Analysis of a competitive prey–predator system with a prey refuge

Gauss's competitive exclusive principle states that two competing species having analogous environment cannot usually occupy the same space at a time but in order to exploit their common environment in a different manner, they can co-exist only when they are active in different times. On the other hand, several studies on predators in various natural and laboratory situations have shown that competitive coexistence can result from predation in a way by resisting any one prey species from becoming sufficiently abundant to outcompete other species such that the predator makes the coexistence possible. It has also been shown that the use of refuges by a fraction of the prey population exerts a stabilizing effect in the interacting population dynamics. Further, the field surveys in the Sundarban mangrove ecosystem reveal that two detritivorous fishes, viz. Liza parsia and Liza tade (prey population) coexist in nature with the presence of the predator fish population, viz. Lates calcarifer by using refuges.     

Parametric Analysis of a Predator–prey System Stabilized by a Top Predator

We present a complete parametric analysis of a predator–prey system influenced by a top predator. We study ecosystems with abundant nutrient supply for the prey where the prey multiplication can be considered as proportional to its density. The main questions we examine are the following: (1) Can the top predator stabilize such a system at low densities of prey? (2) What possible dynamic behaviors can occur? (3) Under which conditions can the top predation result in the system stabilization? We use a system of two nonlinear ordinary differential equations with the density of the top predator as a parameter. The model is investigated with methods of qualitative theory of ODEs and the theory of bifurcations. The existence of 12 qualitatively different types of dynamics and complex structure of the parametric space are demonstrated. Our studies of phase portraits and parametric diagrams show that a top predator can be an important factor leading to stabilization of the predator-prey system with abundant nutrient supply. Although the model here is applied to the plankton communities with fish (or carnivorous zooplankton) as the top trophic level, the general form of the equations allows applications of our results to other ecological systems.     

ABRF-ESRG’03: Analysis of a PVDF-Bound Known Protein with a Homogeneous Amino-Terminus

The Association of Biomolecular Resource Facilities 2003 Edman Sequencing Research Group (ABRF-ESRG’03) sample is the 15th in a series of studies designed to allow participating members to evaluate their abilities to analyze the N-terminus of a protein or peptide using automated Edman degradation chemistry. It is a follow-up study to the ESRG’02 sample, which was a single protein with a heterogeneous N-terminus. Both the 2002 and 2003 samples were obtained from the same protein complex and were resolved by SDS-PAGE followed by electrophoretic transfer to PVDF membrane. The ABRF-ESRG’03 sample had an apparent molecular weight of 49 kDa and a single N-terminus, with initial yields of approximately 2 pmol. Participants were asked to sequence 25 residues and return their results to the ESRG for analysis along with two completed surveys and an area/pmol table for repetitive and initial yield calculations. Data for 46 responses are presented which include initial yields, repetitive yields, sequencer performance, and ability to identify the protein.     

Chemical Analysis of a “Miller-Type” Complex Prebiotic Broth

We have analyzed the chemical variety obtained by Miller-Urey-type experiments using nuclear magnetic resonance (NMR) spectroscopy and coherent anti-Stokes Raman scattering (CARS) spectroscopy, gas chromatography followed by mass spectrometry (GC/MS) and two-dimensional gas chromatography followed by mass spectrometry (GCxGC/MS). In the course of a running Miller-Urey-type experiment, a hydrophobic organic layer emerged besides the hydrophilic aqueous phase and the gaseous phase that were initially present. The gas phase mainly consisted of aromatic compounds and molecules containing C≡C?or?C≡N triple bonds. The hydrophilic phase contained at least a few thousands of different molecules, primarily distributed in a range of 50 and 500 Da. The hydrophobic phase is characterized by carbon-rich, oil-like compounds and their amphiphilic derivatives containing oxygen with tensioactive properties. The presence of a wide range of oxidized molecules hints to the availability of oxygen radicals. We suggest that they intervene in the formation of alkylated polyethylene glycol (PEG) in the oil/water interface. CARS spectroscopy revealed distinct vibrational molecular signatures. In particular, characteristic spectral bands for cyanide compounds were observed if the broth was prepared with electric discharges in the gaseous phase. The characteristic spectral bands were absent if discharges were released onto the water surface. NMR spectroscopy on the same set of samples independently confirmed the observation. In addition, NMR spectroscopy revealed overall high chemical variability that suggests strong non-linearities due to interdependent, sequential reaction steps.     

