gebhart/patrepeval huggingface dataset:
Sensitizers in EUV chemically amplified resist: mechanism of sensitivity improvement (2018)

EUV lithography utilizes photons with 91.6 eV energy to ionize resists, generate secondary electrons, and enable electron driven reactions that produce acid in chemically amplified photoresist. Efficiently using the available photons is of key importance. Unlike DUV lithography, where photons are selectively utilized by photoactive compounds, photons at 13.5nm wavelength ionize almost all materials. Nevertheless, specific elements have a significantly higher atomic photon-absorption cross section at 91.6 eV. To increase photon absorption, sensitizer molecules, containing highly absorbing elements, can be added to photoresist formulations. These sensitizers have gained growing attention in recent years, showing significant sensitivity improvement. But there are few experimental evidences that the sensitivity improvement is due to the higher absorption only, as adding metals salts into the resist formulation can induce other mechanisms, like modification of the dissolution rate, potentially affecting patterning performance. In this work, we used different sensitizers in chemically amplified resist. We measured experimentally the absorption of EUV light, the acid yield, the dissolution rate and the patterning performance of the resists. Surprisingly, the absorption of EUV resist was decreased with addition of metal salt sensitizers. Nevertheless, the resist with sensitizer showed a higher acid yield. Sensitizer helps achieving higher PAG conversion to acid, notably due to an increase of the secondary electron generation. Patterning data confirm a significant sensitivity improvement, but at the cost of roughness degradation at high sensitizer loading. This can be explained by the chemical distribution of the sensitizer in the resist combined with a modification of the dissolution contrast, as observed by Dissolution Rate Monitor.
Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly (2011)

Heat tolerance of DNA origami structures has been improved about 30 °C by photo-cross-linking of 8-methoxypsoralen. To demonstrate one of its applications, the cross-linked origami were used for higher-temperature self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-cross-linked origami at lower-temperature. By contrast, at higher-temperature annealing, native non-cross-linked tiles did not self-assemble to yield the desired product; however, they formed a nonspecific broken structure.
Is Obesity a Disease of the Blood-Brain Barrier? Physiological, Pathological, and Evolutionary Considerations (2003)

Leptin has emerged as a major regulator of body adiposity. The majority of humans with obesity have a resistance to leptin. Human and rodent studies indicate that the major cause of this resistance arises from an impaired ability of leptin to cross the blood-brain barrier, with lesser roles played by receptor and post-receptor defects. Evidence from baboons living in the wild is consistent with the hypothesis that during most of evolution serum levels of leptin were much lower than those currently considered normal. Leptin may have evolved to signal to the brain when caloric reserves were adequate to engage in reproductive and other behaviors not immediately concerned with acquisition of calories. The leptin transporter is a regulated system, with the rate of transport being increased by alpha(1) adrenergic agents and decreased by starvation. Impaired regulation of the transporter or impairments in transporter production could underlie the resistance caused by transporter defects. Evolutionary pressures would not have selected against such impairments if leptin levels were lower than those typically seen in Western society. A model that could explain how leptin transporter resistance can be acquired is presented.
Regulation of cytokine secretion by cystic fibrosis airway epithelial cells (1993)

Chronic airway inflammation is an important feature of cystic fibrosis (CF), markedly influencing morbidity and mortality. We wanted to assess the contribution of the respiratory epithelium in the mediation of local inflammatory events, and, more particularly, its regulating role through cytokine secretion. We have studied the regulation of interleukin-6 and 8 (IL-6 and IL-8) production by the SV40 transformed airway epithelial cell line JME/CF15 (homozygous for the deletion of Phe 508). We show that unstimulated JME/CF15 cells secrete IL-6 and IL-8. Neutrophil chemotactic activity (NCA) is detected in supernatants. The secretion of IL-6 and IL-8 is increased following stimulation of the JME/CF15 cells by IL-1 beta and neutrophil elastase. Lipopolysaccharide and granulocyte macrophage colony stimulating factor (GM-CSF) have no effect on secretion of IL-6 or IL-8. Neutrophil elastase inactivates recombinant human IL-6 at 37 degrees C in vitro, but has no effect at 4 degrees C, suggesting a proteolytic effect of elastase on IL-6. IL-8 activity remains preserved, even after prolonged exposure to elastase. Our data suggest that the airway epithelium may play an active role in the mediation of neutrophil chemotaxis. Local production of IL-8 in response to elastase and IL-1 beta, together with the inactivation of the anti-inflammatory protein IL-6, may result in a significant upregulation of airway inflammation in cystic fibrosis.
Abstract 3212: Metastatic breast cancer cell communication within a pro-dormancy bone marrow niche (2015)

