gebhart/patrepeval huggingface dataset:
Cold atmospheric plasma treatment selectively targets head and neck squamous cell carcinoma cells (2014)

The treatment of locoregional recurrence (LRR) of head and neck squamous cell carcinoma (HNSCC) often requires a combination of surgery, radiation therapy and/or chemotherapy. Survival outcomes are poor and the treatment outcomes are morbid. Cold atmospheric plasma (CAP) is an ionized gas produced at room temperature under laboratory conditions. We have previously demonstrated that treatment with a CAP jet device selectively targets cancer cells using in vitro melanoma and in vivo bladder cancer models. In the present study, we wished to examine CAP selectivity in HNSCC in vitro models, and to explore its potential for use as a minimally invasive surgical approach that allows for specific cancer cell or tumor tissue ablation without affecting the surrounding healthy cells and tissues. Four HNSCC cell lines (JHU-022, JHU-028, JHU-029, SCC25) and 2 normal oral cavity epithelial cell lines (OKF6 and NOKsi) were subjected to cold plasma treatment for durations of 10, 30 and 45 sec, and a helium flow of 20 l/min-1 for 10 sec was used as a positive treatment control. We showed that cold plasma selectively diminished HNSCC cell viability in a dose-response manner, as evidenced by MTT assays; the viability of the OKF6 cells was not affected by the cold plasma. The results of colony formation assays also revealed a cell-specific response to cold plasma application. Western blot analysis did not provide evidence that the cleavage of PARP occurred following cold plasma treatment. In conclusion, our results suggest that cold plasma application selectively impairs HNSCC cell lines through non-apoptotic mechanisms, while having a minimal effect on normal oral cavity epithelial cell lines.
Evaluation of Formability in Bending/Hemming of Aluminum Alloys Using Plane-Strain Tensile Tests (2009)

This paper presents a fundamental study for the characterization of formability in bending/hemming, or “bendability/hemmability,” of automotive aluminum alloys. Based on the strain/stress nature of the hemline (bent corner) surfaces, maximum surface strain was proposed as the hemming fracture criterion, and it is believed that bendability/hemmability of aluminum alloys can be directly approximated by the fracture strains from plane-strain tensile tests. The criterion was verified by comparing hemming and plane-strain tensile experiments on AA6111-T4 and AAx611-T4 with fracture strains measured, respectively, via a modified angled line method and thickness reductions. After a verification of material hardening laws, the identified failure criterion was implemented into 2D and 3D finite element hemming simulations for fracture predictions. The findings provide the basis for the design of aluminum hems under formality constraints, and it is expected that the fundamental theory and established methodology are applicable to bendability/hemmability evaluations for general sheet materials.
Finite Bias Anomaly in the Subgap Conductance of Superconductor-GaAs Junctions (1997)

We measure the subgap conductance across a superconductor-GaAs junction at low temperature. Below $T\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}4\mathrm{K}$ we observe a zero bias conductance peak. For the first time, we observe that at even lower temperatures ( $T\ensuremath{\le}0.8\mathrm{K}$), the conductance peak is shifted to a finite voltage. Application of a magnetic field restores a zero bias conductance peak. This is consistent with theoretical predictions for superconducting-semiconducting junctions in the regime where the contact conductance is larger than the coherent semiconductor conductance.
High energy density battery based on complex hydrides (2023)

A battery and process of operating a battery system is provided using high hydrogen capacity complex hydrides in an organic non-aqueous solvent that allows the transport of hydride ions such as AlH.sub.4.sup.- and metal ions during respective discharging and charging steps.
Impact of mass drug administration campaigns depends on interaction with seasonal human movement (2018)

Seasonal movement patterns of high-risk groups should be taken into consideration when selecting the optimum timing of MDA campaigns.
Numerical Simulation of Stress Evolution in Lithium Manganese Dioxide Particles due to Coupled Phase Transition and Intercalation (2010)

