gebhart/patrepeval huggingface dataset:
Butyrate Activates the WAF1/Cip1 Gene Promoter through Sp1 Sites in a p53-negative Human Colon Cancer Cell Line (1997)

Butyrate is a well known colonic luminal short chain fatty acid, which arrests cell growth and induces differentiation in various cell types. We examined the effect of butyrate on the expression of WAF1/Cip1, a potent inhibitor of cyclin-dependent kinases, and its relation to growth arrest in a p53-mutated human colon cancer cell line WiDr. Five millimolar butyrate completely inhibited the growth of WiDr and caused G1-phase arrest. WAF1/Cip1 mRNA was rapidly induced within 3 h by treatment with 5.0 mM butyrate, and drastic WAF1/Cip1 protein induction was detected. Using several mutant WAF1/Cip1 promoter fragments, we found that the butyrate-responsive elements are two Sp1 sites at -82 and -69 relative to the transcription start site. We also found that a TATA element at -46 and two overlapping consensus Sp1 sites at -60 and -55 are essential for the basal promoter activity of WAF1/Cip1. These findings suggest that butyrate arrests the growth of WiDr by activating the WAF1/Cip1 promoter through specific Sp1 sites in a p53-independent fashion.
High Affinity Antigen Recognition of the Dual Specific Variants of Herceptin Is Entropy-Driven in Spite of Structural Plasticity (2011)

The antigen-binding site of Herceptin, an anti-human Epidermal Growth Factor Receptor 2 (HER2) antibody, was engineered to add a second specificity toward Vascular Endothelial Growth Factor (VEGF) to create a high affinity two-in-one antibody bH1. Crystal structures of bH1 in complex with either antigen showed that, in comparison to Herceptin, this antibody exhibited greater conformational variability, also called "structural plasticity". Here, we analyzed the biophysical and thermodynamic properties of the dual specific variants of Herceptin to understand how a single antibody binds two unrelated protein antigens. We showed that while bH1 and the affinity-improved bH1-44, in particular, maintained many properties of Herceptin including binding affinity, kinetics and the use of residues for antigen recognition, they differed in the binding thermodynamics. The interactions of bH1 and its variants with both antigens were characterized by large favorable entropy changes whereas the Herceptin/HER2 interaction involved a large favorable enthalpy change. By dissecting the total entropy change and the energy barrier for dual interaction, we determined that the significant structural plasticity of the bH1 antibodies demanded by the dual specificity did not translate into the expected increase of entropic penalty relative to Herceptin. Clearly, dual antigen recognition of the Herceptin variants involves divergent antibody conformations of nearly equivalent energetic states. Hence, increasing the structural plasticity of an antigen-binding site without increasing the entropic cost may play a role for antibodies to evolve multi-specificity. Our report represents the first comprehensive biophysical analysis of a high affinity dual specific antibody binding two unrelated protein antigens, furthering our understanding of the thermodynamics that drive the vast antigen recognition capacity of the antibody repertoire.
Changes in amino acid and nucleotide pools of Rhodospirillum rubrum during switch-off of nitrogenase activity initiated by NH4+ or darkness (1987)

Amino acid and nucleotide pools were measured in nitrogenase-containing Rhodospirillum rubrum cultures during NH4+- or dark-induced inactivation (switch-off) of the Fe protein. A big increase in the glutamine pool size preceded NH4+ switch-off of nitrogenase activity, but the glutamine pool remained unchanged during dark switch-off. Furthermore, methionine sulfoximine had no effect on the rate of dark switch-off, suggesting that glutamine plays no role in this process. In the absence of NH4+ azaserine, an inhibitor of glutamate synthate, raised glutamine pool levels sufficiently to initiate switch-off in vivo. While added NH4+ substantially increased the size of the nucleotide pools in N-limited cells, the kinetics of nucleotide synthesis were all similar and followed (rather than preceded) Fe protein inactivation. Darkness had little effect on nucleotide pool sizes. Glutamate pool sizes were also found to be important in NH4+ switch-off because of the role of this molecule as a glutamine precursor. Much of the diversity reported in the observations on NH4+ switch-off appears to be due to variations in glutamate pool sizes prior to the NH4+ shock. The nitrogen nutritional background is an important factor in determining whether darkness initiates nitrogenase switch-off; however, no link has yet been established between this and NH4+ (glutamine) switch-off.
Process-improved RRAM cell performance and reliability and paving the way for manufacturability and scalability for high density memory application (2012)

