest the possibility that HSA may be involved in the development of felbamate toxicity either by antigen formation or as a route of detoxification of 2-phenylpropenal.
Investigation of Silicon Saw Damage Removal and Surface Texturing Using KOH for next Generation Silicon Solar Cells (2014)

Silicon solar cells are the dominating technology in photovoltaics (PV) industry and have a market share of more than 85% of the modules produced for roof top installations.
TrkB is responsible for EMT transition in malignant pleural effusions derived cultures from adenocarcinoma of the lung (2013)

Lung cancer is the leading cause of cancer-related mortality worldwide. Recent evidence indicates that tumors contain a subpopulation of cancer stem cells (CSCs) that are responsible for tumor maintenance and spread. CSCs have recently been linked to the occurrence of epithelial-to-mesenchymal transition (EMT). Neurotrophins (NTs) are growth factors that regulate the biology of embryonic stem cells and cancer cells, but still little is known about the role NTs in the progression of lung cancer. In this work, we investigated the role of the NTs and their receptors using as a study system primary cell cultures derived from malignant pleural effusions (MPEs) of patients with adenocarcinoma of the lung. We assessed the expression of NTs and their receptors in MPE-derived adherent cultures vs. spheroids enriched in CSC markers. We observed in spheroids a selectively enhanced expression of TrkB, both at the mRNA and protein levels. Both K252a, a known inhibitor of Trk activity, and a siRNA against TrkB strongly affected spheroid morphology, induced anoikis and decreased spheroid forming efficiency. Treatment with neurotrophins reversed the inhibitory effect of K252a. Importantly, TrkB inhibition caused loss of vimentin expression as well as that of a set of transcription factors known to be linked to EMT. These ex vivo results nicely correlated with an inverse relationship between TrkB and E-cadherin expression measured by immunohistochemistry in a panel of lung adenocarcinoma samples. We conclude that TrkB is involved in full acquisition of EMT in lung cancer, and that its inhibition results in a less aggressive phenotype.
Starting point designs for freeform four-mirror systems (2018)

Driven by the development of freeform four-mirror solutions, we review and compare analytical methods to generate starting point designs with various states of correction, surface types, symmetry, and obscuration. The advantages and disadvantages of each are examined. We have combined several concepts and techniques from the literature to analytically generate unobscured freeform starting point designs that are corrected through the third-order image degrading aberrations. The surfaces in these starting point designs are described as base off-axis conics that image stigmatically for the central field point, also known as Cartesian reflectors, with an aspheric departure “cap” (quartic with the aperture) added to the Cartesian reflectors. Tilt angles are chosen to cancel field-asymmetric field-linear astigmatism and unobscure the system. Paraxial data from an equivalent on-axis system are used to solve a system of linear equations to determine the magnitude of the aspheric departure “caps” that are placed on top of the base Cartesian reflectors, in order to eliminate the remaining third-order image degrading aberrations. In this approach, each aspheric departure “cap” is centered about the intersection of the optical-axis-ray, also known as the base ray, with the base surface, rather than being centered about the axis of rotational invariance.
ChemInform Abstract: Iron‐Mediated Allylic Substitutions with Complete Chirality Transfer. Synthesis of Functionalized γ‐Substituted Alkenylsulfones of High Enantiomeric Purity. (1996)

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.
Increased mucosal CD4+ T-cell activation following vaccination with an adenoviral vector in rhesus macaques (2012)

Background The possibility that vaccination with Adenoviral vectors increased mucosal T-cell activation remains a central hypothesis to explain the potential enhancement of HIV acquisition within the STEP trial. Modeling this within rhesus macaques is complicated because human Adenoviruses, including Adenovirus type 5 (HAd5), do not productively infect macaques. We created a vector based upon a naturally occurring rhesus macaque Adenovirus (SAdV7) to test whether vaccination with as pecies-specific Adenoviral vector enhances mucosal T-cell activation within the natural host.
Survival Point Estimate Prediction in Matched and Non-Matched Case-Control Subsample Designed Studies (2005)

Providing information about the risk of disease and clinical factors that may increase or decrease a patient's risk of disease is standard medical practice. Although case-control studies can provide evidence of strong associations between diseases and risk factors, clinicians need to be able to communicate to patients the age-specific risks of disease over a defined time interval for a set of risk factors.\nAn estimate of absolute risk cannot be determined from case-control studies because cases are generally chosen from a population whose size is not known (necessary for calculation of absolute risk) and where duration of follow-up is not known (necessary for calculation of incidence). This problem can sometimes be overcome by using a nested case-control design.\nWe have collected data on a National Cancer Institute funded population-based cohort study. This study contains a matched set of cases and controls within the cohort. This design is more cost-efficient than a full cohort study since expensive predictor variables (genomic measures, sex hormone levels, mammographic breast density) are measured on all of the cases, but on only a sample of the cohort who did not develop the outcome of interest (the controls). In addition, this design avoids the potential biases of conventional case-control studies that draw cases and controls from different populations. Importantly, the presence or absence of the outcome of interest has been established for the entire cohort within the same time period.\nThe specifics of the sampling in our study do not adhere to the assumptions for absolute risk estimation methods previously developed in the literature. Here we introduce a novel method which provides locally efficient estimators to predict the absolute risk of a cohort from measures only taken on the matched case-control participants. The proposed method is evaluated using simulation studies and survival data from women with ductal carcinoma in situ, a non-invasive form of breast cancer. A generalization of the proposed method is related to other similar sampling designs such as nested case-control, case-cohort, and two-stage case-control.