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https://www.readbyqxmd.com/read/28922399/probing-eukaryotic-cell-mechanics-via-mesoscopic-simulations
#1
Kirill Lykov, Yasaman Nematbakhsh, Menglin Shang, Chwee Teck Lim, Igor V Pivkin
Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular components plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28912262/diastolic-pressure-difference-to-classify-pulmonary-hypertension-in-the-assessment-of-heart-transplant-candidates
#2
Stephen P Wright, Yasbanoo Moayedi, Farid Foroutan, Suhail Agarwal, Geraldine Paradero, Ana C Alba, Jay Baumwol, Susanna Mak
BACKGROUND: The diastolic pressure difference (DPD) is recommended to differentiate between isolated postcapillary and combined pre-/postcapillary pulmonary hypertension (Cpc-PH) in left heart disease (PH-LHD). However, in usual practice, negative DPD values are commonly calculated, potentially related to the use of mean pulmonary artery wedge pressure (PAWP). We used the ECG to gate late-diastolic PAWP measurements. We examined the method's impact on calculated DPD, PH-LHD subclassification, hemodynamic profiles, and mortality...
September 2017: Circulation. Heart Failure
https://www.readbyqxmd.com/read/28904551/suppressive-effect-of-the-n-hexane-extract-of-litsea-japonica-fruit-flesh-on-monosodium-iodoacetate-induced-osteoarthritis-in-rats
#3
Seung-Hyung Kim, Hye-Jin Choi, Won-Kyung Yang, Ji-Eun Lee, Ju-Hyun Cho, In-Jae Park, Sunyoung Park, Bo-Kyung Park, Mirim Jin
We examined the antiosteoarthritic effect of the n-hexane extract of Litsea japonica fruit flesh (LJF-HE) in a rat model of monosodium-iodoacetate- (MIA-) induced osteoarthritis. LJF-HE significantly reduced the difference in weight-bearing capabilities of the hind paws between healthy and MIA-treated rats. Histological examination of the knee joints indicated that LJF-HE suppressed cartilage and bone destruction. Additionally, there were decreases in the expression of matrix metalloproteinase-2 and metalloproteinase-9 and cyclooxygenase-2 in the joints...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28886630/dissipative-particle-dynamics-systematic-parametrization-using-water-octanol-partition-coefficients
#4
Richard L Anderson, David J Bray, Andrea S Ferrante, Massimo G Noro, Ian P Stott, Patrick B Warren
We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i...
September 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28882448/paenibacillus-ihbetae-sp-nov-a-cold-adapted-antimicrobial-producing-bacterium-isolated-from-high-altitude-suraj-tal-lake-in-the-indian-trans-himalayas
#5
Shashi Kiran, Mohit Kumar Swarnkar, Shanmugam Mayilraj, Rupinder Tewari, Arvind Gulati
The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852(T) and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852(T) and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596(T) (97.8% and 97...
August 16, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28868066/distinguishing-depressive-pseudodementia-from-alzheimer-disease-a-comparative-study-of-hippocampal-volumetry-and-cognitive-tests
#6
Sevki Sahin, Tugba Okluoglu Önal, Nilgun Cinar, Meral Bozdemir, Rahmi Çubuk, Sibel Karsidag
BACKGROUND AND AIM: Depressive pseudodementia (DPD) is a condition which may develop secondary to depression. The aim of this study was to contribute to the differential diagnosis between Alzheimer disease (AD) and DPD by comparing the neurocognitive tests and hippocampal volume. MATERIALS AND METHODS: Patients who met criteria of AD/DPD were enrolled in the study. All patients were assessed using the Wechsler Memory Scale (WMS), clock-drawing test, Stroop test, Benton Facial Recognition Test (BFRT), Boston Naming Test, Mini-Mental State Examination (MMSE), and Geriatric Depression Scale (GDS)...
May 2017: Dementia and Geriatric Cognitive Disorders Extra
https://www.readbyqxmd.com/read/28857572/asymmetric-polymersomes-from-an-oil-in-oil-emulsion-a-computer-simulation-study
#7
Shanlong Li, Yinglin Zhang, Hong Liu, Chunyang Yu, Yongfeng Zhou, Deyue Yan
Asymmetric vesicles are valuable for understanding and mimicking cell and practical biomedicine applications. Recently, a very straightforward methodology for fabricating asymmetric polymersome was developed by Lodge's group through the coassembly of polystyrene-b-poly(ethylene oxide) (PS-b-PEO) and polybutadiene-b-poly(ethylene oxide) (PB-b-PEO) block copolymers at the interface of a polystyrene/polybutadiene/chloroform (PS/PB/CHCl3) emulsion. However, the in-depth microscopic mechanism for the formation of asymmetric polymersomes remains unclear...