Abstract Distant metastases are the major cause of death from breast cancer. In estrogen receptor positive (ER+) breast cancer (BC) in particular, metastatic relapse can occur years after initial treatment, suggesting that disseminated tumor cells have a prolonged dormant phase before becoming proliferative. A major site of early disease dissemination and metastatic relapse of ER+ BC is the bone, although the critical signals that allow circulating breast cancer cells (BCCs) to identify bone marrow (BM) vasculature, enter the tissue, and tether to the BM microenvironment (BMM) are little understood. Investigating these interactions of BCCs with the BMM, however, could enable us to target the key biologic determinants allowing safe harbor for metastases within bone. To address the features of breast tumors associated with late recurrence, but not confounded by variations in systemic treatment, we compiled breast tumor gene expression data from 4,767 patients and established a discovery cohort consisting of 743 lymph node-negative patients who did not receive systemic neoadjuvant or adjuvant therapy. Using this data set, we found that expression of E-selectin ligands and CXCR4 were significantly elevated in ER+ tumors that had late recurrences. Based on these observations, we used intravital fluorescence microscopy to study the precise functions of E-selectin ligands and CXCR4 (SDF-1 receptor) in tumor metastasis in in vivo xenograft models and found that these play distinct roles in ER+ BCC migration in the BMM. Using highly specific E-selectin (GMI-1271) and CXCR4 (AMD3100) inhibitors, we determined that E-selectin interactions were critical for BCC entry into bone, while CXCR4/SDF-1 interactions anchored BCCs to the BMM. CXCR4 inhibition led to significant mobilization of BC micrometastases from the BMM into the peripheral circulation. Moreover, we found that dormant and proliferating BCCs occupy distinct regions of the BMM, with dormant BCCs predominantly found in SDF-1 and E-selectin rich regions and thus highly susceptible to AMD3100 mobilization. These findings shed light on how dormant and proliferating BCCs interact with the BMM and suggest new interventions to break the foothold of dormant BC micrometastases in bone. Citation Format: Trevor T. Price, Clara H. Lee, Qing Cheng, H. Kim Lyerly, William E. Fogler, John L. Magnani, Dorothy A. Sipkins. Metastatic breast cancer cell communication within a pro-dormancy bone marrow niche. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3212. doi:10.1158/1538-7445.AM2015-3212
Physicians' attitudes and practices toward CPR training in family members of patients with coronary heart disease. (1985)

A survey of 482 physicians practicing in central and western Massachusetts was carried out to examine attitudes and reported practices toward cardiopulmonary resuscitation (CPR) training for family members of patients with coronary heart disease (CHD). Seventy-nine per cent of physicians felt that CPR training was important for the family members of patients with CHD yet only 6 per cent actually provided information about CPR to families. Further studies are indicated to determine why physician behavior is at odds with their stated beliefs and to guide appropriate remedial action.
The N-end Rule (1995)

