gebhart/patrepeval huggingface dataset:
Design, experimentation and computerized automated data analysis of synergistic drug combinations against xenograft tumors by Taxotere and T900607 (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

4944 

Quantitative determination of synergistic/antagonistic combinations of antitumor agents in vitro in terms of isobologram and combination index (CI) is relatively easy to be carried out using computer simulation. However, drug combination against xenograft tumor is frequently complicated by variability, experimental size, experimental optimization and cost. This paper demonstrates how to overcome these difficulties by using microtubule targeting antitumor agents, Taxotere (TXT) and [T900607][1] (T607), as examples and using the median-effect principle (Chou) and the CI method (Chou-Talalay). We have succeeded in quantitative determination and antitumor synergism of these two drugs without enhancement of toxicity. This conclusion is reached with i) constant ratio combination (diagonal scheme); ii) previously established optimal conditions (doses, schedule and route) and with determining tumor size and body weight changes; and iii) the use of new computer software “CompuSyn” (Chou & Martin, 2003). In all, only 72 nude mice were used and about 2 months were spent for each experiment. Human colon carcinoma HCT-116 xenografts were implanted on day 0, and i.v. treatment, Q3Dx4 and x3 were started on day 14 with TXT (3, 5, 6, 7 mg/kg) and/or T607 (15, 25, 30, 35mg/kg) on day 14, 17, 20, 23, 32, 35 and 38, (n=6). Computerized analysis indicates that synergism (CI<1) occurred on day 32 with increasing synergism on D35 as indicated by the Fa-CI plots and the isobologram. Surprisingly, body weight decreases during and after combination treatment were less than those treated with each drug alone. This is considered a rare incidence of mutual protection in toxicity. Computer simulation of dose-reduction index (DRI) indicates that TXT doses can be reduced by 1.8-fold and T607 doses can be reduced by 4.5-fold when compared with each drug alone for a given degree of tumor suppression. Thus, decreases in dose led to decrease in toxicity while not compromising therapeutic effects. In a similar experiment with human mammary carcinoma MX-1 xenografts, T607 (25-35mg/kg) and TXT (7.5-15mg/kg) Q3Dx4, i.v. were given on D7, 10, 13 and 16. Increasing therapeutic synergism was observed on 16, 19 and 21. On D19, T607 (30mg/kg) and TXT (15mg/kg) resulted in 0/6 and 2/4 tumor disappearance, respectively, whereas in combination 5/5 tumor disappearance was observed. These results suggest that in vivo drug combinations can be conducted efficiently and synergy can be quantitatively determined, and that combination of TXT and T-607 for clinical development is warranted.

 [1]: /lookup/external-ref?link_type=GEN&access_num=T900607&atom=%2Fcanres%2F65%2F9_Supplement%2F1167.3.atom
Interaction of 2D materials with liquids: wettability, electrochemical properties, friction, and emerging directions (2020)

Abstract The emergence of two-dimensional (2D) materials as functional surfaces for sensing, electronics, mechanics, and other myriad applications underscores the importance of understanding 2D material–liquid interactions. The thinness and environmental sensitivity of 2D materials induce novel surface forces that drive liquid interactions. This complexity makes fundamental 2D material–liquid interactions variable. In this review, we discuss the (1) wettability, (2) electrical double layer (EDL) structure, and (3) frictional interactions originating from 2D material–liquid interactions. While many 2D materials are inherently hydrophilic, their wettability is perturbed by their substrate and contaminants, which can shift the contact angle. This modulation of the wetting behavior enables templating, filtration, and actuation. Similarly, the inherent EDL at 2D material–liquid interfaces is easily perturbed. This EDL modulation partially explains the wettability modulation and enables distinctive electrofluidic systems, including supercapacitors, energy harvesters, microfluidic sensors, and nanojunction gating devices. Furthermore, nanoconfinement of liquid molecules at 2D material surfaces arising from a perturbed liquid structure results in distinctive hydrofrictional behavior, influencing the use of 2D materials in microchannels. We expect 2D material–liquid interactions to inform future fields of study, including modulation of the chemical reactivity of 2D materials via tuning 2D material–liquid interactions. Overall, 2D material–liquid interactions are a rich area for research that enables the unique tuning of surface properties, electrical and mechanical interactions, and chemistry.
Time Series Characterization of Gaming Workload for Runtime Power Management (2013)

