A common neighbor based technique to detect protein complexes in PPI networks

Detection of protein complexes by analyzing and understanding PPI networks is an important task and critical to all aspects of cell biology. We present a technique called PROtein COmplex DEtection based on common neighborhood (PROCODE) that considers the inherent organization of protein complexes as well as the regions with heavy interactions in PPI networks to detect protein complexes. Initially, the core of the protein complexes is detected based on the neighborhood of PPI network. Then a merging strategy based on density is used to attach proteins and protein complexes to the core-protein complexes to form biologically meaningful structures. The predicted protein complexes of PROCODE was evaluated and analyzed using four PPI network datasets out of which three were from budding yeast and one from human. Our proposed technique is compared with some of the existing techniques using standard benchmark complexes and PROCODE was found to match very well with actual protein complexes in the benchmark data. The detected complexes were at par with existing biological evidence and knowledge.     

The severity of psychiatric disorders

The issue of the severity of psychiatric disorders has great clinical importance. For example, severity influences decisions about level of care, and affects decisions to seek government assistance due to psychiatric disability. Controversy exists as to the efficacy of antidepressants across the spectrum of depression severity, and whether patients with severe depression should be preferentially treated with medication rather than psychotherapy. Measures of severity are used to evaluate outcome in treatment studies and may be used as meaningful endpoints in clinical practice. But, what does it mean to say that someone has a severe illness? Does severity refer to the number of symptoms a patient is experiencing? To the intensity of the symptoms? To symptom frequency or persistence? To the impact of symptoms on functioning or on quality of life? To the likelihood of the illness resulting in permanent disability or death? Putting aside the issue of how severity should be operationalized, another consideration is whether severity should be conceptualized similarly for all illnesses or be disorder specific. In this paper, we examine how severity is characterized in research and contemporary psychiatric diagnostic systems, with a special focus on depression and personality disorders. Our review shows that the DSM‐5 has defined the severity of various disorders in different ways, and that researchers have adopted a myriad of ways of defining severity for both depression and personality disorders, although the severity of the former was predominantly defined according to scores on symptom rating scales, whereas the severity of the latter was often linked with impairments in functioning. Because the functional impact of symptom‐defined disorders depends on factors extrinsic to those disorders, such as self‐efficacy, resilience, coping ability, social support, cultural and social expectations, as well as the responsibilities related to one's primary role function and the availability of others to assume those responsibilities, we argue that the severity of such disorders should be defined independently from functional impairment.     

How Methylammonium Cations and Chlorine Dopants Heal Defects in Lead Iodide Perovskites

Lead tri‐iodide methylammonium (MAPbI₃) perovskite polycrystalline materials show complex optoelectronic behavior, largely because their 3D semiconducting inorganic framework is strongly perturbed by the organic cations and ubiquitous structural or chemical inhomogeneities. Here, a newly developed time‐dependent density functional theory‐based theoretical formalism is taken advantage of. It treats electron–hole and electron–nuclei interactions on the same footing to assess the many‐body excited states of MAPbI₃ perovskites in their pristine state and in the presence of point chemical defects. It is shown that lead and iodine vacancies yield deep trap states that can be healed by dynamic effects, namely rotation of the methylammonium cations in response to point charges, or through slight changes in chemical composition, namely by introducing a tiny amount of chlorine dopants in the defective MAPbI₃. The theoretical results are supported by photoluminescence experiments on MAPbI_3?mCl_m and pave the way toward the design of defect‐free perovskite materials with optoelectronic performance approaching the theoretical limits.     

On the Balance of Intercalation and Conversion Reactions in Battery Cathodes

A thermodynamic analysis of the driving forces is presented for intercalation and conversion reactions in battery cathodes across a range of possible working ion, transition metal, and anion chemistries. Using this body of results, the importance of polymorph selection as well as chemical composition on the ability of a host cathode to support intercalation reactions is analyzed. It is found that the accessibility of high energy charged polymorphs in oxides generally leads to larger intercalation voltages favoring intercalation reactions, whereas sulfides and selenides tend to favor conversion reactions. Furthermore, it is observed that Cr‐containing cathodes favor intercalation more strongly than those with other transition metals. Finally, it is concluded that two‐electron reduction of transition metals (as is possible with the intercalation of a 2 + ion) will favor conversion reactions in the compositions studied.     

On the dynamics of one-prey-n-predator impulsive reaction-diffusion predator–prey system with ratio-dependent functional response

In this paper, a one-prey-n-predator impulsive reaction-diffusion periodic predator–prey system with ratio-dependent functional response is investigated. On the basis of the upper and lower solution method and comparison theory of differential equation, sufficient conditions on the ultimate boundedness and permanence of the predator–prey system are established. By constructing an appropriate auxiliary function, the conditions for the existence of a unique globally stable positive periodic solution are also obtained. Examples and numerical simulations are presented to verify the feasibility of our results. A discussion is conducted at the end.     

Livestock exclusion alters plant species composition in fen meadows

Questions

Our study evaluated how species composition and plant traits that indicate functioning condition in fens responded to grazing cessation over time in an arid ecosystem of the western US. The specific questions addressed were: (i) how does livestock exclusion influence species composition in fens; (ii) is grazing cessation associated with shifts in species functional traits that indicate fen condition; and (iii) what is the pattern of response to livestock exclusion over time?

Location

Plumas National Forest, California, US.

Methods

We studied paired fenced and unfenced study sites in two fens to examine the effects of livestock exclusion. Parallel transects were established at each site, and plant species and ground cover were repeatedly surveyed, once prior to and multiple times following treatment, using 0.01 m² frequency frames. We used NMDS to analyse species composition, RLQ and fourth‐corner analysis to evaluate species functional traits and environmental variables, and linear mixed effects models to examine differences in responses between fenced and unfenced study sites over time.

Results

After fencing, we observed unexpected shifts in species composition and plant functional traits. Grazed sites were associated with peat‐forming obligate wetland, moss and sedge species, while fenced sites were characterized by non‐peat‐forming facultative upland, and upland forb, grass and early seral species. Species composition also varied between sites and sample years.

Conclusions

We found that livestock exclusion strongly affects plant species composition in fens, including promoting species with functional traits that indicate a loss of functioning condition, such as ruderal and upland species. Possible explanations for these observed shifts include: (1) biomass accumulation in the absence of herbivory, (2) competitive exclusion in fenced sites, (3) succession, (4) the abiotic conditions of our study sites, particularly hydrology and nutrient status, and (5) interactions among these factors. We conclude that degradation of fen wetlands caused by livestock grazing in the arid western US may not be reversed by excluding livestock alone.