2,717 research outputs found
Universal time-dependent deformations of Schrodinger geometry
We investigate universal time-dependent exact deformations of Schrodinger
geometry. We present 1) scale invariant but non-conformal deformation, 2)
non-conformal but scale invariant deformation, and 3) both scale and conformal
invariant deformation. All these solutions are universal in the sense that we
could embed them in any supergravity constructions of the Schrodinger invariant
geometry. We give a field theory interpretation of our time-dependent
solutions. In particular, we argue that any time-dependent chemical potential
can be treated exactly in our gravity dual approach.Comment: 24 pages, v2: references adde
Dense active matter model of motion patterns in confluent cell monolayers
Epithelial cell monolayers show remarkable displacement and velocity
correlations over distances of ten or more cell sizes that are reminiscent of
supercooled liquids and active nematics. We show that many observed features
can be described within the framework of dense active matter, and argue that
persistent uncoordinated cell motility coupled to the collective elastic modes
of the cell sheet is sufficient to produce swirl-like correlations. We obtain
this result using both continuum active linear elasticity and a normal modes
formalism, and validate analytical predictions with numerical simulations of
two agent-based cell models, soft elastic particles and the self-propelled
Voronoi model together with in-vitro experiments of confluent corneal
epithelial cell sheets. Simulations and normal mode analysis perfectly match
when tissue-level reorganisation occurs on times longer than the persistence
time of cell motility. Our analytical model quantitatively matches measured
velocity correlation functions over more than a decade with a single fitting
parameter.Comment: updated version accepted for publication in Nat. Com
Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes.
Background: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study, we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients and in combination with bioinformatics analysis to evaluate the utility of selected differentially expressed miRNAs in the serum as potential OA biomarkers. Methods: Serum samples were collected from 12 primary OA patients, and 12 healthy individuals were screened using the Agilent Human miRNA Microarray platform interrogating 2549 miRNAs. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs. Expression levels of selected miRNAs were validated by quantitative real-time PCR (qRT-PCR) in all serum and in articular cartilage samples from OA patients (n = 12) and healthy individuals (n = 7). Bioinformatics analysis was used to investigate the involved pathways and target genes for the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to controls. Two hundred and five miRNAs (73.5%) were upregulated and 74 (26.5%) downregulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC) > 0.8 and p < 0.05. Bioinformatics analysis in the 77 miRNAs revealed that their target genes were involved in multiple signaling pathways associated with OA, among which FoxO, mTOR, Wnt, pI3K/akt, TGF-β signaling pathways, ECM-receptor interaction, and fatty acid biosynthesis. qRT-PCR validation in seven selected out of the 77 miRNAs revealed 3 significantly downregulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p, and hsa-miR-140-3p) in the serum of OA patients, which were in silico predicted to be enriched in pathways involved in metabolic processes. Target-gene analysis of hsa-miR-140-3p, hsa-miR-33b-3p, and hsa-miR-671-3p revealed that InsR and IGFR1 were common targets of all three miRNAs, highlighting their involvement in regulation of metabolic processes that contribute to OA pathology. Hsa-miR-140-3p and hsa-miR-671-3p expression levels were consistently downregulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A serum miRNA signature was established for the first time using high density resolution miR-arrays in OA patients. We identified a three-miRNA signature, hsa-miR-140-3p, hsa-miR-671-3p, and hsa-miR-33b-3p, in the serum of OA patients, predicted to regulate metabolic processes, which could serve as a potential biomarker for the evaluation of OA risk and progression.Peer reviewedFinal Published versio
Magnetic structure and field-dependent magnetic phase diagram of Ni2In-type PrCuSi
The magnetic structure of the ternary equiatomic intermetallic compound PrCuSi is investigated using neutron powder diffraction experiments in 0 T as well as in external magnetic fields up to 2 T. The PrCuSi compound crystallizes in the hexagonal Ni2In-type structure, in the space group P63/mmc. In this structure, cationic ordering of Cu and Si takes place. The antiferromagnetic phase transition in the Pr sublattice takes place at K in 0 T. Under an external magnetic field of 2 T, a field-induced ferromagnetic phase is observed. Magnetoelastic coupling is evidenced by an increase in the unit cell volume. Clear signatures of a mixed antiferromagnetic and ferromagnetic phase in weak, intermediate fields, 0.4–0.8 T, are obtained from the present study. Using the present set of experimental data, we construct the H − T phase diagram of PrCuSi
Back reaction effects on the dynamics of heavy probes in heavy quark cloud
We holographically study the effect of back reaction on the hydrodynamical
properties of strongly coupled super Yang-Mills (SYM) thermal
plasma. The back reaction we consider arises from the presence of static heavy
quarks uniformly distributed over SYM plasma. In order to
study the hydrodynamical properties, we use heavy quark as well as heavy
quark-antiquark bound state as probes and compute the jet quenching parameter,
screening length and binding energy. We also consider the rotational dynamics
