Inference of natural selection from ancient DNA.

Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods

Dietary zinc supplementation of 3xTg-AD mice increases BDNF levels and prevents cognitive deficits as well as mitochondrial dysfunction

The overall effect of brain zinc (Zn2+) in the progression and development of Alzheimer's disease (AD) is still not completely understood. Although an excess of Zn2+ can exacerbate the pathological features of AD, a deficit of Zn2+ intake has also been shown to increase the volume of amyloid plaques in AD transgenic mice. In this study, we investigated the effect of dietary Zn2+ supplementation (30 p.p.m.) in a transgenic mouse model of AD, the 3xTg-AD, that expresses both β amyloid (Aβ)- and tau-dependent pathology. We found that Zn2+ supplementation greatly delays hippocampal-dependent memory deficits and strongly reduces both Aβ and tau pathology in the hippocampus. We also evaluated signs of mitochondrial dysfunction and found that Zn2+ supplementation prevents the age-dependent respiratory deficits we observed in untreated 3xTg-AD mice. Finally, we found that Zn2+ supplementation greatly increases the levels of brain-derived neurotrophic factor (BDNF) of treated 3xTg-AD mice. In summary, our data support the idea that controlling the brain Zn2+ homeostasis may be beneficial in the treatment of AD

Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness

Synchronized oscillation is very commonly observed in many neuronal systems and might play an important role in the response properties of the system. We have studied how the spontaneous oscillatory activity affects the responsiveness of a neuronal network, using a neural network model of the visual cortex built from Hodgkin-Huxley type excitatory (E-) and inhibitory (I-) neurons. When the isotropic local E-I and I-E synaptic connections were sufficiently strong, the network commonly generated gamma frequency oscillatory firing patterns in response to random feed-forward (FF) input spikes. This spontaneous oscillatory network activity injects a periodic local current that could amplify a weak synaptic input and enhance the network's responsiveness. When E-E connections were added, we found that the strength of oscillation can be modulated by varying the FF input strength without any changes in single neuron properties or interneuron connectivity. The response modulation is proportional to the oscillation strength, which leads to self-regulation such that the cortical network selectively amplifies various FF inputs according to its strength, without requiring any adaptation mechanism. We show that this selective cortical amplification is controlled by E-E cell interactions. We also found that this response amplification is spatially localized, which suggests that the responsiveness modulation may also be spatially selective. This suggests a generalized mechanism by which neural oscillatory activity can enhance the selectivity of a neural network to FF inputs

Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease

Huanglongbing (HLB) or “citrus greening” is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production

Dynamic Effective Connectivity of Inter-Areal Brain Circuits

Anatomic connections between brain areas affect information flow between neuronal circuits and the synchronization of neuronal activity. However, such structural connectivity does not coincide with effective connectivity (or, more precisely, causal connectivity), related to the elusive question “Which areas cause the present activity of which others?”. Effective connectivity is directed and depends flexibly on contexts and tasks. Here we show that dynamic effective connectivity can emerge from transitions in the collective organization of coherent neural activity. Integrating simulation and semi-analytic approaches, we study mesoscale network motifs of interacting cortical areas, modeled as large random networks of spiking neurons or as simple rate units. Through a causal analysis of time-series of model neural activity, we show that different dynamical states generated by a same structural connectivity motif correspond to distinct effective connectivity motifs. Such effective motifs can display a dominant directionality, due to spontaneous symmetry breaking and effective entrainment between local brain rhythms, although all connections in the considered structural motifs are reciprocal. We show then that transitions between effective connectivity configurations (like, for instance, reversal in the direction of inter-areal interactions) can be triggered reliably by brief perturbation inputs, properly timed with respect to an ongoing local oscillation, without the need for plastic synaptic changes. Finally, we analyze how the information encoded in spiking patterns of a local neuronal population is propagated across a fixed structural connectivity motif, demonstrating that changes in the active effective connectivity regulate both the efficiency and the directionality of information transfer. Previous studies stressed the role played by coherent oscillations in establishing efficient communication between distant areas. Going beyond these early proposals, we advance here that dynamic interactions between brain rhythms provide as well the basis for the self-organized control of this “communication-through-coherence”, making thus possible a fast “on-demand” reconfiguration of global information routing modalities

