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Empirical free energy calculation: Comparison to calorimetric data

Zhiping Weng, Charles Delisi, Sandor Vajda
1997 Protein Science  
., 1996; Weng et ai., 1996) .  ...  Weng et al. ' v c is determined from hydrocarbon (vapor) to water transfer free energies.  ... 
doi:10.1002/pro.5560060918 pmid:9300497 pmcid:PMC2143797 fatcat:qcvx7znetraybeglaci5tck6sq

Protein therapeutics: promises and challenges for the 21st century

Zhiping Weng, Charles DeLisi
2002 Trends in Biotechnology  
Acknowledgement Zhiping Weng is partially supported by NSF grant DBI#0078194.  ...  Chen and Weng further developed the FFT algorithm with a target function that is tolerant to conformation changes. They performed a comprehensive study on 28 distinct protein-protein complexes.  ... 
doi:10.1016/s0167-7799(01)01846-7 pmid:11742675 fatcat:r2iv3nfjcfdhrbmfxbx5fmgvay

Prediction of protein complexes using empirical free energy functions

Zhiping Weng, Sandor Vajda, Charles Delisi
2008 Protein Science  
Weng et al.  ...  Weng et al.  ... 
doi:10.1002/pro.5560050406 pmid:8845751 pmcid:PMC2143396 fatcat:pw3ezkyl6vbedk4vvqxpo4ne2m

Rapid evolution by spontaneous mutation increases genetic diversity facilitating plant population survival [article]

Henning Nottebrock, Mao-Lun Weng, Matthew T Rutter, Charles B. Fenster
2018 bioRxiv   pre-print
Using a mechanistic eco-evolutionary trait-based neighborhood-model, we quantify the impact of mutations on spatial interactions to better understand the potential effect of niche evolution through mutations on the population dynamics of Arabidopsis thaliana. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000
more » ... , including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale, survival is enhanced but reproduction is decreased when a genotype is surrounded by different genotypes. At large-scale, seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. Mutations may provide a mechanism for plants to quickly evolve niches and may drive competition, facilitation and selection with profound consequences for future population and community dynamics.
doi:10.1101/497610 fatcat:7ghualf23jcvzcyiotpole2upe

Free Energy Landscapes of Encounter Complexes in Protein-Protein Association

Carlos J. Camacho, Zhiping Weng, Sandor Vajda, Charles DeLisi
1999 Biophysical Journal  
., 1997b; Weng et al., 1997) .  ... 
doi:10.1016/s0006-3495(99)77281-4 pmid:10049302 pmcid:PMC1300098 fatcat:frg7cqhwmbb2ln6rmecvvu5ofy

Mutation bias shapes gene evolution in Arabidopsis thaliana [article]

J Grey Monroe, Thanvi Srikant, Pablo Carbonell-Bejerano, Moises Exposito-Alonso, Mao-Lun Weng, Matthew T Rutter, Charles B Fenster, Detlef Weigel
2020 bioRxiv   pre-print
(b) High-quality de novo mutations called in this investigation (total number = mutations here + Weng et al. 2019.) (c) Visualization of raw data and high confidence set.  ... 
doi:10.1101/2020.06.17.156752 fatcat:xor7tdjpwzbhjoiigh2t4y5cpu

Effects of Mineral Nutrition on Components of Reproduction in Clarkia ungucilata

Frank Vasek, Vincent Weng, Robert Beaver, Charles Huszar
1987 Aliso  
An experiment was conducted to determine the effects of nutritional level and flower location on factors related to flower, pollen, and ovule production, and to determine what developmental patterns would be modified to mediate any observed changes. Plants subjected to high nutrient levels developed larger leaves, more branches, more flowers on both the main stem and the branches, and opened their first flowers 6 days sooner than plants at lower levels of nutrients. Total flower number
more » ... from 72.2 to 626 .8 per plant, with most of the increase produced on the primary branches. The number of pollen grains in the entire androecium averaged 14,685, but significantly increased with higher nutrient levels and decreased with the stage of plant maturity (nodal position on the plant). The number of ovules also increased with nutrient level and decreased with maturity stage. Average ovule number decreased from about 129 in flowers at nodes produced early in the growth cycle to about 100 in flowers produced at later nodes. Despite highly significant plasticity in numbers of both pollen and ovules, the Pollen/ Ovule Ratio (average 132.7) did not vary significantly with either nutrient level or plant maturity stage. Path analysis, which decomposes correlation coefficients into direct and indirect effects of factors influencing development, indicated that nutrient level had a very strong direct effect on the number of primary branches and on the number of primary-branch flowers, as well as very strong indirect effects on the latter. The primary-branch flowers directly determined over 67% of the total flower number, and indirectly determined about 24%jointly with secondary-branch flowers, and over 3% jointly with main-stem flowers. The direct effects of secondary-branch flowers and mainstem flowers were 3.8% and 0.3%, respectively. The relationship among components of yield is slightly additive. Direct determination of yield was 74.6% by the number of flowers per plant, 0.6% by the number of ovules per flower, 3.8% by the number of seeds per ovule, and 1.1 % by the weight per seed. The proportion of yield jointly determined by flower number and the developed seeds per ovule was 15.3%. It was concluded that allocation of resources increases to both male and female functions under conditions of high nutrient levels, and pollen/ ovule ratios are consistent within a plant despite significant plasticity in numbers of pollen grains and ovules.
doi:10.5642/aliso.19871104.15 fatcat:7cm54vlg65axzgfvwicibpll5q