Runtime power management using dynamic voltage and frequency scaling (DVFS) has been extensively studied for video processing applications. But there is only a little work on game power management although gaming applications are now widely run on battery-operated portable devices like mobile phones. Taking a cue from video power management, where PID controllers have been successfully used, they were recently applied to game workload prediction and DVFS. However, the use of hand-tuned PID controller gains on relatively short game plays left open questions on the robustness of the controller and the sensitivity of prediction quality on the choice of the gain values. In this paper, we try to systematically answer these questions. We first show that from the space of PID controller gain values, only a small subset leads to good game quality and power savings. Further, the choice of this set highly depends on the scene and the game application. For most gain values the controller becomes unstable, which can lead to large oscillations in the processor’s frequency setting and thereby poor results. We then study a number of time series models, such as a Least Mean Squares (LMS) Linear Predictor and its generalizations in the form of Autoregressive Moving Average (ARMA) models. These models learn most of the relevant model parameters iteratively as the game progresses, thereby dramatically reducing the complexity of manual parameter estimation. This makes them deployable in real setups, where all game plays and even game applications are not a priori known. We have evaluated each of these models (PID, LMS, and ARMA) for a variety of games—ranging from Quake II to more recent closed-source games such as Crysis, Need for Speed—Shift and World in Conflict—with very encouraging results. To the best of our knowledge, this is the first work that systematically explores (a) the feasibility of manually tuning PID controller parameters for power management, (b) time series models for workload prediction for gaming applications, and (c) power management for closed-source games.
Relationship between maximum acceptable work time and physical workload (2002)

For safe job design, it is necessary to know the maximum acceptable work time (MAWT) for a given workload. The aim was to establish the relationship between MAWT and physical workload. Cycling tests at six different work rates relative to personal maximum working capacity were performed by 12 young adults in the laboratory. The oxygen uptake (VO(2)) in the per cent maximum aerobic capacity (%VO(2max)), relative heart rate (RHR) and relative oxygen uptake (RVO(2)) were collected throughout the test. MAWT was determined by observing the heart rate data during the test. The results showed that MAWT was negatively correlated with %VO(2max), RHR and RVO(2) (p < 0.01). Three exponential regression models were obtained and all their R(2) > 0.80. These models suggest that long-hour shifts (> 10 h) should assign a lower work intensity than for an 8-h workday. It is also logical that the workload limit for a 4-h work shift could be set at about 10% VO(2max) higher than the suggested limit for an 8-h workday.
Cardiorespiratory dynamics during sinusoidal and impulse exercise in man. (1983)

Dynamic characteristics of ventilation, cardiac output, and gas exchange during sinusoidally varying work rates for the periods from 1 to 12 min and impulse work rate with a duration of 10 sec were studied on five healthy men in an upright position. Changes in work rate were given by controlling externally the electromagnetic braking system of a bicycle ergometer. Stroke volume, heart rate, and cardiac output during exercise were determined continuously by using an automated impedance cardiograph. Breath by breath determination in minute ventilation, respiratory frequency, tidal volume, oxygen consumption, carbon dioxide output, end-tidal pressures of oxygen and carbon dioxide, and gas exchange ratio were conducted. From these and steady-state response data amplitude and phase relations between each variable and the input work loads were obtained utilizing the frequency analysis techniques. The response characteristics to sinusoidal stimuli were well represented by first-order models with time constants for VE, VCO2, VO2, and Q averaging 75, 67, 52, and 36 sec, respectively. The kinetics of HR closely resembled that of Q. There was a close link between both the dynamics of VE and VCO2. On the other hand, the responses to impulse stimuli were better described by second-order models in which fast and slow response components were connected in parallel. However, the contribution of the fast component to total response was small. Although this response may support in its form the neuro-humoral concept to explain exercise hyperpnea, a tight linkage was observed between VE and VCO2 responses to impulse stimuli. Thus, hyperpnea during the unsteady-state of exercise may be explained by the cardiodynamic hypothesis.
Auditing Black-box Models by Obscuring Features (2016)