Lithium manganese dioxide particles undergo a significant volume change after transition from the cubic to the tetragonal phase. The transition may cause severe damage in cathode materials and capacity fade. This paper proposes a volume expansion and diffusion model to evaluate stresses due to phase transition. A three-dimensional finite element approach is developed to account for coupled phase transition and intercalation effects, which is applicable to arbitrary particle geometries. The study shows that the stress levels are closely related to particle geometry, lithium diffusivity, and input current density. The stress due to phase transition is roughly an order of magnitude higher than that due to intercalation in the cubic phase. However, the interaction kinetics still plays an important role on the stress distribution because it affects the concentration profile and emergence of phase transition. Lower diffusivity and higher current density induce a larger gradient in the lithium concentration and lead to higher stress levels.
Well-Organized Dense Arrays of Nanodomains in Thin Films of Poly(dimethylsiloxane)-b-poly(lactide) Diblock Copolymers (2013)

Thin films with well-organized arrays of densely packed nanodomains were fabricated from poly(dimethylsiloxane)-b-poly(dl-lactide) (DL) diblock copolymers. As a consequence of the unusually large Flory–Huggins interaction parameter between these repeat units, domains with sizes ∼10 nm are routinely generated using low molar mass diblock copolymers. Different morphologies are easily accessible by judiciously adjusting the block composition, garnering dot patterns (from spheres) and line patterns (from parallel cylinders) in a facile manner. The strong incompatibility also allows retention of order at relatively low molar mass even with high degrees of compositional asymmetry (e.g., fL ∼ 0.15). Block copolymers with various compositions are shown to form well-organized morphologies on various substrates and thermal annealing readily enhanced long-range order. All block copolymers were prepared on a >10 g scale, and the processing conditions are compatible with the current infrastructure of the microelectronics industry, demonstrating a strong potential for commercial relevance.
Direct reconstruction of CT-based attenuation correction images for PET with cluster-based penalties (2013)

Extremely low-dose CT acquisitions for the purpose of PET attenuation correction will have a high level of noise and biasing artifacts due to factors such as photon starvation. This work explores a priori knowledge appropriate for CT iterative image reconstruction for PET attenuation correction. We investigate the maximum a posteriori (MAP) framework with cluster-based, multinomial priors for the direct reconstruction of the PET attenuation map. The objective function for direct iterative attenuation map reconstruction was modeled as a Poisson log-likelihood with prior terms consisting of quadratic (Q) and mixture (M) distributions. The attenuation map is assumed to have values in 4 clusters: air+background, lung, soft tissue, and bone. Under this assumption, the MP was a mixture probability density function consisting of one exponential and three Gaussian distributions. The relative proportion of each cluster was jointly estimated during each voxel update of direct iterative coordinate decent (dICD) method. Noise-free data were generated from NCAT phantom and Poisson noise was added. Reconstruction with FBP (ramp filter) was performed on the noise-free (ground truth) and noisy data. For the noisy data, dICD reconstruction was performed with the combination of different prior strength parameters (β and γ) of Q- and M-penalties. The combined quadratic and mixture penalties reduces the RMSE by 18.7% compared to post-smoothed iterative reconstruction and only 0.7% compared to quadratic alone. For direct PET attenuation map reconstruction from ultra-low dose CT acquisitions, the combination of quadratic and mixture priors offers regularization of both variance and bias and is a potential method to derive attenuation maps with negligible patient dose. However, the small improvement in quantitative accuracy relative to the substantial increase in algorithm complexity does not currently justify the use of mixture-based PET attenuation priors for reconstruction of CT images for PET attenuation correction.
Abstract 4819: Evaluation of PTEN status in circulating tumor cells (CTCs) and matched tumor tissue from castrate-resistant prostate cancer (CRPC) patients (2014)