Here for the first time we discuss RRAM cell performance and reliability through process improvement. Excellent post-cycling (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> ) retention and post-bake retention and endurance have been achieved for the optimized process conditions. The optimized RRAM cells show potential for manufacturability and scalability for high density memory application.
Cost of leukopenia and neutropenia in metastatic breast cancer within last 12, 36, and 60 months using a curated disease model (2019)

(2019). Cost of leukopenia and neutropenia in metastatic breast cancer within last 12, 36, and 60 months using a curated disease model. Journal of Drug Assessment: Vol. 8, Abstracts from the Seventh Annual National Association of Specialty Pharmacy (NASP) Meeting, pp. 23-23.
Paramagnetic colloids: Chaotic routes to clusters and molecules (2018)

We present computer simulations and experiments on dilute suspensions of superparamagnetic particles subject to rotating magnetic fields. We focus on chains of four particles and their decay routes to stable structures. At low rates, the chains track the external field. At intermediate rates, the chains break up but perform a periodic (albeit complex) motion. At sufficiently high rates, the chains generally undergo chaotic motion at short times and decay to either closely packed clusters or more dispersed, colloidal molecules at long times. We show that the transition out of the chaotic states can be described as a Poisson process in both simulation and experiment.
On an evaluation of tracking performance improvement by SMC-PHD filter with intensity image of pedestrians detection over on-board camera using neural network (2014)

Performance evaluation of multiple pedestrian tracking with/without the particle filter technique has been conducted by proposing some elaborated criteria for evaluation in terms of 1) detection evaluation for each frame, and 2) tracking evaluation for each image sequence. We cope with non-triviality on performance evaluate of multiple pedestrians detection and tracking under the situation of having false positive and false negative, true positive and true negative, and swapping of tracking targets with respect to different pedestrians as well as among false tracks and true tracks. Evaluation results with comparison among A) Nearest Neighbour(NN), B) Plain mode of particle filter, and C) Weighted model of particle filter are summarized as follows. By truth detection rate criterion, A) NN is the worst performance, while B) Plain is better than C) Weighted. By Swapping ID criterion, performance is improved by B) Plain and C) Weighted with C) being slightly better than B). However, by the criterion of termination of tracking, B) and C) are not necessarily better than A), rather worse than A), and B) Plain is worse than C) Weighted. This means that short term tracking performance has been improved by particle filter. Also, an elaboration in C) Weighted to consider the change of target size improve the performance than B) Plain.
Hematogenous Proteus Mirabilis Osteomyelitis (1983)

Hematogenous gram negative infection of the long bones can present a confusing clinical picture that may delay treatment or lead to an inappropriate choice of initial treatment, and thereby compromise the resuit. This report emphasizes the common clinical features of this condition: previous urinary or gastrointestinal tract instrumentation, a long history of diffuse pain, swelling, and tenderness of the affected limb, weight loss and anorexia, and a potentially nondiagnostic radiographic appearance.
Kernel methods, syntax and semantics for relational text categorization (2008)

Previous work on Natural Language Processing for Information Retrieval has shown the inadequateness of semantic and syntactic structures for both document retrieval and categorization. The main reason is the high reliability and effectiveness of language models, which are sufficient to accurately solve such retrieval tasks. However, when the latter involve the computation of relational semantics between text fragments simple statistical models may result ineffective. In this paper, we show that syntactic and semantic structures can be used to greatly improve complex categorization tasks such as determining if an answer correctly responds to a question. Given the high complexity of representing semantic/syntactic structures in learning algorithms, we applied kernel methods along with Support Vector Machines to better exploit the needed relational information. Our experiments on answer classification on Web and TREC data show that our models greatly improve on bag-of-words.
Partitioning, Persistence, and Accumulation in Digested Sludge of the Topical Antiseptic Triclocarban during Wastewater Treatment (2006)