September 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28853329/artificial-biomembrane-morphology-a-dissipative-particle-dynamics-study
#8
Matthew Becton, Rodney Averett, Xianqiao Wang
Artificial membranes mimicking biological structures are rapidly breaking new ground in the areas of medicine and soft-matter physics. In this endeavor, we use dissipative particle dynamic (DPD) simulation to investigate the morphology and behavior of lipid-based biomembranes under conditions of varied lipid density and self-interaction. Our results show that a less-than-normal initial lipid density does not create the traditional membrane; but instead results in the formation of a 'net', or at very low densities, a series of disparate 'clumps' similar to the micelles formed by lipids in nature...
August 30, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28835573/higher-tissue-levels-of-thymidylate-synthase-determined-by-elisa-are-associated-with-poor-prognosis-of-patients-with-lung-cancer
#9
Takayuki Shiina, Gaku Saito, Takao Sakaizawa, Hiroyuki Agatsuma, Yoshiaki Tominaga, Akira Hyogotani, Kazutoshi Hamanaka, Masayuki Toishi, Keiichiro Takasuna, Ryoichi Kondo, Kazuo Yoshida, Ken-Ichi Ito
Thymidylate synthase (TS) is essential in thymidylate biosynthesis and DNA replication. Dihydropyrimidine dehydrogenase (DPD) is a rate-limiting enzyme in pyrimidine catabolism and is important in catabolism of 5-fluorouracil (5-FU). The significance of TS and DPD expressed in lung cancer remains controversial. Here we analyzed the relationship between TS and DPD expression and clinicopathological features of lung cancer. Enzyme-linked immunosorbent assays (ELISAs) were used to measure TS and DPD levels in paired tumor and non-tumor lung tissues obtained from 168 patients (107 adenocarcinomas, 39 squamous cell carcinomas, and 22 others), who had operations at the Shinshu University Hospital from 2004 to 2007 and were followed up for a median of 57...
August 2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28821458/dipeptidyl-peptidase-iv-and-quorum-sensing-signaling-in-biofilm-related-virulence-of-prevotella-aurantiaca
#10
Dareen Fteita, Ahmed Ali Musrati, Eija Könönen, Xiaochu Ma, Mervi Gürsoy, Markus Peurla, Eva Söderling, Herman O Sintim, Ulvi Kahraman Gürsoy
Biofilm formation and dipeptidyl peptidase IV (DPPIV) enzyme activity contribute to the virulence of oral bacteria, and these virulence factors are partly regulated by quorum sensing signaling system. We recently demonstrated that estradiol regulates growth properties and DPPIV activity of Prevotella intermedia, Prevotella nigrescens, and Prevotella pallens. Here, we examined the DPPIV dependency of biofilm formation of Prevotella aurantiaca. Three strains (two clinical strains AHN 37505 and 37552 and the type strain CCUG 57723) were incubated in three estradiol concentrations (30, 90, and 120 nmol/L)...
August 15, 2017: Anaerobe
https://www.readbyqxmd.com/read/28810734/adsorption-and-depletion-regimes-of-a-nonionic-surfactant-in-hydrophilic-mesopores-an-experimental-and-simulation-study
#11
Dirk Müter, Gernot Rother, Henry Bock, Martin Schoen, Gerhard H Findenegg
Adsorption and aggregation of nonionic surfactants at oxide surfaces has been studied extensively in the past, but only for concentrations below and near the critical micelle concentration. Here we report an adsorption study of a short-chain surfactant (C6E3) in porous silica glass of different pore sizes (7.5 to 50 nm), covering a wide composition range up to 50 wt % in a temperature range from 20 °C to the LCST. Aggregative adsorption is observed at low concentrations, but the excess concentration of C6E3 in the pores decreases and approaches zero at higher bulk concentrations...