Abstract Background: PTEN loss occurs frequently in prostate cancer and may trigger progression to CRPC through activation of the PI3K/AKT pathway. A blood-based assay that determines PTEN status in CRPC patients could enable informed treatment decisions such as the use of a PI3K-targeted therapy. Here we examined the relationship between PTEN status in CTCs and matched archival and fresh tumor biopsies in 43 CRPC patients. Methods: Nucleated cells from CRPC patient blood were plated onto glass slides and subjected to IF staining and CTC identification by high-speed fluorescent scanners at Epic Sciences. CTCs were identified as CK+/CD45- cells with intact DAPI nuclei, and samples with ≥4 CTCs per 2 slides (74%) were then tested for PTEN by FISH. Heterozygous loss was defined as a decrease in PTEN copies (PTEN &amp;lt; CEP10 and &amp;lt; 2 copies) and homozygous loss as zero PTEN copies. PTEN IHC in tissue was stained using CST clone 138G6 and H-scores ≤ 200 counted as loss. Results: Heterozygous or homozygous loss of PTEN by FISH was observed in 16 of 43 patients (37%) by CTC analysis. In addition to loss of PTEN, changes in ploidy were frequently observed and broad heterogeneity seen both within and between patients. The PTEN status in CTCs correlated strongly with the PTEN status in metastatic tissue: All 10 patients that exhibited homozygous PTEN loss in CTCs showed concordant homozygous PTEN loss in fresh biopsies. This correlation extended to three patients that showed correlated mixed homozygous and hemizygous PTEN loss populations in CTCs and tissue. “Drift or change” in PTEN status from archival to fresh biopsies occurred in 15 patients, In 12 of these patients, PTEN status in CTCs was reflective of the status in fresh tissue. Together with PTEN evaluation, the analysis of androgen receptor expression by immunofluorescence and ERG rearrangements by FISH proved feasibility of multiplex biomarker assessment in CTCs. This analysis demonstrated heterogeneity of AR phenotypes and a positive association of ERG rearrangements and PTEN loss in CTCs, consistent with literature reports. Conclusion: Our results illustrate the potential for using CTCs as a non-invasive, real-time biopsy to determine a patient's current PTEN status. PTEN status will be determined using these assays in an ongoing AKT inhibitor Phase II trial. Citation Format: Elizabeth Punnoose, Eric Tucker, Edith Szafer-Glusman, Jin Zhu, Dena Marrinucci, Jessica Louw, Florence Lee, Mikel Kitchen, Natalee Bales, Lukas Amler, Hartmut Koeppen, Premal Patel, Yibing Yan, Ruth Riisnaes, Gerhardt Attard, Johann de Bono. Evaluation of PTEN status in circulating tumor cells (CTCs) and matched tumor tissue from castrate-resistant prostate cancer (CRPC) patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4819. doi:10.1158/1538-7445.AM2014-4819
Novel Fluorescence Competition Assay for Retinoic Acid Binding Proteins (2018)

Vitamin A derived retinoid compounds have multiple, powerful roles in the cellular growth and development cycle and, as a result, have attracted significant attention from both academic and pharmaceutical research in developing and characterizing synthetic retinoid analogues. Simplifying the hit development workflow for retinoid signaling will improve options available for tackling related pathologies, including tumor growth and neurodegeneration. Here, we present a novel assay that employs an intrinsically fluorescent synthetic retinoid, DC271, which allows direct measurement of the binding of nonlabeled compounds to relevant proteins. The method allows for straightforward initial measurement of binding using existing compound libraries and is followed by calculation of binding constants using a dilution series of plausible hits. The ease of use, high throughput format, and measurement of both qualitative and quantitative binding offer a new direction for retinoid-related pharmacological development.
Hemogenic endothelium generates mesoangioblasts that contribute to several mesodermal lineages in vivo (2014)

