Weighted persistent homology for biomolecular data analysis

In this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be assigned to vertices (atom centers), edges (bonds), or higher order simplexes (cluster of atoms), depending on the biomolecular structure, function, and dynamics properties. Further, we propose the first localized weighted persistent homology (LWPH). Inspired by the great success of element specific persistent homology (ESPH), we do not treat biomolecules as an inseparable system like all previous weighted models, instead we decompose them into a series of local domains, which may be overlapped with each other. The general persistent homology or weighted persistent homology analysis is then applied on each of these local domains. In this way, functional properties, that are embedded in local structures, can be revealed. Our model has been applied to systematically studying DNA structures. It has been found that our LWPH based features can be used to successfully discriminate the A-, B-, and Z-types of DNA. More importantly, our LWPH based PCA model can identify two configurational states of DNA structure in ion liquid environment, which can be revealed only by the complicated helical coordinate system. The great consistence with the helical-coordinate model demonstrates that our model captures local structure variations so well that it is comparable with geometric models. Moreover, geometric measurements are usually defined in very local regions. For instance, the helical-coordinate system is limited to one or two basepairs. However, our LWPH can quantitatively characterize structure information in local regions or domains with arbitrary sizes and shapes, where traditional geometrical measurements fail.Comment: 27 pages; 18 figure

Avalanche dynamics in Bak-Sneppen evolution model observed with standard distribution width of fitness

We introduce the standard distribution width of fitness to characterize the global and individual features of a ecosystem in the Bak-Sneppen evolution model. Through tracking this quantity in evolution, a different hierarchy of avalanche dynamics, $w_{0}$ avalanche is observed. The corresponding gap equation and the self-organized threshold $w_{c}$ are obtained. The critical exponents $\tau ,$ $\gamma$and $\rho$, which describe the behavior of the avalanche size distribution, the average avalanche size and the relaxation to attractor, respectively, are calculated with numerical simulation. The exact master equation and $\gamma$ equation are derived. And the scaling relations are established among the critical exponents of this new avalanche.Comment: 14 pages, 3 figure

Can springs cut canyons into rock?

Amphitheater-headed valleys on Earth and Mars are often assumed to result from erosion by emerging spring water (i.e., seepage erosion or groundwater sapping) rather than by surface runoff. The origin of such valleys has implications for landscape evolution on Earth and the hydrologic cycle and associated potential for life on other planets. In this paper we explore the evidence for seepage erosion in bedrock to address whether valley morphology can be used as a diagnostic indicator of seepage erosion. Seepage erosion is an important process in loose sediment where hydraulic forces cause grain detachment, often resulting in amphitheater-headed valleys. However, the extension of these processes to resistant rock is uncertain. In sedimentary rocks, groundwater might control the shape and rate of valley formation. It is possible, however, that seepage plays only a secondary role to runoff processes. This seems likely in basaltic valleys on Earth, where little evidence exists for seepage erosion. Since the ability of seepage to erode bedrock valleys remains unclear and because many amphitheater-headed valleys were probably carved by other processes, seepage erosion should not be inferred based solely on valley form

An interferometric complementarity experiment in a bulk Nuclear Magnetic Resonance ensemble

We have experimentally demonstrated the interferometric complementarity, which relates the distinguishability $D$ quantifying the amount of which-way (WW) information to the fringe visibility $V$ characterizing the wave feature of a quantum entity, in a bulk ensemble by Nuclear Magnetic Resonance (NMR) techniques. We primarily concern on the intermediate cases: partial fringe visibility and incomplete WW information. We propose a quantitative measure of $D$ by an alternative geometric strategy and investigate the relation between $D$ and entanglement. By measuring $D$ and $V$ independently, it turns out that the duality relation $D^{2}+V^{2}=1$ holds for pure quantum states of the markers.Comment: 13 page, 5 PS figure

Comparison of patients undergoing switching versus augmentation of antipsychotic medications during treatment for schizophrenia

It is often difficult to determine whether a patient may best benefit by augmenting their current medication or switching them to another. This post-hoc analysis compares patients’ clinical and functional profiles at the time their antipsychotic medications were either switched or augmented. Adult outpatients receiving oral antipsychotic treatment for schizophrenia were assessed during a 12-month international observational study. Clinical and functional measures were assessed at the time of first treatment switch/augmentation (0–14 days prior) and compared between Switched and Augmented patient groups. Due to low numbers of patients providing such data, interpretations are based on effect sizes. Data at the time of change were available for 87 patients: 53 Switched and 34 Augmented. Inadequate response was the primary reason for treatment change in both groups, whereas lack of adherence was more prevalent in the Switched group (26.4% vs 8.8%). Changes in clinical severity from study initiation to medication change were similar, as indicated by Clinical Global Impressions–Severity scores. However, physical and mental component scores of the 12-item Short-Form Health Survey improved in the Augmented group, but worsened in the Switched group. These findings suggest that the patient’s worsening or lack of meaningful improvement prompts clinicians to switch antipsychotic medications, whereas when patients show some improvement, clinicians may be more likely to try bolstering the improvements through augmentation. Current findings are consistent with physicians’ stated reasons for switching versus augmenting antipsychotics in the treatment of schizophrenia. Confirmation of these findings requires further research

Experimental Implementation of Hogg's Algorithm on a Three-Quantum-bit NMR Quantum Computer

Using nuclear magnetic resonance (NMR) techniques with three-qubit sample, we have experimentally implemented the highly structured algorithm for the 1-SAT problem proposed by Hogg. A simplified temporal averaging procedure was employed to the three-qubit spin pseudo-pure state. The algorithm was completed with only a single evaluation of structure of the problem and the solutions were found with probability 100%, which outperform both unstructured quantum and the best classical search algorithm.Comment: Revtex, 14 pages and 1 table, 4 EPS figure

Evaluation of the impact of the voucher and accreditation approach on improving reproductive behaviors and status in Cambodia

Background: Cost of delivering reproductive health services to low-income populations will always require total or partial subsidization by government and/or development partners. Broadly termed “demand-side financing” or “output-based aid,” these strategies include a range of interventions that channel government or donor subsidies to the user rather than the service provider. Initial pilot assessments of reproductive health voucher programs suggest that they can increase access, reduce inequities, and enhance program efficiency and service quality. However, there is a paucity of evidence describing how these programs function in different settings for various reproductive health services. Methods/Design: Population Council, funded by the Bill and Melinda Gates Foundation, intends to generate evidence around the “voucher and accreditation” approaches to improving the reproductive health of low-income women in Cambodia. The study comprises four populations: facilities, providers, women of reproductive age using facilities, and women and men who have been pregnant and/or used family planning within the previous 12 months. The study will be carried out in a sample of 20 health facilities that are accredited to provide maternal and newborn health and family planning services to women holding vouchers from operational districts in three provinces: Kampong Thom, Kampot, and Prey Veng and a matched sample of non-accredited facilities in three other provinces. Health facility assessments will be conducted at baseline and endline to track temporal changes in quality of care, client out-of-pocket costs, and utilization. Facility inventories, structured observations, and client exit interviews will be used to collect comparable data across facilities. Health providers will also be interviewed and observed providing care. A population survey of about 3,000 respondents will also be conducted in areas where vouchers are distributed and similar non-voucher locations. Discussion: A quasi-experimental study will investigate the impact of the voucher approach on improving reproductive health behaviors, reproductive health status, and reducing inequities at the population level and assess effects on access, equity, and quality of care at the facility level. If the voucher scheme in Cambodia is found effective, it may help other countries adopt this approach for improving utilization and access to reproductive health and family planning services