Chemical Analysis of a “Miller-Type” Complex Prebiotic Broth

In a famous experiment Stanley Miller showed that a large number of organic substances can emerge from sparking a mixture of methane, ammonia and hydrogen in the presence of water (Miller, Science 117:528–529, 1953). Among these substances Miller identified different amino acids, and he concluded that prebiotic events may well have produced many of Life’s molecular building blocks. There have been many variants of the original experiment since, including different gas mixtures (Miller, J Am Chem Soc 77:2351–2361, 1955; Oró Nature 197:862–867, 1963; Schlesinger and Miller, J Mol Evol 19:376–382, 1983; Miyakawa et al., Proc Natl Acad Sci 99:14,628–14,631, 2002). Recently some of Miller’s remaining original samples were analyzed with modern equipment (Johnson et al. Science 322:404–404, 2008; Parker et al. Proc Natl Acad Sci 108:5526–5531, 2011) and a total of 23 racemic amino acids were identified. To give an overview of the chemical variety of a possible prebiotic broth, here we analyze a “Miller type” experiment using state of the art mass spectrometry and NMR spectroscopy. We identify substances of a wide range of saturation, which can be hydrophilic, hydrophobic or amphiphilic in nature. Often the molecules contain heteroatoms, with amines and amides being prominent classes of molecule. In some samples we detect ethylene glycol based polymers. Their formation in water requires the presence of a catalyst. Contrary to expectations, we cannot identify any preferred reaction product. The capacity to spontaneously produce this extremely high degree of molecular variety in a very simple experiment is a remarkable feature of organic chemistry and possibly prerequisite for Life to emerge. It remains a future task to uncover how dedicated, organized chemical reaction pathways may have arisen from this degree of complexity.     

What's in a crowd? Analysis of face-to-face behavioral networks

The availability of new data sources on human mobility is opening new avenues for investigating the interplay of social networks, human mobility and dynamical processes such as epidemic spreading. Here we analyze data on the time-resolved face-to-face proximity of individuals in large-scale real-world scenarios. We compare two settings with very different properties, a scientific conference and a long-running museum exhibition. We track the behavioral networks of face-to-face proximity, and characterize them from both a static and a dynamic point of view, exposing differences and similarities. We use our data to investigate the dynamics of a susceptible-infected model for epidemic spreading that unfolds on the dynamical networks of human proximity. The spreading patterns are markedly different for the conference and the museum case, and they are strongly impacted by the causal structure of the network data. A deeper study of the spreading paths shows that the mere knowledge of static aggregated networks would lead to erroneous conclusions about the transmission paths on the dynamical networks.     

Longitudinal Data Analysis with Event Time as a Covariate

We consider the estimation of a nonparametric smooth function of some event time in a semiparametric mixed effects model from repeatedly measured data when the event time is subject to right censoring. The within-subject correlation is captured by both cross-sectional and time-dependent random effects, where the latter is modeled by a nonhomogeneous Ornstein–Uhlenbeck stochastic process. When the censoring probability depends on other variables in the model, which often happens in practice, the event time data are not missing completely at random. Hence, the complete case analysis by eliminating all the censored observations may yield biased estimates of the regression parameters including the smooth function of the event time, and is less efficient. To remedy, we derive the likelihood function for the observed data by modeling the event time distribution given other covariates. We propose a two-stage pseudo-likelihood approach for the estimation of model parameters by first plugging an estimator of the conditional event time distribution into the likelihood and then maximizing the resulting pseudo-likelihood function. Empirical evaluation shows that the proposed method yields negligible biases while significantly reduces the estimation variability. This research is motivated by the project of hormone profile estimation around age at the final menstrual period for the cohort of women in the Michigan Bone Health and Metabolism Study.     

Analysis of Phaseolus–Rhizobium interactions in a subsistence farming system

Poor bean yields in the Cunha region of the Mata Atlântica ecosystem in the state of São Paulo, Brazil, are associated with low agronomic inputs, plant disease, and soil erosion. To identify sustainable farming practices that increase production and maximize biological N2 fixation (BNF), the effects of soil fertility and plant cultivar on seed yield and root nodule formation were measured under standard agronomic practices. Results from 16 sites showed that fertilizing with lime and molybdenum increased seed yields to 370% for the landrace Serro Azul. In addition to increased yields, plants grown with fertilizer had more nodules. Marked strains of Rhizobium tropici were tested under controlled environments. An indicator strain of Rhizobium containing the gusA marker gene was used. Our results verify that the indicator strain CM-255 GusA+Hup+ had a high capacity to associate with the five bean varieties tested. Fertilization with P, K, S + micronutrients and liming were essential for better nodulation by the indicator strain. Under low fertility conditions, the landrace variety Serro Azul was poorly nodulated, when associated with native strains or with the indicator strain. However, under better soil fertility conditions, nodulation of Serro Azul by the marked Rhizobium strain was increased. The commercial variety Carioca 80SH showed no increase in nodulation (nodule number).     

Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster

SUMMARY The Hox gene cluster is renowned for its role in developmental patterning of embryogenesis along the anterior–posterior axis of bilaterians. Its supposed evolutionary sister or paralog, the ParaHox cluster, is composed of Gsx, Xlox, and Cdx, and also has important roles in anterior–posterior development. There is a debate as to whether the cnidarians, as an outgroup to bilaterians, contain true Hox and ParaHox genes, or instead the Hox‐like gene complement of cnidarians arose from independent duplications to those that generated the genes of the bilaterian Hox and ParaHox clusters. A recent whole genome analysis of the cnidarian Nematostella vectensis found conserved synteny between this cnidarian and vertebrates, including a region of synteny between the putative Hox cluster of N. vectensis and the Hox clusters of vertebrates. No syntenic region was identified around a potential cnidarian ParaHox cluster. Here we use different approaches to identify a genomic region in N. vectensis that is syntenic with the bilaterian ParaHox cluster. This proves that the duplication that gave rise to the Hox and ParaHox regions of bilaterians occurred before the origin of cnidarians, and the cnidarian N. vectensis has bona fide Hox and ParaHox loci.     

OPERATING ROOM DEATHS—An Analysis of Mortality in a Veterans Administration Hospital Over a Ten-Year Period

A study of operating room and recovery room deaths which occurred during a ten-year period from 1948 through 1957 at one hospital revealed that there were 59 deaths associated with 57,132 surgical procedures.Factors which directly influenced the rate of operating room and recovery room death were the age of the patient and the length of operating time. Seventy-five per cent of the deaths occurred in cases in which the operation took longer than one hour. Combined anesthesia techniques may have indirectly contributed to death in some cases.Complications of operation requiring another surgical procedure sometimes occur. In this series, reoperation proved to be more hazardous in terms of mortality rate than did single operations. This is not surprising for most complications occur in the poorer risk patients.The operating room death rate steadily increased during the ten-year period studied. This increasing death rate can largely be attributed to the more intricate operations which are being done on poorer risk patients. The use of the curariform drugs had no influence on the increasing death rate.     

Biochemical Analysis of a β-d-Xylosidase and a Bifunctional Xylanase-Ferulic Acid Esterase from a Xylanolytic Gene Cluster in Prevotella ruminicola 23