Data-trained predictive models are widely used to assist in decision making. But they are used as black boxes that output a prediction or score. It is therefore hard to acquire a deeper understanding of model behavior: and in particular how different attributes influence the model prediction. This is very important when trying to interpret the behavior of complex models, or ensure that certain problematic attributes (like race or gender) are not unduly influencing decisions. 
In this paper, we present a technique for auditing black-box models: we can study the extent to which existing models take advantage of particular features in the dataset without knowing how the models work. We show how a class of techniques originally developed for the detection and repair of disparate impact in classification models can be used to study the sensitivity of any model with respect to any feature subsets. 
Our approach does not require the black-box model to be retrained. This is important if (for example) the model is only accessible via an API, and contrasts our work with other methods that investigate feature influence like feature selection. We present experimental evidence for the effectiveness of our procedure using a variety of publicly available datasets and models. We also validate our procedure using techniques from interpretable learning and feature selection.
Modulation of IgA, IgE, and IgG Fc receptor expression on human mononuclear phagocytes by 1α,25-dihydroxyvitamin D3 and cytokines (1995)

The effects of 1 alpha,25-dihydroxyvitamin D3/calcitriol on the expression of Fc receptors (FcR) for IgA (Fc alpha R), IgE (Fc epsilon RII), and IgG (Fc gamma R) on human peripheral blood monocytes and the cell lines U937, THP-1, and Mono Mac-6, in combination with various cytokines, was examined by flow cytometry. On both monocyte-derived macrophages and the myelomonocytic cell lines, Fc alpha R/CD89 expression was induced by calcitriol alone and additively in combination with tumor necrosis factor-alpha (TNF-alpha), interferon-gamma (IFN-gamma), and granulocyte-macrophage colony-stimulating factor. Constitutive and interleukin-4 (IL-4)-driven Fc epsilon RII/CD23 expression was markedly diminished on calcitriol-treated U937 cells and monocytes. Fc epsilon RII was also triggered by IFN-gamma, TNF-alpha, and IL-6 on all the cell lines, an effect blocked by calcitriol. On monocytes, the basal level and IFN-gamma-induced Fc gamma RI/CD64 expression was down-regulated by calcitriol and IL-4. The expression of Fc gamma RII/CD32 on monocytes was strongly suppressed by calcitriol. Transforming growth factor-beta induced Fc gamma RIII/CD16 on monocytes, an effect opposed by calcitriol. The ability of calcitriol-treated monocytes to phagocytose IgG-sensitized ox erythrocytes was diminished. Our results demonstrate that calcitriol, alone or in combination with cytokines, modulates Fc alpha R, Fc epsilon RII, Fc gamma RI, and Fc gamma RII expression on human mononuclear phagocytes, as well as Fc gamma R-mediated phagocytosis.
Chemical synthesis of cellulose by utilizing enzymatic polymerization. (1993)

The first successful chemical synthesis of cellulose is mainly reviewed in connection with related synthetic organic reactions in the carbohydrate chemistry field. The synthesis is a completely novel polymerization, which uses cellulose as catalyst for the polymerization of β-D-cellobiosyl fluoride substrate monomer. The product of the water-insoluble part had DP22 and a similar structure with natural cellulose, characterized by CP/MAS 13C NMR, IR spectra as well as X-ray analysis. This enzymatic polymerization technique is expected to contribute to glycotechnology to prepare new oligo- and poly-saccharides.
The <i>de Novo</i> Reference Genome and Transcriptome Assemblies of the Wild Tomato Species <i>Solanum chilense</i> Highlights Birth and Death of NLR Genes Between Tomato Species (2019)