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Soohyun Lee, Simon Kasif, Zhiping Weng, Charles R. Cantor, Richard Mayeux
2008 PLoS ONE  
Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations
more » ... s). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results: We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0,1%. Conclusions: Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.
doi:10.1371/journal.pone.0003906 pmid:19093001 pmcid:PMC2600609 fatcat:uyfxnnkqj5cmxilq5rvt32mudy

ON CONTROL OF RESIST FILM UNIFORMITY IN THE MICROLITHOGRAPHY PROCESS

Ho Weng Khuen, Lee Lay Lay, Charles Schaper
2002 IFAC Proceedings Volumes  
A new approach to improve resist thickness uniformity through the softbake process is proposed. Using in-situ thickness measurements, a multi-zone bakeplate and sliding mode control algorithm, the temperature distributions of the bakeplate is manipulated in real-time to reduce the resist thickness non-uniformity. Constraints on the bakeplate temperature are imposed to prevent the decomposition of photoactive compound in the resist. Hence the sliding mode control is implemented in a cascaded
more » ... rol structure. The resist thickness non-uniformity is reduced to less than 10 angstroms across individual wafers and from wafer-to-wafer.
doi:10.3182/20020721-6-es-1901.01154 fatcat:5jcee56kwza6zg3xx6ve6pxyeq

Release of acidic store calcium is required for effective priming of the NLRP3 inflammasome [article]

Nick Platt, Dawn Shepherd, Yuzhe Weng, Grant Charles Churchill, Antony Galione, Frances M. Platt
2022 bioRxiv   pre-print
The lysosome is a dynamic signaling organelle that is critical for cell functioning. It is a regulated calcium store that can contribute to Ca2+-regulated processes via both local calcium release and more globally by influencing ER Ca2+release. Here, we provide evidence from studies of an authentic mouse model of the lysosomal storage disease Niemann-Pick Type C (NPC) that has reduced lysosomal Ca2+ levels, and genetically modified mice in which the two-pore lysosomal Ca2+ release channel
more » ... are deleted that lysosomal Ca2+ signaling is required for normal pro-inflammatory responses. We demonstrate that production of the pro-inflammatory cytokine IL-1beta via the NLRP3 inflammasome is significantly reduced in murine Niemann-Pick Type C, the inhibition is selective because secretion of TNF alpha is not diminished, and it is a consequence of inefficient inflammasome priming. Synthesis of precursor ProIL-1 beta is significantly reduced in macrophages genetically deficient in the lysosomal protein Npc1, which is mutated in most clinical cases of NPC, and in wild type cells in which Npc1 activity is pharmacologically inhibited. Comparable reductions in ProIL-1 beta generation were measured in vitro and in vivo by macrophages genetically altered to lack expression of the two-pore lysosomal Ca2+ release channels Tpcn1 or Tpcn2. These data demonstrate a requirement for lysosome-dependent Ca2+ signaling in the generation of specific pro-inflammatory responses.
doi:10.1101/2022.01.06.475262 fatcat:a5b6pxw72raabgfklalrrja6wq

Nonlinear evolution of stimulated scattering near 1/4 critical density

Charles F. Wu, Yao Zhao, Su-Ming Weng, Min Chen, Zheng-Ming Sheng
2019 Wuli xuebao  
非均匀等离子体中1/4临界密度附近受 激散射的非线性演化 * 吴钟书 1) 赵耀 2) † 翁苏明 1) 陈民 1) 盛政明 1)3) 1) (上海交通大学物理与天文学院, 激光等离子体教育部重点实验室, 上海 200240) 2) (中国科学院上海光学精密机械研究所高功率激光物理联合实验室, 上海 201800) 3) (李政道研究所, 上海 200240)
doi:10.7498/aps.68.20190883 fatcat:kslw6jsdx5d4lmfydv5selxowe