Prevotella ruminicola 23 is an obligate anaerobic bacterium in the phylum Bacteroidetes that contributes to hemicellulose utilization within the bovine rumen. To gain insight into the cellular machinery that this organism elaborates to degrade the hemicellulosic polymer xylan, we identified and cloned a gene predicted to encode a bifunctional xylanase-ferulic acid esterase (xyn10D-fae1A) and expressed the recombinant protein in Escherichia coli. Biochemical analysis of purified Xyn10D-Fae1A revealed that this protein possesses both endo-β-1,4-xylanase and ferulic acid esterase activities. A putative glycoside hydrolase (GH) family 3 β-d-glucosidase gene, with a novel PA14-like insertion sequence, was identified two genes downstream of xyn10D-fae1A. Biochemical analyses of the purified recombinant protein revealed that the putative β-d-glucosidase has activity for pNP-β-d-xylopyranoside, pNP-α-l-arabinofuranoside, and xylo-oligosaccharides; thus, the gene was designated xyl3A. When incubated in combination with Xyn10D-Fae1A, Xyl3A improved the release of xylose monomers from a hemicellulosic xylan substrate, suggesting that these two enzymes function synergistically to depolymerize xylan. Directed mutagenesis studies of Xyn10D-Fae1A mapped the catalytic sites for the two enzymatic functionalities to distinct regions within the polypeptide sequence. When a mutation was introduced into the putative catalytic site for the xylanase domain (E280S), the ferulic acid esterase activity increased threefold, which suggests that the two catalytic domains for Xyn10D-Fae1A are functionally coupled. Directed mutagenesis of conserved residues for Xyl3A resulted in attenuation of activity, which supports the assignment of Xyl3A as a GH family 3 β-d-xylosidase.β-1,4-linked xylopyranose is the principal component of plant cell wall hemicellulose, which represents the second largest reservoir of fixed carbon in the biosphere (11, 30, 34, 38, 42, 72). The catabolic breakdown of hemicellulose thus represents a critical step in the recycling of carbon in nature and has been targeted as a subject of intense research with respect to renewable energy resources. Two enzymes of principal importance for recycling hemicellulosic material are endo-1,4-β-xylanases (EC 3.2.1.8), which cleave the xylan backbone, and β-d-xylosidases (EC 3.2.1.37), which cleave xylose monomers from the nonreducing end of xylo-oligosaccharides (17).Prevotella ruminicola 23 is an important member of the anaerobic rumen microbiota (60) that contributes to the utilization of noncellulosic polysaccharides, such as starch and xylan (15, 25, 35, 55). Despite its documented importance in rumen physiology, relatively little is known about the cellular machinery that P. ruminicola 23 employs to harvest energy from hemicellulosic substrates. Several studies have explored the carbohydrate active enzymes from the related taxon Prevotella bryantii B₁4 (previously classified as P. ruminicola B₁4) (25, 27, 28, 50, 52, 66, 73); however, less is known about the xylanolytic system that P. ruminicola 23 elaborates. These two species share 88.9% nucleotide identity in their 16S rRNA genes (1,473 nucleotides aligned); however, there is evidence that these two species exhibit differences in their xylanolytic systems (2). Two xylanases from P. ruminicola 23 have been characterized: a 66-kDa xylanase with significant sequence identity to glycoside hydrolase (GH) family 5 endoglucanases (69, 70) and an 80-kDa xylanase related to GH family 10 endoxylanases which possesses a 260-amino-acid insertion within the putative catalytic domain (25). Recently, the draft genome sequence for P. ruminicola 23 has been obtained (http://www.tigr.org/tdb/rumenomics/), and a large number of GHs have been identified. Consistent with the predicted role of P. ruminicola 23 in hemicellulose degradation, many of these genes appear to encode enzymes important for hemicellulose depolymerization and utilization.In this study, we report the biochemical properties for two GHs with unique domain architectures from P. ruminicola 23. These two enzymes function synergistically to release monomeric sugars from a complex hemicellulosic substrate, xylan. This study, therefore, provides important insight into the molecular strategies for xylan depolymerization by P. ruminicola 23.     

Has Large-Scale Named-Entity Network Analysis Been Resting on a Flawed Assumption?

The assumption that a name uniquely identifies an entity introduces two types of errors: splitting treats one entity as two or more (because of name variants); lumping treats multiple entities as if they were one (because of shared names). Here we investigate the extent to which splitting and lumping affect commonly-used measures of large-scale named-entity networks within two disambiguated bibliographic datasets: one for co-author names in biomedicine (PubMed, 2003–2007); the other for co-inventor names in U.S. patents (USPTO, 2003–2007). In both cases, we find that splitting has relatively little effect, whereas lumping has a dramatic effect on network measures. For example, in the biomedical co-authorship network, lumping (based on last name and both initials) drives several measures down: the global clustering coefficient by a factor of 4 (from 0.265 to 0.066); degree assortativity by a factor of ∼13 (from 0.763 to 0.06); and average shortest path by a factor of 1.3 (from 5.9 to 4.5). These results can be explained in part by the fact that lumping artificially creates many intransitive relationships and high-degree vertices. This effect of lumping is much less dramatic but persists with measures that give less weight to high-degree vertices, such as the mean local clustering coefficient and log-based degree assortativity. Furthermore, the log-log distribution of collaborator counts follows a much straighter line (power law) with splitting and lumping errors than without, particularly at the low and the high counts. This suggests that part of the power law often observed for collaborator counts in science and technology reflects an artifact: name ambiguity.     

Decompressive Hemicraniectomy in a South American Population – Morbidity and Outcomes Analysis

Background

Malignant cerebral artery strokes have a poor prognosis, with nearly 80% of mortality in some series despite intensive care. After a large randomized trial, decompressive hemicraniectomy has been performed more often in stroke patients. Here, we describe patients in a tertiary teaching hospital in Brazil, emphasizing the impact of age on outcomes.

Methods

A retrospective cohort of patients, with malignant strokes which received a decompressive hemicraniectomy, from paper and electronic medical records, from January 2010 to December 2013 was divided into two groups according to age.

Results

The final analysis included 60 patients. The overall mortality was higher among patients older than 60 yrs (67% vs. 41%; p = 0.039), whose group also had a worse outcome (76% with mRS 5 or 6) at 90 days (OR 3.91 CI95% 1.30–11.74), whereas only 24% had mRS of 0–4 (p = 0.015). All patients who presented with sepsis died (p = 0.003). The incidence of pulmonary infection was very high in the elderly group (76%) with significant intergroup differences (p = 0.027, OR 8.32 CI95% 0.70–98.48).