The topical antiseptic agent triclocarban (TCC) is a common additive in many antimicrobial household consumables, including soaps and other personal care products. Long-term usage of the mass-produced compound and a lack of understanding of its fate during sewage treatment motivated the present mass balance analysis conducted at a typical U.S. activated sludge wastewater treatment plant featuring a design capacity of 680 million liters per day. Using automated samplers and grab sampling, the mass of TCC contained in influent, effluent, and digested sludge was monitored by isotope dilution liquid chromatography (tandem) mass spectrometry. The average mass of TCC (mean +/- standard deviation) entering and exiting the plant in influent (6.1 +/- 2.0 microg/L) and effluent (0.17 +/- 0.03 microg/ L) was 3737 +/- 694 and 127 +/- 6 g/d, respectively, indicating an aqueous-phase removal efficiency of 97 +/- 1%. Tertiary treatment by chlorination and sand filtration provided no detectable benefit to the overall removal. Due to strong sorption of TCC to wastewater particulate matter (78 +/- 11% sorbed), the majority of the TCC mass was sequestered into sludge in the primary and secondary clarifiers of the plant. Anaerobic digestion for 19 days did not promote TCC transformation, resulting in an accumulation of the antiseptic compound in dewatered, digested municipal sludge to levels of 51 +/- 15 mg/kg dry weight (2815 +/- 917 g/d). In addition to the biocide mass passing through the plant contained in the effluent (3 +/- 1%), 76 +/- 30% of the TCC input entering the plant underwent no net transformation and instead partitioned into and accumulated in municipal sludge. Based on the rate of beneficial reuse of sludge produced by this facility (95%), which exceeds the national average (63%), study results suggest that approximately three-quarters of the mass of TCC disposed of by consumers in the sewershed of the plant ultimately is released into the environment by application of municipal sludge (biosolids) on land used in part for agriculture.
Growth of Legionella pneumophila in continuous culture (1985)

A method was developed to grow Legionella pneumophila in continuous culture. A chemostat was used to simulate nutrient-limited, submaximal growth in the natural environmental and to provide a precisely controlled growth regimen. Cultures grew under forced aeration under conditions yielding up to 38% saturation of dissolved oxygen; supplemental CO2 (5%) at the same gas flow rates as ambient air had no effect on culture growth. Pleomorphism was observed during growth under all conditions. Pigment was produced only at D less than 0.03 h-1. Catalase was produced at higher growth rates but not at higher temperatures. The pathogenicity was unaffected by altering either the growth rate or the growth temperature.
Cancer Stem Cell-Based Models of Colorectal Cancer Reveal Molecular Determinants of Therapy Resistance (2016)

Colorectal cancer stem cells (CSCs) have been shown to be responsible for tumor propagation, metastatic dissemination, and relapse. However, molecular pathways present in CSCs, as well as mechanisms of therapy resistance, are mostly unknown. Taking advantage of genetically characterized CSC lines derived from colorectal tumors, this study provides an extensive analysis of CSC response to EGFR-targeted therapy in vivo and an overview of factors implicated in therapy response or resistance. Furthermore, the implementation of a biobank of molecularly annotated CSC lines provides an innovative resource for future investigations in colorectal cancer.
File allocation in distributed systems (1976)

The problem of allocating files in a computer network is a complex combinatorial problem due to the number of integer design parameters involved. These parameters include system cost, number of copies of each file to be stored, and sites at which the copies should be stored. The tradeoffs between these parameters are discussed. The design problem is formulated as an integer programming problem. A branch and bound algorithm is proposed to solve the problem. A linear programming formulation which ignores integer restrictions (and allows a fraction of a file to reside at a site) is shown to yield integer solutions in most cases. In other words integer restrictions are satisfied automatically. A near-optimal heuristic is presented, along with computational results. An efficient method to solve the file allocation problem for medium-scale networks is proposed.
Tailoring the local electronic structure of heterogenized rhodium carbon dioxide photoreduction catalyst to optimize their performance (2017)

