Quantitative Biology

To analyze the bacteriostatic effect of Chinese traditional herbal medicines on E. coli, total 35 different preparations (decoction, volatile oil and distillate) of Chinese traditional herbal medicines were tested using plate culture method. The results showed that 18 preparations of traditional Chinese herbal medicines have different inhibition effect on E. coli in vitro. The results also revealed that different process and combination affect the bacteriostatic effect and different medicines could be used in singles or combined to treat E.coli disease

Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic material that exist in all breathingcreatures. This biomolecule (DNA) comprehends the genetic material obligatory for the operational and expansion of all personified lives. To save DNA data of single person we require 10CD-ROMs.Moreover, this size is increasing constantly, and more and more sequences are adding in the public databases. This abundant increase in the sequence data arise challenges in the precise information extraction from this data. Since many data analyzing and visualization tools do not support processing of this huge amount of data. To reduce the size of DNA and protein sequence, many scientists introduced various types of sequence compression algorithms such as compress or gzip, Context Tree Weighting (CTW), Lampel Ziv Welch (LZW), arithmetic coding, run-length encoding and substitution method etc. These techniques have sufficiently contributed to minimizing the volume of the biological datasets. On the other hand, traditional compression techniques are also not much suitable for the compression of these types of sequential data. In this paper, we have explored diverse types of techniques for compression of large amounts of DNA Sequence Data. In this paper, the analysis of techniques reveals that efficient techniques not only reduce the size of the sequence but also avoid any information loss. The review of existing studies also shows that compression of a DNA sequence is significant for understanding the critical characteristics of DNA data in addition to improving storage efficiency and data transmission. In addition, the compression of the protein sequence is a challenge for the research community. The major parameters for evaluation of these compression algorithms include compression ratio, running time complexity etc.

Purpose: To explore the issue of counterintuitive data via analysis of a representative case and further discussion of those situations in which the data appear to be inconsistent with current knowledge. Case: 844 postoperative CABG patients, who were extubated within 24 hours of surgery were identified in a critical care database (MIMIC-III). Nurse elicited pain scores were documented throughout their hospital stay on a scale of 0 to 10. Levels were tracked as mean, median, and maximum values, and categorized as no (0/10), mild (1-3), moderate (4-6) and severe pain (7-10). Regression analysis was employed to analyze the relationship between pain scores and outcomes of interest (mortality and hospital LOS). After covariate adjustment, increased levels of pain were found to be associated with lower mortality rates and reduced hospital LOS. Conclusion: These counterintuitive results for post-CABG pain related outcomes have not been previously reported. While not representing strong enough evidence to alter clinical practice, confirmed and reliable results such as these should serve as a research trigger and prompt further studies into unexpected associations between pain and patient outcomes. With the advent of frequent secondary analysis of electronic health records, such counterintuitive data results are likely to become more frequent. We discuss the issue of counterintuitive data in extended fashion, including possible reasons for, and approaches to, this phenomenon.

Here we develop an approach to bio-structural robustness integrated with structure-function relationship in a unified conceptual and methodological framework, and envision its study using adequate computational and experimental methods. To distinguish this structural robustness from the abstract organizational robustness of systems, we call it anapedesis, and define it as the scale-independent property of biological objects, from biomolecules to organisms, to deform and recover while minimizing and/or repairing the damage produced by stretch. We propose to study the consequences of deformation of biological objects closer to their structural and/or functional failure than previously considered relevant. We show that structural robustness is present as a basic principle in many facets of biomedicine: many pathological conditions may derive from the failure of molecules, cells and their higher-order assemblies to maintain robustness against deformation. Furthermore, structural robustness could have been the key selective criterion during pre-biotic evolution and afterwards, and its universality can be demonstrated by modeling using genetic algorithms. Thus, the specific investigation of bio-structural robustness as anapedesis could help the solving of fundamental problems of biology and medicine.

The discovery of past spikes in atmospheric radiocarbon activity, caused by major solar energetic particle events, has opened up new possibilities for high-precision chronometry. The two spikes, or Miyake Events, have now been widely identified in tree-rings that grew in the years 775 and 994 CE. Furthermore, all other plant material that grew in these years would also have incorporated the anomalously high concentrations of radiocarbon. Crucially, some plant-based artefacts, such as papyrus documents, timber beams and linen garments, can also be allocated to specific positions within long, currently unfixed, historical sequences. Thus, Miyake Events represent a new source of tie-points that could provide the means for anchoring early chronologies to the absolute timescale. Here, we explore this possibility, outlining the most expeditious approaches, the current challenges and obstacles, and how they might best be overcome.

In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some pos- sible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover (PP) (Charadrius melodus) and Red Knot (RK) (Calidris canutus). To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed ap- peared quite different. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species.