August 29, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28799231/efficacy-of-daratumumab-based-therapies-in-patients-with-relapsed-refractory-multiple-myeloma-treated-outside-of-clinical-trials
#12
Arjun Lakshman, Jithma P Abeykoon, Shaji K Kumar, S Vincent Rajkumar, David Dingli, Francis K Buadi, Wilson I Gonsalves, Nelson Leung, Angela Dispenzieri, Taxiarchis V Kourelis, Ronald S Go, Martha Q Lacy, Miriam A Hobbs, Yi Lin, Rahma Warsame, John Lust, Amie L Fonder, Yi L Hwa, Suzanne R Hayman, Stephen J Russell, Robert A Kyle, Morie A Gertz, Prashant Kapoor
Outside of clinical trials, experience with daratumumab-based combination therapies (DCTs) using bortezomib (V)/lenalidomide (R)/pomalidomide (P), and dexamethasone (d) in relapsed/refractory multiple myeloma (RRMM) is limited. We reviewed the outcomes of 126 patients who received ≥ 1 cycle of any DCT. Median age at DCT initiation was 67 (range, 43-93) years. High-risk cytogenetics was present in 33% patients. Median number of prior therapies was 4 (range, 1-14) and time to first DCT from diagnosis was 4...
August 11, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28798969/a-dissipative-particle-dynamics-simulation-study-on-phase-diagrams-for-the-self-assembly-of-amphiphilic-hyperbranched-multiarm-copolymers-in-various-solvents
#13
Haina Tan, Chunyang Yu, Zhongyuan Lu, Yongfeng Zhou, Deyue Yan
Self-assembly of amphiphilic hyperbranched multiarm copolymers (HMCs) has shown great potential for preparing all kinds of delicate supramolecular structures in all scales and dimensions in solution. However, theoretical studies on the influencing factors for the self-assembly of HMCs have been greatly lagging behind. The phase diagram of HMCs in selective solvents is very necessary but has not been disclosed up to now. Here, the self-assembly of HMCs with different hydrophilic fractions in various solvents was studied systematically by using dissipative particle dynamics (DPD) simulations...
August 11, 2017: Soft Matter
https://www.readbyqxmd.com/read/28782462/concentrations-of-ctx-i-ctx-ii-dpd-and-pyd-in-the-urine-as-a-biomarker-for-the-diagnosis-of-temporomandibular-joint-osteoarthritis-a-preliminary-study
#14
Soo-Min Ok, Seung-Min Lee, Hae Ryoun Park, Sung-Hee Jeong, Ching-Chang Ko, Yong-Il Kim
OBJECTIVES: The aim of this study was to identify a marker for temporomandibular joint (TMJ) osteoarthritis (OA) diagnosis by comparing the concentrations of urinary pyridinoline (PYD), deoxypyridinoline (DPD), and C-terminal telopeptides type I collagen (CTX-I), and CTX-II of TMJ OA patients with those of a non-symptomatic group. METHODS: PYD, DPD, CTX-I, and CTX-II concentrations in the urine of 36 non-symptomatic subjects and 31 TMJ OA subjects were analyzed...
August 7, 2017: Cranio: the Journal of Craniomandibular Practice
https://www.readbyqxmd.com/read/28756316/dissipative-particle-dynamics-simulations-reveal-the-ph-driven-micellar-transition-pathway-of-monorhamnolipids
#15
Jianchang Xu, ZhiKun Wang, Jianbang Gao, Chunling Li, Shuangqing Sun, Songqing Hu
Dissipative particle dynamics (DPD) simulation has been used to study the effect of pH on the morphology transition of micelles assembled by monorhamnolipids (monoRLs). Results show that micellar structures and transition modes with increasing mass concentrations are multiform due to the changeable hydrophilicity of pH-responsive beads at different pH levels. Various chaotic multilayer aggregations of monoRLs are observed at low pH (pH<4.0) whereas well-ordered single-layer structures are obtained at high pH (pH>7...