SSCI-VIDE+ING+FWI:JEC:DFA
Handheld multispectral dual-axis confocal microscope for cervical cancer screening (2013)

Our work demonstrates a MEMS based handheld dual-axis confocal microscope for cervical cancer screening. Imaging demonstration is performed with plant and animal tissue biopsies. The data is collected and displayed in real time with 2-5 Hz frame rates.
Advanced interconnect challenges beyond 5nm and possible solutions (2021)

As the on-chip interconnect scales down to below 30nm pitch, it faces challenges in all aspects of performance, yield, and cost. Performance degradation caused by electron scattering in narrow Cu damascene lines, combined with slow barrier/liner scaling is a big concern. In order to reduce the resistivity of damascene Cu lines, grain size and interface engineering are being investigated, as well as a new liner that can enable more aggressive thickness scaling. To improve capacitance, k-value reduction of dielectric films by damage recovery during process integration is being studied. Yield loss is mainly attributed to micro bridge, also known as stochastic printing failures of EUV lithography, or scaling induced Cu void or bridge defects. New photoresists or etch process recipes are being explored in order to address the micro bridge. Cu-fill friendly damascene profile is being introduced to suppress Cu void defects. Since rising BEOL cost is a critical challenge, single EUV patterning to replace double patterning is being actively investigated. In parallel to the conventional scaling, disruptive interconnect architectural changes such as backside power distribution network, and innovative materials such as alternative conductors, and 2D barriers / liners need to be considered.
High temperature behavior of poly[bis(2,2,2-trifluoroethoxy)phosphazene] (1999)

Mesomorphic features of poly[bis(2,2,2-trifluoroethoxy)phosphazene] (PBFP) with high (≈107) and low (≈104) molecular weights have been investigated by X-ray diffraction techniques, differential scanning calorimetry optical and electron microscopy, and small-angle X-ray scattering. Characterization measurements were made from room temperature to ≈300°C, which is well above Tm, the designated melting temperature of PBFP. The wide angle X-ray scattering (WAXS) may be interpreted in support of some kind of “nano-scale order” persisting above the isotropization temperature, Tm, of this polymer. There is other evidence to the contrary, namely the optical isotropicity between crossed-polars (depicts melting) and the absence of discrete small angle X-ray scattering (SAXS) under these same conditions. An attempt is made here to establish if these features above Tm are related to molecular weight.
Efficacy of venetoclax as targeted therapy for relapsed/refractory t(11;14) multiple myeloma (2017)

Venetoclax is a selective, orally bioavailable BCL-2 inhibitor that induces cell death in multiple myeloma (MM) cells, particularly in those harboring t(11;14), which express high levels of BCL-2 relative to BCL-X<sub>L</sub> and MCL-1. In this phase 1 study, patients with relapsed/refractory MM received venetoclax monotherapy. After a 2-week lead-in with weekly dose escalation, daily venetoclax was given at 300, 600, 900, or 1200 mg in dose-escalation cohorts and 1200 mg in the safety expansion. Dexamethasone could be added on progression during treatment. Sixty-six patients were enrolled (30, dose-escalation cohorts; 36, safety expansion). Patients received a median of 5 prior therapies (range, 1-15); 61% were bortezomib and lenalidomide double refractory, and 46% had t(11;14). Venetoclax was generally well tolerated. Most common adverse events included mild gastrointestinal symptoms (nausea [47%], diarrhea [36%], vomiting [21%]). Cytopenias were the most common grade 3/4 events, with thrombocytopenia (32%), neutropenia (27%), anemia (23%), and leukopenia (23%) reported. The overall response rate (ORR) was 21% (14/66), and 15% achieved very good partial response or better (≥VGPR). Most responses (12/14 [86%]) were reported in patients with t(11;14). In this group, ORR was 40%, with 27% of patients achieving ≥VGPR. Biomarker analysis confirmed that response to venetoclax correlated with higher <i>BCL2:BCL2L1</i> and <i>BCL2:MCL1</i> mRNA expression ratios. Venetoclax monotherapy at a daily dose up to 1200 mg has an acceptable safety profile and evidence of single-agent antimyeloma activity in patients with relapsed/refractory MM, predominantly in patients with t(11;14) abnormality and those with a favorable <i>BCL2</i> family profile. Registered at www.clinicaltrials.gov: #NCT01794520.
ChemInform Abstract: A New Convenient Synthesis of Aroyl Cyanides via the Formation of Cyanohydrin Nitrate Intermediates. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Brokerage Commission Schedules (1993)