of heavy probe quark in the back-reacted plasma and analyse associated energy
loss. We observe that the presence of back reaction enhances the energy-loss in
the thermal plasma. Finally, we show that there is no effect of angular drag on
the rotational motion of quark-antiquark bound state probing the back reacted
thermal plasma.Comment: 29 pages, 21 figure
Global parameter estimation methods for stochastic biochemical systems
<p>Abstract</p> <p>Background</p> <p>The importance of stochasticity in cellular processes having low number of molecules has resulted in the development of stochastic models such as chemical master equation. As in other modelling frameworks, the accompanying rate constants are important for the end-applications like analyzing system properties (e.g. robustness) or predicting the effects of genetic perturbations. Prior knowledge of kinetic constants is usually limited and the model identification routine typically includes parameter estimation from experimental data. Although the subject of parameter estimation is well-established for deterministic models, it is not yet routine for the chemical master equation. In addition, recent advances in measurement technology have made the quantification of genetic substrates possible to single molecular levels. Thus, the purpose of this work is to develop practical and effective methods for estimating kinetic model parameters in the chemical master equation and other stochastic models from single cell and cell population experimental data.</p> <p>Results</p> <p>Three parameter estimation methods are proposed based on the maximum likelihood and density function distance, including probability and cumulative density functions. Since stochastic models such as chemical master equations are typically solved using a Monte Carlo approach in which only a finite number of Monte Carlo realizations are computationally practical, specific considerations are given to account for the effect of finite sampling in the histogram binning of the state density functions. Applications to three practical case studies showed that while maximum likelihood method can effectively handle low replicate measurements, the density function distance methods, particularly the cumulative density function distance estimation, are more robust in estimating the parameters with consistently higher accuracy, even for systems showing multimodality.</p> <p>Conclusions</p> <p>The parameter estimation methodologies described in this work have provided an effective and practical approach in the estimation of kinetic parameters of stochastic systems from either sparse or dense cell population data. Nevertheless, similar to kinetic parameter estimation in other modelling frameworks, not all parameters can be estimated accurately, which is a common problem arising from the lack of complete parameter identifiability from the available data.</p
A long-term survivor of repeated inguinal nodes recurrence of papillary serous adenocarcinoma of CUP: case report
BACKGROUND: Tumor spread beyond the peritoneal cavity in cases of papillary serous adenocarcinoma of the unknown primary (CUP) is a rare late event and carries a poor prognosis. CASE PRESENTATION: A 71-year-old female was referred to our hospital because of a large right inguinal tumor with biopsy evidence of carcinoma as well as an elevated serum CA125 (cancer antigen 125). She underwent complete resection of the right inguinal tumor and multiple pelvic tumors, which involved the rectum, ovary and uterus. Pathological examination revealed the tumors to be metastases of a papillary serous adenocarcinoma with a psammoma body of CUP. On the 28th postoperative day, newly developed asymptomatic small left inguinal node metastases in the setting of a normal CA125 level were removed. Four and a half years after the primary resection, the CA125 level increased again and newly developed asymptomatic metastases were found in the right deep inguinal nodes and extirpated at that time. All surgical resections followed the modified FAM (5FU, Adriamycin; ADM, MMC) regimen, including protracted dairy oral administration of UFT or 5'-FDUR, Cimetidine and PSK (protein-bound polysaccharide K) as an immunomodulator or biological response modifier in conjunction with intermittent one-day continuous infusion (ADM+MMC) or intermittent single bolus injection of ADM+MMC. At present, the patient has been living in good health for almost 7 years with no evidence of relapse. CONCLUSION: Aggressive resection surgery followed by effective adjuvant chemotherapy is necessary for surviving long time without relapse of poorly prognostic patients with metastases outside of the abdominal cavity from peritoneal papillary serous adenocarcinomas
Acidic preconditioning protects endothelial cells against apoptosis through p38- and Akt-dependent Bcl-xL overexpression
To analyze the underlying cellular mechanisms of adaptation to ischemia-induced apoptosis through short acidic pretreatment, i.e. acidic preconditioning (APC), Wistar rat coronary endothelial cells (EC) were exposed for 40 min to acidosis (pH 6.4) followed by a 14 h recovery period (pH 7.4) and finally treated for 2 h with simulated in vitro ischemia (glucose-free anoxia at pH 6.4). APC led to a transient activation of p38 and Akt kinases, but not of JNK and ERK1/2 kinases, which was accompanied by significant reduction of the apoptotic cell number, caspase-12/-3 cleavage and Bcl-xL overexpression. These effects of APC were completely abolished by prevention of Akt- or p38-phosphorylation during APC. Furthermore, knock-down of Bcl-xL by siRNA-transfection also abolished the anti-apoptotic effect of APC. Therefore, APC leads to protection of EC against ischemic apoptosis by activation of Akt and p38 followed by overexpression of Bcl-xL, which is a key anti-apoptotic mechanism of APC
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