The effects of problem-oriented policing on crime and disorder

Problem-oriented Policing (POP) was first introduced by Herman Goldstein in 1979. The approach was one of a series of responses to a crisis in effectiveness and legitimacy in policing that emerged in the 1970s and 1980s. Goldstein argued that police were not being effective in preventing and controlling crime because they had become too focused on the “means” of policing and had neglected the “goals” of preventing and controlling crime and other community problems. Goldstein argued that the unit of analysis in policing must become the “problem” rather than calls or crime incidents as was the case during that period. POP has had tremendous impact on American policing, and is now one of the most widely implemented policing strategies in the US. To synthesize the extant problem-oriented policing evaluation literature and assess the effects of problem-oriented policing on crime and disorder Eligible studies had to meet three criteria: (1) the SARA model was used for a problemoriented policing intervention; (2) a comparison group was included; (3) at least one crime or disorder outcome was reported with sufficient data to generate an effect size. The unit of analysis could be people or places. Several strategies were used to perform an exhaustive search for literature fitting the eligibility criteria. First, a keyword search was performed on an array of online abstract databases. Second, we reviewed the bibliographies of past reviews of problem-oriented policing. Third, we performed forward searches for works that have cited seminal problem-oriented policing studies. Fourth, we performed hand searches of leading journals in the field. Fifth, we searched the publications of several research and professional agencies. Sixth, after finishing the above searches we e-mailed the list of studies meeting our eligibility criteria to leading policing scholars knowledgeable in the area of problem-oriented policing to ensure we had not missed any relevant studies. For our ten eligible studies, we provide both a narrative review of effectiveness and a meta-analysis. For the meta-analysis, we coded all primary outcomes of the eligible studies and we report the mean effect size (for studies with more than one primary outcome, we averaged effects to create a mean), the largest effect, and the smallest effect. Because of the heterogeneity of our studies, we used a random effects model. Based on our meta-analysis, overall problem-oriented policing has a modest but statistically significant impact on reducing crime and disorder. Our results are consistent when examining both experimental and quasi-experimental studies. Conclusions: We conclude that problem-oriented policing is effective in reducing crime and disorder, although the effect is fairly modest. We urge caution in interpreting these results because of the small number of methodologically rigorous studies on POP and the diversity of problems and responses used in our eligible studies

Police-initiated diversion for youth to prevent future delinquent behavior: a systematic review

BackgroundOverly punitive responses to youth misconduct may have the unintended consequence ofincreasing the likelihood of future delinquency; yet, overly lenient responses may fail to serveas a corrective for the misbehavior. Police diversion schemes are a collection of strategiespolice can apply as an alternative to court processing of youth. Police-initiated diversionschemes aim to reduce reoffending by steering youth away from deeper penetration into thecriminal justice system and by providing an alternative intervention that can help youthaddress psychosocial development or other needs that contribute to their problem behavior.ObjectivesThe objective of this review was to synthesize the evidence on the effectiveness of pre-courtinterventions involving police warning or counseling and release, and cautioning schemes inreducing delinquent behavior.Search methodsA combination of 26 databases and websites were searched. References of relevant reviewswere also scanned to identify studies. We also consulted with experts in the field. Searcheswere executed by two reviewers and conducted between August 2016 and January 2017.Selection criteriaOnly experimental and quasi-experimental designs were eligible for this review. All quasiexperimentaldesigns must have had a comparison group similar to the police diversionintervention group with respect to demographic characteristics and prior involvement indelinquent behavior (i.e., at similar risk for future delinquent behavior). Additionally, studiesmust have included youth participants between 12 and 17 years of age who either underwenttraditional system processing or were diverted from court processing through a police-leddiversion program. Studies were also eligible if delinquency-related outcomes, includingofficial and non-official (self-report or third-party reporting) measures of delinquency werereported.Data collection and analysisThis study used meta-analysis to synthesize results across studies. This method involvedsystematic coding of study features and conversion of study findings into effect sizesreflecting the direction and magnitude of any police-led diversion effect. There were 19independent evaluations across the 14 primary documents coded for this review. From this,we coded 67 effect sizes of delinquent behavior post diversion across 31 diversion-traditionalprocessing comparisons. We analyzed these comparisons using two approaches. The firstapproach selected a single effect size per comparison based on a decision rule and the secondused all 67 effect sizes, nesting these within comparison condition and evaluation design.ResultsThe general pattern of evidence is positive, suggesting that police-led diversion modestlyreduces future delinquent behavior of low-risk youth relative to traditional processing.Authors’ conclusionsThe findings from this systematic review support the use of police-led diversion for low-riskyouth with limited or no prior involvement with the juvenile justice system. Thus, policedepartments and policy-makers should consider diversionary programs as part of the mix ofsolutions for addressing youth crime