ABSTRACT It is generally optimal for risk‐sharing reasons to base a charge for information on the signal realization. When this is not possible, a charge based on the amount of trading, a brokerage commission, may be a good alternative. The optimal brokerage commission schedule is derived for a risk‐neutral information seller faced with risk‐averse purchasers who may differ in their risk aversion. Revenues from the brokerage commission are compared with those from a fixed charge for information and the optimal mutual fund management fee.
Evaluation of dual-energy radiography with a digital x-ray detector (2001)

Dual-energy imaging has been proposed as a method for producing material-specific images, thus permitting separate examination of bone and soft-tissue structures. Interesting clinical results, particularly for chest, have been presented usually for screen-film or phosphor plate detectors and with single exposure. The purpose of the paper is to investigate double exposure dual-energy with a digital X-Ray detector. The study is performed with a CCD-based large field digital X-Ray detector (Paladio detector, Apelem) installed on a remote table. Dual exposure is feasible on this detector with little registration problem because we have a very short delay (&lt; 0.5 s) between two acquisitions. For each examination, two radiographs are acquired at two different high and low energies and with adapted X-ray tube filtrations. X-ray generator energy voltages and filtrations are optimized in order to obtain thin energy peak spectra with good spectral separation (50 keV), much better than with single exposure systems. Tissue decomposition images are estimated from both acquisitions. The decomposition process is helped by the nice spectral separation. Scatter correction, applied to the raw dual-exposure acquisitions, provides an improvement of tissue decomposition. Results are shown for a chest phantom.
Evodiamine Mitigates Cellular Growth and Promotes Apoptosis by Targeting the c-Met Pathway in Prostate Cancer Cells (2020)

Evodiamine (EVO) is an indoloquinazoline alkaloid that exerts its various anti-oncogenic actions by blocking phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt), mitogen-activated protein kinase (MAPK), c-Met, and nuclear factor kappa B (NF-κB) signaling pathways, thus leading to apoptosis of tumor cells. We investigated the ability of EVO to affect hepatocyte growth factor (HGF)-induced c-Met/Src/STAT3 activation cascades in castration-resistant prostate cancer (CRPC). First, we noted that EVO showed cytotoxicity and anti-proliferation activities in PC-3 and DU145 cells. Next, we found that EVO markedly inhibited HGF-induced c-Met/Src/STAT3 phosphorylation and impaired the nuclear translocation of STAT3 protein. Then, we noted that EVO arrested the cell cycle, caused apoptosis, and downregulated the expression of various carcinogenic markers such as B-cell lymphoma 2 (Bcl-2), B-cell lymphoma-extra large (Bcl-xL), cyclin D1, cyclooxygenase 2 (COX-2), survivin, vascular endothelial growth factor (VEGF), and matrix metallopeptidases 9 (MMP-9). Moreover, it was observed that in cPC-3 and DU145 cells transfected with c-Met small interfering RNA (siRNA), Src/STAT3 activation was also mitigated and led to a decrease in EVO-induced apoptotic cell death. According to our results, EVO can abrogate the activation of the c-Met/Src/STAT3 signaling axis and thus plays a role as a robust suppressor of tumor cell survival, proliferation, and angiogenesis.
Ultrasonic wave propagation in fiber-reinforced solids containing voids (1977)

Calculated results are presented for ultrasonic wave propagation in fiber-reinforced composite material containing voids, where the fiber reinforcement is unidirectional. Both elastically isotropic and anisotropic fibers are considered. The propagation direction is taken as normal to the fiber length and expressions are obtained for the longitudinal- and shear-wave velocities as a function of composite void and fiber volume fraction. The results exhibit reasonable behavior and a comparison of calculated data and such experimental data as are available shows fair agreement.