The embryonic endothelium is a known source of hematopoietic stem cells. Moreover, vessel-associated progenitors/stem cells with multilineage mesodermal differentiation potential, such as the 'embryonic mesoangioblasts', originate in vitro from the endothelium. Using a genetic lineage tracing approach, we show that early extra-embryonic endothelium generates, in a narrow time-window and prior to the hemogenic endothelium in the major embryonic arteries, hematopoietic cells that migrate to the embryo proper, and are subsequently found within the mesenchyme. A subpopulation of these cells, distinct from embryonic macrophages, co-expresses mesenchymal and hematopoietic markers. In addition, hemogenic endothelium-derived cells contribute to skeletal and smooth muscle, and to other mesodermal cells in vivo, and display features of embryonic mesoangioblasts in vitro. Therefore, we provide new insights on the distinctive characteristics of the extra-embryonic and embryonic hemogenic endothelium, and we identify the putative in vivo counterpart of embryonic mesoangioblasts, suggesting their identity and developmental ontogeny.
Observer-based techniques in ripple correlation control applied to power electronic systems (2002)

Ripple correlation control is a general optimization method for use with power electronic interfaced systems. The method relies on gradient information extracted from the ripple associated with these systems. The variable to be optimized and the variable that the optimization is being performed with respect to, must both be available to the controller. This paper discusses ways of dealing with the difficulties that arise when these signals cannot be measured due to dynamics within the system.
Genetic and metabolic status of NGF-deprived sympathetic neurons saved by an inhibitor of ICE family proteases. (1996)

Sympathetic neurons undergo programmed cell death (PCD) when deprived of NGF. We used an inhibitor to examine the function of interleukin-1 beta-converting enzyme (ICE) family proteases during sympathetic neuronal death and to assess the metabolic and genetic status of neurons saved by such inhibition. Bocaspartyl(OMe)-fluoromethylketone (BAF), a cell-permeable inhibitor of the ICE family of cysteine proteases, inhibited ICE and CPP32 (IC50 approximately 4 microM) in vitro and blocked Fas-mediated apoptosis in thymocytes (EC50 approximately 10 microM). At similar concentrations, BAF also blocked the NGF deprivation-induced death of rat sympathetic neurons in culture. Compared to NGF-maintained neurons, BAF-saved neurons had markedly smaller somas and maintained only basal levels of protein synthesis; readdition of NGF restored growth and metabolism. Although BAF blocked apoptosis in sympathetic neurons, it did not prevent the fall in protein synthesis or the increase in the expression of c-jun, c-fos, and other mRNAs that occur during neuronal PCD, implying that the ICE-family proteases function downstream of these events during PCD.NGF and BAF rescued sympathetic neurons with an identical time course, suggesting that NGF, in addition to inhibiting metabolic and genetic events associated with neuronal PCD, can act posttranslationally to abort apoptosis at a time point indistinguishable from the activation of cysteine proteases. Both poly-(ADP ribose) polymerase and pro-ICE and Ced-3 homolog-1 (ICH-1) appear to be cleaved in a BAF-inhibitable manner, although the majority of pro-CPP32 appears unchanged, suggesting that ICH-1 is activated during neuronal PCD. Potential implications of these findings for anti-apoptotic therapies are discussed.
Extent of neutrophil (NTP) infiltration in benign lymph nodes (LNs) to predict survival in patients with muscle-invasive bladder cancer (MIBC). (2013)