The N-end rule relates the in vivo half-life1 of a protein to the identity of its N-terminal residue (Varshavsky 1992). Similar but distinct versions of the N-end rule have been shown to operate in all organisms examined, from mammals to fungi and bacteria. I summarize the current understanding of the N-end rule pathway and describe some of the recent methods that utilize the N-end rule. &#13;\n&#13;\nFeatures of a protein that confer metabolic instability are called degradation signals, or degrons (Varshavsky 1991). The essential component of one degron, the first to be identified, is a destabilizing N-terminal residue of a protein (Bachmair et al. 1986). This signal is called the N-degron. The N-end rule (defined above) results from the existence of N-degrons containing different destabilizing residues (Varshavsky 1992). In eukaryotes, the N-degron comprises two determinants: a destabilizing N-terminal residue and an internal lysine (or lysines) of a substrate. The lysine residue is the site of formation of a multiubiquitin chain, which is required for the degradation of at least some N-end rule substrates (Bachmair and Varshavsky 1989; Hill et al. 1993; Dohmen et al. 1994). Ubiquitin (Ub) is a 76-residue protein whose covalent conjugation to other proteins (often in the form of a multi-Ub chain) plays a role in a number of processes, primarily through routes that involve protein degradation (for review, see Finley and Chau 1991; Gottesman and Maurizi 1992; Hershko and Ciechanover 1992; Jentsch 1992; Varshavsky 1992, 1995a; Parsell and Lindquist 1993; Vierstra 1993; Ciechanover 1994; Gonda 1994; Hochstrasser 1995).
Modeling Ewing sarcoma tumors in vitro with 3D scaffolds (2013)

The pronounced biological influence of the tumor microenvironment on cancer progression and metastasis has gained increased recognition over the past decade, yet most preclinical antineoplastic drug testing is still reliant on conventional 2D cell culture systems. Although monolayer cultures recapitulate some of the phenotypic traits observed clinically, they are limited in their ability to model the full range of microenvironmental cues, such as ones elicited by 3D cell-cell and cell-extracellular matrix interactions. To address these shortcomings, we established an ex vivo 3D Ewing sarcoma model that closely mimics the morphology, growth kinetics, and protein expression profile of human tumors. We observed that Ewing sarcoma cells cultured in porous 3D electrospun poly(ε-caprolactone) scaffolds not only were more resistant to traditional cytotoxic drugs than were cells in 2D monolayer culture but also exhibited remarkable differences in the expression pattern of the insulin-like growth factor-1 receptor/mammalian target of rapamycin pathway. This 3D model of the bone microenvironment may have broad applicability for mechanistic studies of bone sarcomas and exhibits the potential to augment preclinical evaluation of antineoplastic drug candidates for these malignancies.
Dependence of oil stability index of fatty compounds on their structure and concentration and presence of metals (2003)

Abstract During storage and use, vegetable oil‐derived industrial products such as biodiesel and biodegradable lubricants can be subjected to conditions that promote oxidation of their unsaturated components. The materials arising during oxidation and subsequent degradation can seriously impair the quality and performance of such products. Therefore, oxidative stability is a significant issue facing these vegetable oil‐derived products, and enhanced understanding of the influence of various components of vegetable oils and storage parameters is necessary. In this work, the oil stability index (OSI) was used for assessing oxidation of monoalkyl esters of FA by varying several parameters. Neat fatty compounds and prepared mixtures thereof were studied for assessing the influence of compound structure and concentration. Small amounts of more highly unsaturated compounds had a disproportionately strong effect on oxidative stability. The recently developed concept of bis‐allylic equivalents correlated more closely than the iodine value with the OSI times of mixtures of fatty esters. The OSI times of free acids were shorter than those of the corresponding alkyl esters. The presence of copper, iron, and nickel also reduced oxidative stability, but their effect was less than the presence of more highly unsaturated fatty compounds. Of these metals, copper had the strongest catalytic effect on OSI time. OSI may be an alternative to long‐term storage tests for determining the influence of extraneous materials such as metals on oxidative stability.
Effective Gaussian mixture learning for video background subtraction (2005)

Adaptive Gaussian mixtures have been used for modeling nonstationary temporal distributions of pixels in video surveillance applications. However, a common problem for this approach is balancing between model convergence speed and stability. This paper proposes an effective scheme to improve the convergence rate without compromising model stability. This is achieved by replacing the global, static retention factor with an adaptive learning rate calculated for each Gaussian at every frame. Significant improvements are shown on both synthetic and real video data. Incorporating this algorithm into a statistical framework for background subtraction leads to an improved segmentation performance compared to a standard method.
Efficacy of Total Lymphoid Irradiation in Intractable Rheumatoid Arthritis (1985)