Committee Selection with a Weight Constraint Based on a Pairwise Dominance Relation [chapter]

Charles Delort, Olivier Spanjaard, Paul Weng
2011 Lecture Notes in Computer Science  
This paper is devoted to a knapsack problem with a cardinality constraint when dropping the assumption of additive representability [10] . More precisely, we assume that we only have a classification of the items into ordered classes. We aim at generating the set of preferred subsets of items, according to a pairwise dominance relation between subsets that naturally extends the ordering relation over classes [4, 16] . We first show that the problem reduces to a multiobjective knapsack problem
more » ... th cardinality constraint. We then propose two polynomial algorithms to solve it, one based on a multiobjective dynamic programming scheme and the other on a multiobjective branch and bound procedure. We conclude by providing numerical tests to compare both approaches.
doi:10.1007/978-3-642-24873-3_3 fatcat:hvq2ad5spfeyvovk4o3ikmit5u

Internal Support of Tissue-Engineered Cartilage

Carlos A. Arévalo-Silva, Roland D. Eavey, Yilin Cao, Martin Vacanti, Yulai Weng, Charles A. Vacanti
2000 Archives of Otolaryngology - Head and Neck Surgery  
Vacanti, Weng, and C. A. Vacanti), and the Department of Pathology (Dr M. Vacanti), University of Massachusetts Medical Center, Worcester.  ... 
doi:10.1001/archotol.126.12.1448 pmid:11115280 fatcat:ihbq2sl4ibbk3lsetpsbn5hcmm

Effect of Flow Rate and Viscosity on Complex Fracture Development in UFM Model [chapter]

Olga Kresse, Xiaowei Weng, Dimitry Chuprakov, Romain Prioul, Charles Cohe
2013 Effective and Sustainable Hydraulic Fracturing  
A recently developed unconventional fracture model (UFM * ) is able to simulate complex fracture networks propagation in a formation with pre-existing natural fractures. Multiple fracture branches can propagate at the same time and crisscross each other. The behaviour of a hydraulic fracture when it intersects a natural fracture, whether being arrested, crossing, creating an offset, or dilating the natural fracture, plays a key role in predicting the resulting fracture footprint,
more » ... , and improving production evaluation. It is therefore critical to properly model the fracture interaction in a complex fracture model such as UFM. A new crossing model, called OpenT, taking into account the effect of flow rate and fluid viscosity on the hydraulic/natural fracture crossing behaviour is integrated in UFM simulator. The previous fracture crossing model is primarily based on the stress field at the approaching hydraulic fracture tip and its interaction with the natural fracture. A new elasticity solution for the fracture contact has been developed. The new OpenT semi-analytical crossing model quantifies the localized stress field induced in the natural fracture and in the rock and evaluates the size and length of open and shear slippage zones along the natural fracture. The natural fracture activation and stress field near the intersection point are strongly dependent on the contacting hydraulic fracture opening and thus on fluid flow rate and viscosity. This new model is validated against laboratory experimental results and an advanced numerical model. In this paper we present the results of several test cases showing the influence of injection rate and fluid viscosity on the generated hydraulic fracture footprint in formations with pre-© 2013 Kresse et al.; licensee InTech. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. existing natural fractures. The influence of the stress field anisotropy, intersection angle, as well as natural fractures properties are also important and are discussed. The results are then compared with the simulations using the previous crossing model which does not account for the influence of fluid properties. Effective and Sustainable Hydraulic Fracturing 184 Effect of Flow Rate and Viscosity on Complex Fracture Development in UFM Model http://dx.
doi:10.5772/56406 fatcat:vy5q3mnj5ffqdbxr5semrt74oy

Pleiotropy is associated with fitness consequences of new mutations in mutation accumulation lines [article]

Sydney Kreutzmann, Elizabeth Pompa, Nhan D. Nguyen, Liya Tilahun, Matthew T. Rutter, Mao-Lun Weng, Charles B. Fenster, Carrie F. Olson-Manning
2021 bioRxiv   pre-print
These lines have shed light on the distribution of phenotypic effects (Chang and Shaw 2003; Shaw, Geyer, and Shaw 2002; Weng et al. 2021) , the mutational spectrum (Weng et al. 2019; Schrider et al.  ...  These lines have accumulated an average of 17 mutations over 30 generations of mutation accumulation (Weng et al. 2019) .  ... 
doi:10.1101/2021.06.28.450192 fatcat:o3y5gowgijcjfig5yygaq3pvd4
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