e15522 Background: In preclinical models, NTPs appear to establish a pre-metastatic niche that fosters the invasion of metastases (Kowanetz et al. PNAS 2010). This observation still requires clinical validation in MIBC. Methods: Benign LN tissue was obtained from patients (pts) who had undergone cystectomy and LN dissection for documented MIBC. Immunohistochemical (IHC) staining for CD15 (a NTP marker) was performed. Interleukin-17 (IL-17) and phosphorylated signal transducer and activator of transcription 3 (pSTAT3), putative mediators of NTP recruitment, were assessed through the same method (Laan et al. J Immunol 1999; Fielding et al. J Immunol 2008). Positively staining cells were counted and averaged over 8 high power fields. Pts were stratified by the median cell count for each biomarker. Analyses of overall survival (OS) were performed using the Kaplan-Meier method and log-rank test. Results: Of 55 pts with MIBC, 19 pts received no neoadjuvant chemotherapy (NAC), while 36 pts had received NAC with either GC (n=17) or MVAC (n=19). CD15 and IL-17 expression was significantly lower in pts with prior NAC (P&lt;0.001 for both), while expression of pSTAT3 was similar in both groups. Furthermore, across the whole cohort, a strong association was seen between expression of CD15 and IL-17 (r=0.73, P&lt;0.001). Amongst patients with no prior NAC, median OS was higher in those pts with low CD15 v high CD15 (158.7 mos v 36.9 mos, P=0.02), and low pSTAT3 v high pSTAT3 (NR v 106.4 mos, P=0.04). Median OS was numerically higher in pts with low IL-17 v high IL-17 (114.5 v 36.9 mos; P=0.14). Patients with both low CD15/IL-17 had a particularly favorable outcome. Amongst pts with prior exposure to NAC, no difference in survival was noted based on CD15, pSTAT3 or IL-17. Conclusions: NTP recruitment to benign LNs (potentially mediated by IL-17) may be prognostic of OS in pts with MIBC who have not received NAC. Bolstered by these findings, the prognostic value of NTP recruitment will be examined prospectively in SWOG 1011, a trial comparing limited v extended LN dissection in pts with MIBC.
Organopalladium Reactions in Combinatorial Chemistry (2005)

The authors present a comprehensive review of the instances of the use of water in palladium catalysts and examine the three major protocols used. An outline of the function of water is included. The chapter features the recent progress in the chemistry of solid-bound Pd-catalyzed processes, with a focus on those customarily carried out in a homogeneous system, especially carbon–carbon bond-forming reactions. The review consists of three parts: rationale and need for immobilizing palladium on a solid support; comparison of various palladium immobilization systems; and applications for these solid-bound palladium catalysts in organic chemistry. Some of the authors' personal speculations about the future of this burgeoning field are also included. An extensive overview on the use of Pd-catalyzed and Pd-mediated reactions in solid phase combinatorial chemistry and parallel synthesis is provided. The discussion of reactions on soluble polymers such as MeO–PEG (polyethylene glycol) and some modern separation techniques (fluorous phase developments) are covered in three parts. The first part presents Pd-catalyzed and Pd-mediated transformations on solid support without cleaving off any higher molecular weight compound from the support. Techniques for the attachment of building blocks and simple group transformations, such as hydrogenation reactions, are also included. The second part covers cleavage reactions that give rise to soluble products as well as transformations that occur after the cleavage step. Finally, new separation techniques that enhance the throughput for automated parallel synthesis is reviewed.
Alignment characterization in micro and nano technologies (2005)

The use of lasers as probe sources is very extended in micro and nano technologies. Therefore, the characterization of the beam is critical for the utter development of the measurement. Typically, the beam is projected on the detectors using optical elements and lenses. The alignment procedure is not always very good, and the difficulties increases when infrared radiation is involved. Even with very accurate positioning elements some misalignments are produced. The misalignment is most responsible for the appearance of coma aberration. In the case of a pure Gaussian beam shape they are going to produce a slightly comatic aberrated beam. In this paper we propose a method to characterize the direction and amplitude of this comatic aberration. The method is sensible enough to characterize slightly aberrated beams normally used to deconvolve detector's spatial response. It is based on a statistical analysis of the beam shape in different directions respect to its center. Simulations including the effect of noise are presented too and some applications to micro and nano metrology are exposed.
Iontophoretic device delivery for the localized treatment of pancreatic ductal adenocarcinoma (2020)

Drug delivery to pancreatic tumors is impaired by a unique desmoplastic response and poor tumor vascularization. A drug delivery device capable of overcoming these barriers could provide substantial benefit for patients with pancreatic cancer. In this study, we show that local iontophoretic delivery of folinic acid (leucovorin), fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX) resulted in better tumor response and tolerability compared with i.v. FOLFIRINOX. Given the low systemic exposure of FOLFIRINOX using iontophoretic delivery, it may be possible to use in combination with systemic delivery to treat micrometastatic disease. Local iontophoretic delivery of cytotoxic agents should be considered as a neoadjuvant approach to improve resection rates and outcome in patients with localized and locally advanced pancreatic cancer.