The plants, Althaea officinalis, Tilia cordata and Psidium guaja have been used traditionally to treat respiratory infection symptoms. Flowers of A. officinalis and leaves of T. cordata and P. guaja have been used to treat cough, sore throat, catarrh, oral and pharyngeal mucosa irritation. Therefore, this study was designed to examine the antibacterial and antibiofilm effects of these plants individually as well as in combination, as a formula against respiratory infections causing pathogens. The tested pathogens were Extended Spectrum Beta-Lactamase producing Escherichia coli (ESBL), Beta-Lactamase producing Escherichia coli (BL), Beta-Lactamase producing Klebsiella pneumoniae (BL), Beta-Lactamase producing Pseudomonas aeruginosa (BL), Enterobacter cloacae, and Beta-Lactamase producing Staphylococcus aureus (BL). The tested plants were extracted using ethanol and then fractionated using different polarity solvents (hexane, ethyl acetate and water). Disc diffusion and microdilution (Minimum Inhibitory Concentration) methods were used to evaluate the antibacterial activity while the antibiofilm activity was tested using crystal violet assay. The results showed that A. officinalis and T. cordata extracts and fractions exhibited weak antibacterial activity having MIC values ranged from 6.25 to 12.5 mg/mL. P. guaja exhibited moderate antibacterial activity with MIC values ranged from 6.25 to 1.56 mg/mL. Combination between these plants extracts and fractions in equal proportion provides stronger antibacterial (with MIC values ranged from 6.25 to 0.8 mg/mL) and antibiofilm activities (MBIC50 was 0.2 mg/mL). Therefore, this study provides a valuable scientific knowledge to support the use of plants in combination rather than individually.

Bacopa monnieri was also known as Brahmi. Theses plant has been considered as medicinal plants in Ayurvedic systems for centuries. This present study was carried out to evaluate the antibacterial and antifungal properties of ethanolic, diethyl ether, ethyl acetate, and aqueous extracts of B. monnieri. Agar disc diffusion tests were carried out to determine the antimicrobial effects of ethanolic, diethyl ether, ethyl acetate and aqueous extracts of B. monnieri against Gram-positive (Staphylococcus aureus ATCC 25923), Gram-negative (Escherichia coli ATCC 25922) bacterial strains and antifungal strains (Aspergillus flavus, and Candida albicans). Among the various extracts, diethyl ether extracts of B. monnieri has an antibacterial potency against Staphylococcus aureus (gram positive), and ethyl acetate extract showed effects on E. coli (gram negative) at higher concentrations of 300 microgam mL-1. The ethanolic extract has potent antifungal activity against the fungus (Aspergillus flavus, and Candida albicans) compared to diethyl ether and ethyl acetate-ether. Both extracts (diethyl ether and ethyl acetate) has a minimum antifungal effect while these extracts showed more inhibitory effects on tested bacteria. Inhibitory effects of the aqueous extract were not observed at all concentration (100 microgam mL-1, 200 microgam mL-1and 300 microgam mL-1) against the entire examined bacterial and fungal species. The finding of this study indicates the antibacterial and antifungal activity exhibited by the ethanolic, diethyl ether, and ethyl acetate extract of B. monnieri can be validated to the management of medicinal plant throughout the world.

It is well known that psychoemotional disorders may be accompanied by decreased sociability in humans. It has been shown that repeated social defeats in 10 daily agonistic interactions in male mice led to development of the expressed level of anxiety and to reduction of communication estimated in the elevated plus-maze and partition tests, respectively. In the social interactions test, sociable behavior toward unfamiliar partner and exploratory activity were dramatically decreased in defeated male mice. Avoidance of approaching partner was significantly increased. Demonstration of self-grooming behavior was increased in defeated males. Chronic diazepam treatment (0.5 mg/kg, i.p., 2 weeks) led to significant decrease of anxiety level estimated in the elevated plus maze test and to improvement of communication in the partition test. In the social interaction test diazepam completely restored the level of sociability and exploratory activity and reduced avoidance behavior of approaching partner. Diazepam did not affect self-grooming demonstration. It is concluded that main factor which provokes decrease in communication in defeated male mice is the high level of anxiety. Similarity between changes in social behavior in defeated mice and symptoms of autism in humans is discussed. It is supposed that this behavioral approach may be useful for studying the molecular mechanisms of autistic spectrum disorders, developing under chronic negative social experiences.

There are many functions which are continuous everywhere but non-differentiable at some or all points such functions are termed as unreachable functions. Graphs representing such unreachable functions are called unreachable graphs. For example, ECG is such an unreachable graph. Classical calculus fails in their characterization as derivatives do not exist at the unreachable points. Such unreachable functions can be characterized by fractional calculus as fractional derivatives exist at those unreachable points where classical derivatives do not exist. Definition of fractional derivatives has been proposed by several mathematicians like Grunwald-Letinikov, Riemann-Liouville, Caputo, and Jumarie to develop the theory of fractional calculus. In this paper, we have used Jumarie type fractional derivative and consequently the phase transition (P.T.) which is the difference between left fractional derivative and right fractional derivatives to characterize those points. A comparative study has been done between normal ECG sample and problematic ECG sample (Right Ventricular Hypertrophy) by the help of the above mentioned mathematical tool.