Conclusions

Older patients present more commonly with infections, more disabilities and a higher mortality, highlighting very poor results in elderly population. These results should be proved with a South American trial, and if confirmed, it can impact on future decisions regarding decompressive craniectomy for acute ischemic stroke in our region.     

Cardiac Monitoring in a Community Hospital—Analysis of 18 Months' Experience

Cardiac monitoring facilities have been present in teaching hospital centers for over five years. A substantial decrease in mortality has been observed in monitored patients with acute myocardial infarction. The community hospital system offers a challenge to effective monitoring since many physicians care for patients and often many kinds of therapy are used.After 18 months of operation mortality from myocardial infarction was only 16.6 percent in a community hospital monitoring unit where the majority of the emergency care and resuscitation was carried out by nurses. Vital to this success was the use of standing orders for nurses, requirement of privilege to practice within the monitoring facility and acceptance of the nurse as a therapist in emergency situations.Fourteen patients were successfully resuscitated and were later discharged from the hospital. Four of them had ventricular fibrillation from digitalis intoxication.Patients with shock and severe congestive heart failure continue to be a major unsolved clinical problem. The results indicate that the potentially viable patient with serious electrical disturbances can almost invariably be salvaged.     

Network Analysis of a Comprehensive Knowledge Repository Reveals a Dual Role for Ceramide in Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common cause of senile dementia. Many inflammatory factors such as amyloid-β and pro-inflammatory cytokines are known to contribute to the inflammatory response in the AD brain. Sphingolipids are widely known to have roles in the pathogenesis of inflammatory diseases, where the precise roles for sphingolipids in inflammation-associated pathogenesis of AD are not well understood. Here we performed a network analysis to clarify the importance of sphingolipids and to model relationships among inflammatory factors and sphingolipids in AD. In this study, we have updated sphingolipid signaling and metabolic cascades in a map of AD signaling networks that we named “AlzPathway,” a comprehensive knowledge repository of signaling pathways in AD. Our network analysis of the updated AlzPathway indicates that the pathways related to ceramide are one of the primary pathways and that ceramide is one of the important players in the pathogenesis of AD. The results of our analysis suggest the following two prospects about inflammation in AD: (1) ceramide could play important roles in both inflammatory and anti-inflammatory pathways of AD, and (2) several factors such as Sphingomyelinase and Siglec-11 may be associated with ceramide related inflammation and anti-inflammation pathways in AD. In this study, network analysis of comprehensive knowledge repository reveals a dual role for ceramide in AD. This result provides a clue to clarify sphingolipids related inflammatory and anti-inflammatory pathways in AD.     

Got Milk? Breastfeeding and Milk Analysis of a Mother on Chronic Hemodialysis

Purpose

Women on dialysis rarely become pregnant. However, the overall rate of successful pregnancies is increasing in this patient population and breastfeeding becomes an option for mothers on dialysis. In this study we performed a systematic breast milk composition analysis of a mother on chronic hemodialysis (HD).

Methods

Specimens of breast milk and blood were collected in regular intervals before and after HD from a 39-year old woman starting on day 10 postpartum. Samples were analyzed for electrolytes, retention solutes, nutrients and other laboratory measurements. Breast milk samples from low-risk mothers matched for postpartum age were used as controls.

Results

Significantly higher levels of creatinine and urea were found in pre-HD breast milk when compared to post-HD. A similar post-dialytic decrease was only found for uric acid but not for any other investigated parameter. Conversely, sodium and chloride were significantly increased in post-HD samples. Compared to controls creatinine and urea were significantly higher in pre-HD samples while the difference remained only significant for post-HD creatinine. Phosphate was significantly lower in pre- and post-HD breast milk when compared to controls, whereas calcium showed no significant differences. In terms of nutrient components glucose levels showed a strong trend for a decrease, whereas protein, triglycerides and cholesterol did not differ. Similarly, no significant differences were found in iron, potassium and magnesium content.

Conclusion

To the best of our knowledge this is the first report on a breastfeeding mother on chronic dialysis. Although we found differences in creatinine, urea, sodium, chloride and phosphate, our general analysis showed high similarity of our patient’s breast milk to samples from low-risk control mothers. Significant variations in breast milk composition between pre- and post-HD samples suggest that breastfeeding might be preferably performed after dialysis treatment. In summary, our findings indicate that breastfeeding can be considered a viable option for newborns of mothers on dialysis.