Twenty-six patients participated in a randomized, double-blind study of the efficacy of total lymphoid irradiation in the treatment of intractable rheumatoid arthritis. All 26 patients, for whom therapy with gold compounds and penicillamine had failed, would ordinarily have been considered candidates for cytotoxic or antimetabolite drug therapy. Thirteen patients randomly assigned to receive full-dose total lymphoid irradiation (2000 rad) and 11 patients assigned to receive control low-dose total lymphoid irradiation (200 rad) completed radiotherapy. Alleviation of joint disease activity was significantly greater in the high-dose group as judged by morning stiffness, joint tenderness, and functional assessment (global composite score) at 3 and 6 months after radiotherapy. The high-dose group had a marked reduction in both T-lymphocyte function and numbers, but this finding was not observed in the low-dose group. Complications seen in the high-dose but not low-dose group included transient neutropenia, thrombocytopenia, pericarditis, and pleurisy.
DnaK Plays a Pivotal Role in Tat Targeting of CueO and Functions beside SlyD as a General Tat Signal Binding Chaperone (2007)

The Tat (twin-arginine translocation) system from Escherichia coli transports folded proteins with N-terminal twin-arginine signal peptides across the cytoplasmic membrane. The influence of general chaperones on Tat substrate targeting has not been clarified so far. Here we show that the chaperones SlyD and DnaK bind to a broad range of different Tat signal sequences in vitro and in vivo. Initially, SlyD and GroEL were purified from DnaK-deficient extracts by their affinity to various Tat signal sequences. Of these, only SlyD bound Tat signal sequences also in the presence of DnaK. SlyD and DnaK also co-purified with Tat substrate precursors, demonstrating the binding to Tat signal sequences in vivo. Deletion of dnaK completely abolished Tat-dependent translocation of CueO, but not of DmsA, YcdB, or HiPIP, indicating that DnaK has an essential role specifically for CueO. DnaK was not required for stability of the CueO precursor and thus served in some essential step after folding. A CueO signal sequence fusion to HiPIP was Tat-dependently transported without the need of DnaK, indicating that the mature domain of CueO is responsible for the DnaK dependence. The overall results suggest that SlyD and DnaK are in the set of chaperones that can serve as general Tat signal-binding proteins. DnaK has additional functions that are indispensable for the targeting of CueO.
A tutorial on particle filters for online nonlinear/non-Gaussian Bayesian tracking (2002)

Increasingly, for many application areas, it is becoming important to include elements of nonlinearity and non-Gaussianity in order to model accurately the underlying dynamics of a physical system. Moreover, it is typically crucial to process data on-line as it arrives, both from the point of view of storage costs as well as for rapid adaptation to changing signal characteristics. In this paper, we review both optimal and suboptimal Bayesian algorithms for nonlinear/non-Gaussian tracking problems, with a focus on particle filters. Particle filters are sequential Monte Carlo methods based on point mass (or "particle") representations of probability densities, which can be applied to any state-space model and which generalize the traditional Kalman filtering methods. Several variants of the particle filter such as SIR, ASIR, and RPF are introduced within a generic framework of the sequential importance sampling (SIS) algorithm. These are discussed and compared with the standard EKF through an illustrative example.
Insulin Secretion by Anomers of D-Glucose (1974)

Isolated rat islets were incubated for 5 minutes in the media containing either the alpha or beta anomer of D-glucose (2 milligrams per milliliter). The amounts of secreted insulin and changes of anomers ratio were concomitantly determined. In spite of rapid mutarotation, significantly greater stimulation of insulin secretion was observed by alpha-D-glucose as compared with beta-D-glucose.
Pivotal Roles of CD4+ Effector T cells in Mediating Agonistic Anti-GITR mAb-Induced-Immune Activation and Tumor Immunity in CT26 Tumors (2007)