November 15, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28728692/magnetic-resonance-in-transthyretin%C3%A2-cardiac-amyloidosis
#16
Ana Martinez-Naharro, Thomas A Treibel, Amna Abdel-Gadir, Heerajnarain Bulluck, Giulia Zumbo, Daniel S Knight, Tushar Kotecha, Rohin Francis, David F Hutt, Tamer Rezk, Stefania Rosmini, Candida C Quarta, Carol J Whelan, Peter Kellman, Julian D Gillmore, James C Moon, Philip N Hawkins, Marianna Fontana
BACKGROUND: Cardiac transthyretin amyloidosis (ATTR) is an increasingly recognized cause of heart failure. Cardiac magnetic resonance (CMR), with late gadolinium enhancement (LGE) and T1 mapping, is emerging as a reference standard for diagnosis and characterization of cardiac amyloidosis. OBJECTIVES: The authors used CMR with extracellular volume fraction (ECV) measurement to characterize cardiac involvement in relation to outcome in ATTR. METHODS: Subjects comprised 263 patients with cardiac ATTR corroborated by grade 2 to 3 (99m)Tc-DPD ((99m)Tc-3,3-diphosphono-1,2-propanodicarboxylic acid) cardiac uptake, 17 with suspected cardiac ATTR (grade 1 (99m)Tc-DPD), and 12 asymptomatic individuals with amyloidogenic transthyretin (TTR) mutations...
July 25, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28709282/hybrid-smoothed-dissipative-particle-dynamics-and-immersed-boundary-method-for-simulation-of-red-blood-cells-in-flows
#17
Ting Ye, Nhan Phan-Thien, Chwee Teck Lim, Lina Peng, Huixin Shi
In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. The smoothed dissipative particle dynamics (SDPD), a particle-based method, is one of the easy and flexible methods to model such complex structure fluids. It couples the best features of the smoothed particle hydrodynamics (SPH) and dissipative particle dynamics (DPD), with parameters having specific physical meaning (coming from SPH discretization of the Navier-Stokes equations), combined with thermal fluctuations in a mesoscale simulation, in a similar manner to the DPD...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28689756/sensorimotor-gating-characteristics-of-violent-men-with-comorbid-psychosis-and-dissocial-personality-disorder-relationship-with-antisocial-traits-and-psychosocial-deprivation
#18
Ottilie Sedgwick, Susan Young, Ben Greer, Jack Arnold, Aisling Parsons, Ignazio Puzzo, Mariafatima Terracciano, Mrigendra Das, Veena Kumari
Evidence suggests violence amongst those with psychosis is not aetiologically homogeneous, and that a large proportion of those who engage in violent behaviour have a comorbid antisocial personality disorder. Initial investigations indicate that this subgroup has distinct historical and neuropsychological characteristics, which may indicate diverse treatment needs. This study investigated sensorimotor gating characteristics of violent men with diagnoses of both psychosis and dissocial personality disorder (DPD) (n=21) relative to violent men with psychosis alone (n=12), DPD alone (n=14) and healthy, non-violent male controls (n=27), using the prepulse inhibition (PPI) paradigm...
July 6, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28670884/low-incidence-of-the-dpd-ivs14-1g-a-polymorphism-in-jordanian-breast-and-colorectal-cancer-patients
#19
Mohammad Al-Khateeb, Abdalla Awidi, Kamal Al-Hadidi, Abdelkader Battah
Background: Dihydropyrimidine dehydrogenase (DPD) is a crucial enzyme in the catabolism of 5-fluorouracil (5-FU), a drug that is frequently used in cancer therapy. Patients with deficient DPD activity are at risk of developing severe 5-FU–associated toxicity. One possible cause of deficiency is genetic polymorphisms in the DPD gene, such as IVS14+1G>A. Aim: The present study was conducted to screen for the IVS14+1G>A polymorphism in cancer patients receiving 5-FU and a control group. Methods: A total of 40 cancer patients (30 colorectal cancer (CRC) and 10 breast cancer patients) were enrolled in this study...
June 25, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28669715/lead-substances-selection-using-ghs-approach-for-the-classification-of-mixtures-case-study-of-painting-in-the-work-environment
#20
Kazuhiro Kaneko, Satoko Ishii, Sachio Hosohara, Tsuyoshi Hirata, Motoshi Masuda, Kaori Murasawa, Airi Yamada, Takaaki Tadokoro, Masahiko Hanzawa
We developed a lead substances selection approach based on the concept of mixture classification of UN GHS for the purpose of efficient risk assessment of mixtures consisting of multiple components. Lead substances selection methods are being actively developed in Europe, but these methods are predicated on the regulations and information sources available within Europe and are therefore not readily applicable to countries outside Europe. In this study, the features of the GHS-based approach and the risk assessment results for outdoor painting work as a specific utilization example of the GHS-based approach were described...
June 29, 2017: Regulatory Toxicology and Pharmacology: RTP
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