Wild tomato species, like <i>Solanum chilense</i>, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. <i>S. chilense</i> also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.We generated ∼134 Gb of DNA and 157 Gb of RNA sequence data for <i>S chilense</i>, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% of these gene models are supported by RNA-seq data derived from leaf tissue samples. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% of BUSCO genes. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We find subfamilies of NLRs unique to <i>S. chilense</i> Synteny analysis suggests significant degree of the gene order conservation between the <i>S. chilense</i>, <i>S. lycopersicum</i> and <i>S. pennellii genomes</i>We generated the first genome and transcriptome sequence assemblies for the wild tomato species <i>Solanum chilense</i> and demonstrated their value in comparative genomics analyses. These data are an important resource for studies on adaptation to biotic and abiotic stress in <i>Solanaceae</i>, on evolution of self-incompatibility and for tomato breeding.
Characterization of high molecular mass linear polyacrylamide powder prepared by emulsion polymerization as a replaceable polymer matrix for DNA sequencing by capillary electrophoresis (1998)

In a previous paper, a 2% w/w replaceable high molecular mass linear polyacrylamide solution (high molecular mass LPA) was used to achieve long read-lengths for DNA sequencing by capillary electrophoresis (E. Carrilho et al., Anal. Chem. 1996, 68, 3305-3313). In that work, the polymer was prepared by polymerization in water at 6% w/w, followed by dilution to 2% w/w. In this study, an improved method for preparation of high molecular mass LPA was developed, based on inverse emulsion polymerization. With this polymerization procedure, the LPA results in a molecular mass of approximately 9 MDa, with characteristics of a fine powder of high purity and practically unlimited shelf life. Using size exclusion chromatography (SEC) and viscosity measurements to characterize the polymer, good batch-to-batch reproducibility was found. It was observed that the viscous polymer solutions made from these high molecular mass polymers require careful preparation and handling because the method of dissolution could affect the molecular mass distribution and the resultant separation of DNA components. Solutions containing 2% w/w of LPA made by emulsion polymerization were simple to prepare, resulting in excellent performance as a replaceable matrix for DNA sequencing by capillary electrophoresis. The viscosity of the polymer decreased exponentially when pressure was applied, allowing easy replacement from a capillary using a syringe. With a properly prepared matrix, a read-length of more than 1000 bases in 80 min with an accuracy better than 97%, and better than 99% for the first 800 bases, could be achieved.
Influence of Body Composition, Oral Contraceptive Use, and Physical Activity on Bone Mineral Density in Premenopausal Women (2009)

In premenopausal women, low bone density may reflect attainment of a lower peak bone mass which can increase risk of osteoporosis after menopause. The purpose of this study was to examine the relationship between total body, lumbar spine, and proximal femur bone mineral density (BMD) and body composition and oral contraceptive (OC) use in 18-30 year old women. Sixty-five healthy women, split into groups of oral contraceptive users (OC, n = 36) and non oral contraceptive users (Non-OC, n = 29), completed Baecke physical activity, calcium intake, and menstrual history questionnaires. Total body, AP lumbar spine, and dual proximal femur scans were performed using Dual Energy X-Ray Absorptiometry (DXA). Body composition measures were obtained from the total body scan analysis. No significant differences were found for BMD in OC users and non-users. Bone free lean body mass (BFLBM) and weight were positively correlated to all BMD sites, and fat mass was related to total body and L1-L4 spine BMD (p < 0.05). Stepwise regression analyses determined that weight was a significant predictor for all BMD sites (p < 0.05). When separating the two components of body weight, BFLBM was a significant predictor for all BMD sites, and fat mass only predicted total body BMD. In conclusion, this study indicates that weight and BFLBM are significant contributors to BMD in young healthy premenopausal women, and OC use did not influence the relationship between BMD and BFLBM.
Expression and assembly of largest foreign protein in chloroplasts: oral delivery of human FVIII made in lettuce chloroplasts robustly suppresses inhibitor formation in haemophilia A mice (2017)