Glucocorticoid-induced TNF receptor family related protein (GITR) is a member of the TNFR superfamily. Previous studies have shown that in vivo administration of a GITR agonistic Ab (DTA-1) is able to overcome tolerance and induce tumor rejection in several murine syngeneic tumor models. However, little is known about the in vivo targets and the mechanisms of how this tolerance is overcome in a tumor-bearing host, nor is much known about how the immune network is regulated to achieve this antitumor response. In this study, we demonstrate that the in vivo ligation of GITR on CD4(+) effector T cells renders them refractory to suppression by regulatory T (T(reg)) cells in the CT26 tumor-bearing mouse. GITR engagement on T(reg) cells does not appear to directly abrogate their suppressive function; rather, it increases the expansion of T(reg) cells and promotes IL-10 production, a cytokine important for their suppressive function. Moreover, CD4(+) effector T cells play a crucial role in mediating DTA-1-induced immune activation and expansion of CD8(+), NK, and B cells in the tumor-draining lymph nodes. This includes increased CD69 expression on all of these subsets. In addition, NK and tumor-specific CD8(+) T cells are generated that are cytolytic, which show increased intracellular IFN-gamma production and CD107a mobilization, the latter a hallmark of cytolytic activities that lead to tumor killing.
Wax moth larva (Galleria mellonella): an in vivo model for assessing the efficacy of antistaphylococcal agents (2011)

To investigate whether the wax moth larva, Galleria mellonella, is a suitable host for assessing the in vivo efficacy of antistaphylococcal agents against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) infections. Wax moth larvae were infected with increasing doses of S. aureus to investigate the effect of inoculum size on larval survival. In addition, infected wax moth larvae were treated with daptomycin, penicillin or vancomycin to examine whether these agents were effective against S. aureus and MRSA infections in vivo. Increasing inoculum doses of live S. aureus cells resulted in greater larval mortality, but heat-killed bacteria and cell-free culture filtrates had no detrimental effects on survival. Larval mortality rate also depended on the post-inoculation incubation temperature. After larvae were infected with S. aureus, larval survival was enhanced by administering the antistaphylococcal antibiotics daptomycin or vancomycin. Larval survival increased with increasing doses of the antibiotics. Moreover, penicillin improved survival of larvae infected with a penicillin-susceptible methicillin-susceptible S. aureus (MSSA) strain, but it was ineffective at similar doses in larvae infected with MRSA (penicillin resistant). Daptomycin and vancomycin were also effective when administered to the larvae prior to infection with bacteria. This is the first report to demonstrate that antibiotics are effective in the wax moth larva model for the treatment of infections caused by Gram-positive bacteria. The new wax moth larva model is a useful preliminary model for assessing the in vivo efficacy of candidate antistaphylococcal agents before proceeding to mammalian studies, which may reduce animal experimentation and expense.
Isolation and characterization of a TATA-less promoter for the human beta 3 integrin gene (1994)

Proper expression of the human platelet fibrinogen receptor is necessary for the maintenance of normal hemostasis. This receptor is formed by the heterodimer alpha IIb beta 3, a prototypic member of the integrin family of adhesive molecules. beta 3 is also expressed in other tissues with alpha v as the vitronectin receptor. It was not possible to study the basis for tissue-specific expression of this gene, because the beta 3 gene promoter had not been isolated previously. We have now isolated a 6.0-kb human genomic DNA fragment containing 2.0 kb of sequence 5′ to the beta 3 ATG start codon. This clone also contains sequence encoding the signal peptide of the immature beta 3 protein and 3.0 kb of 3′ intronic sequence. Primer extension and RNase protection studies of poly A+ RNA from a human erythroleukemia (HEL) cell line indicated a major transcription start site 30 bp upstream of the ATG start codon. In an orientation-dependent manner, a 584-bp fragment 5′ to the start codon promotes expression of the chloramphenicol acetyl transferase (CAT) reporter gene in K562 cells. CAT expression from this beta 3 promoter is fivefold above expression from a “promoter-less” control CAT construct. This beta 3 promoter lacks TATA and CAAT cis-acting elements, but there are two Sp1 sites flanking the transcription start site. Other potential transcription factor binding sites are also identified. Phorbol esters (TPA), which increase beta 3 transcription in K562 cells, stimulated transcription from the 584-bp 5′ beta 3 region. The isolation of this beta 3 promoter region should permit a more detailed analysis of its transcriptional regulation.