Inhibitor formation is a serious complication of factor VIII (FVIII) replacement therapy for the X-linked bleeding disorder haemophilia A and occurs in 20%-30% of patients. No prophylactic tolerance protocol currently exists. Although we reported oral tolerance induction using FVIII domains expressed in tobacco chloroplasts, significant challenges in clinical advancement include expression of the full-length CTB-FVIII sequence to cover the entire patient population, regardless of individual CD4<sup>+</sup> T-cell epitope responses. Codon optimization of FVIII heavy chain (HC) and light chain (LC) increased expression 15- to 42-fold higher than the native human genes. Homoplasmic lettuce lines expressed CTB fusion proteins of FVIII-HC (99.3 kDa), LC (91.8 kDa), C2 (31 kDa) or single chain (SC, 178.2 kDa) up to 3622, 263, 3321 and 852 μg/g in lyophilized plant cells, when grown in a cGMP hydroponic facility (Fraunhofer). CTB-FVIII-SC is the largest foreign protein expressed in chloroplasts; despite a large pentamer size (891 kDa), assembly, folding and disulphide bonds were maintained upon lyophilization and long-term storage as revealed by GM1-ganglioside receptor binding assays. Repeated oral gavages (twice/week for 2 months) of CTB-FVIII-HC/CTB-FVIII-LC reduced inhibitor titres ~10-fold (average 44 BU/mL to 4.7 BU/mL) in haemophilia A mice. Most importantly, increase in the frequency of circulating LAP-expressing CD4<sup>+</sup> CD25<sup>+</sup> FoxP3<sup>+</sup> Treg in tolerized mice could be used as an important cellular biomarker in human clinical trials for plant-based oral tolerance induction. In conclusion, this study reports the first clinical candidate for oral tolerance induction that is urgently needed to protect haemophilia A patients receiving FVIII injections.
Removal of Sulfate Ion From AN-107 by Evaporation (2000)

Hanford low-activity waste solutions contain sulfate, which can cause accelerated corrosion of the vitrification melter and unacceptable operating conditions. A method is needed to selectively separate sulfate from the waste. An experiment was conducted to evaluate evaporation for removing sulfate ion from Tank AN-107 low-activity waste. Two evaporation steps were performed. In the first step, the volume was reduced by 55% while in the second step, the liquid volume was reduced another 22%. Analysis of the solids precipitated during these evaporations revealed that large amounts of sodium nitrate and nitrite co-precipitated with sodium sulfate. Many other waste components precipitated as well. It can be concluded that sulfate removal by precipitation is not selective, and thus, evaporation is not a viable option for removing sulfate from the AN-107 liquid.
On the Stability of a Plasma Diode† (1963)

ABSTRACT Appropriate analysis of an earlier derived time-dependent parametric solution for the current-voltage response of a planar plasma diode is found to admit an exact solution so long as the electron transit time is too short to excite the natural resonances of the plasma. This latter concept, applicable to finite plasmas, has apparently not been recognized heretofore, Thus it is possible to observe d.c. response of such a diode above a lower energy region which is unstable and manifests a.c, output ; the nature of the criterion for the transition separating the two regimes is characterized and its modification under certain boundary conditions appraised for the cold plasma limit with allowance, also, for the onset of relativistic effects.
Generation Of Large Spot Arrays From A Single Laser Beam By Multiple Imaging With Binary Phase Gratings (1989)

A simple technique for generating large (100 x 100+) arrays of uniform intensity spots of good contrast is proposed. One application of such spot arrays is as power supplies for optical logic devices in two-dimensional optical computing/switching architectures. This spot generation technique utilizes binary phase gratings both to produce small spot arrays (-20 x 20) and to multiply image them. Since the gratings need produce only small numbers of spots, the design computation and fabrication constraints are simplified. An experimental demonstration of this technique for an 81 x 81 array is presented along with a discussion of potential limitations.
Resolving postoperative neuroinflammation and cognitive decline (2011)

These data reveal the mechanisms for bidirectional communication between the brain and immune system following aseptic trauma. Pivotal molecular mechanisms can be targeted to prevent and/or resolve postoperative neuroinflammation and cognitive decline.