The burden of scrub typhus in India: A systematic review

BackgroundScrub typhus, a vector-borne zoonotic infection caused by the bacteria Orientia tsutsugamushi, is one of the most common and clinically important rickettsial infections worldwide. An estimated one million cases occur annually with a high case fatality rate. Although scrub typhus is a major public health threat in India, the burden and distribution remains unclear. We aimed to estimate the burden of scrub typhus in India.MethodologyWe performed a systematic review of published literature on scrub typhus from India to extract information on epidemiology, morbidity, and mortality. Important databases were searched using keywords and appropriate combinations. We identified observational, interventional, and population-based studies and extracted the data to evaluate the number of cases diagnosed using serology or PCR and the number of deaths due to scrub typhus. We conducted a systematic narrative synthesis to summarize included studies.Principal findingsIn the last decade, there were 18,781 confirmed scrub typhus cases reported in 138 hospital-based studies and two community-based studies. IgM ELISA was used in 122 studies to confirm the cases in majority (89%). The proportion of scrub typhus among acute undifferentiated febrile illness (AUFI) studies was 25.3%, and community seroprevalence was 34.2%. Ninety studies had data published on multiple organ involvement out of which 17.4% of cases had multiple organ dysfunction syndromes, 20.4% patients required ICU admission, and 19.1% needed ventilation. The overall case-fatality rate was 6.3%, and the mortality among those with multi-organ dysfunction syndrome was as high as 38.9%.Conclusion/significanceScrub typhus, a common acute febrile illness in India causing severe morbidity, accounts for a large number of deaths. The burden of the disease has been underappreciated. Early diagnosis and prompt treatment can significantly reduce complications and mortality. Establishing good surveillance and instituting appropriate control measures are urgently needed.     

Assessing the importance of individual habitat patches as irreplaceable connecting elements: An analysis of simulated and real landscape data

Habitat loss and fragmentation are considered to be severe threats to biodiversity, and maintaining natural levels of landscape connectivity may be one of the best responses to these issues. Graph-based habitat availability (reachability) metrics have been shown to be an appropriate method for a multifaceted but coherent landscape connectivity assessment. These metrics can be partitioned into three commensurate fractions (intra, flux, connector) that quantify the different ways in which habitat patches contribute to the overall landscape connectivity and habitat availability. In particular, the connector fraction measures the contribution of patches to the connectivity between other habitat areas as irreplaceable connecting elements or stepping stones. Because many conservation efforts and initiatives are focused on conserving or restoring corridors and other linkages between habitat areas, it is critical to understand more thoroughly the conditions under which investing in these connecting elements is an efficient management strategy. For this purpose, we analysed the contribution of the connector fraction in different simulated habitat patterns under different levels of habitat amount and fragmentation and in natural habitats for endangered forest bird species in Catalonia (Spain). We show that a prominent role of individual stepping stone patches as irreplaceable providers of habitat connectivity and availability arises only under a relatively narrow set of conditions, characterised by low habitat amount, high habitat fragmentation and modest to intermediate species dispersal abilities. We suggest that to support connectivity-related investments, it is necessary to focus on those few species or dispersal distance ranges that are likely to be both most dependent on and most benefited by the conservation or restoration of stepping stone patches. We conclude that the total amount of reachable habitat for a particular species is rarely determined by the contribution of individual connectors as the only dominant factor. Therefore, conservationists should be cautious not to overemphasise the importance of connectivity investments and to balance them with other conservation alternatives and strategies to promote species conservation in heterogeneous landscapes.     

Evaluation of the whole blood lymphocyte transformation assay for scrub typhus exposure: adaptability to field sample collection

The optimal conditions for the determination of exposure to scrub typhus by the whole blood lymphocyte transformation assay was 7 days culture of 10% blood in RPMI 1640 medium supplemented with 10% human AB-negative serum and L-glutamine with 50-200 micrograms protein/ml of Karp, Kato, or Gilliam strain membrane antigen. A simple exponentially decaying linear model shows the decrease in lymphocyte viability, the ability of sensitized cells to be stimulated with PHA mitogen, and the corresponding decrease in stimulation by scrub typhus antigens with increasing time of preincubation on ice. The lower limit of stimulation index for the detection of scrub typhus by whole blood lymphocyte transformation assay was 4.0 with a type I error of 1%.     

Assessing the ecological suitability of the Irish landscape for the Eurasian lynx (Lynx lynx)

Mammal Research - Restoration of natural processes via the reintroduction of locally extinct species is a key component of the rewilding process. In Ireland, the Eurasian lynx (Lynx lynx), an...     

Multidimensional recording (MDR) and data sharing: an ecological open research and educational platform for neuroscience

Primate neurophysiology has revealed various neural mechanisms at the single-cell level and population level. However, because recording techniques have not been updated for several decades, the types of experimental design that can be applied in the emerging field of social neuroscience are limited, in particular those involving interactions within a realistic social environment. To address these limitations and allow more freedom in experimental design to understand dynamic adaptive neural functions, multidimensional recording (MDR) was developed. MDR obtains behavioral, neural, eye position, and other biological data simultaneously by using integrated multiple recording systems. MDR gives a wide degree of freedom in experimental design because the level of behavioral restraint is adjustable depending on the experimental requirements while still maintaining the signal quality. The biggest advantage of MDR is that it can provide a stable neural signal at higher temporal resolution at the network level from multiple subjects for months, which no other method can provide. Conventional event-related analysis of MDR data shows results consistent with previous findings, whereas new methods of analysis can reveal network mechanisms that could not have been investigated previously. MDR data are now shared in the public server Neurotycho.org. These recording and sharing methods support an ecological system that is open to everyone and will be a valuable and powerful research/educational platform for understanding the dynamic mechanisms of neural networks.     

Assessing forest fragmentation in northeastern region (NER) of India using landscape matrices

Northeastern region (NER) of India, one of the largest reserves of forests in India has so far been studied with a view to map the distribution of species or modeling the disturbance regimes and richness analysis. The present study focuses on the importance of regional level studies where the entire NER which is under the threat of forest fragmentation and degradation, is been assessed. In the present study, six historical data sets generated from remote sensing data (1972, 1982, 1987, 1989, 1993 and 1999) are used to assess forest cover loss, shape index and entropy to the degree of forest fragmentation over a multi-decadal period. The assessments have been carried out in the open (40–10% canopy density) and close (>40% canopy density) forest cover classes. The range of shape index and deviation from the actual mean in open forest and closed forest were computed separately. The patches among two categories were further analyzed based on patch area into six classes; ranging from <1 km² to >500 km². This also indicates variability of the forest patches. It is noteworthy that patches of area within 1–10 km² and 10–50 km² have been severely fragmented. This loss could be attributed to the shifting cultivation practice where the patches of moderate size are cultivated by group of families. The present study could give an insight to the patch configuration and composition in terms of shape index and the Shannon's entropy index.     

Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data

The goal of landscape genetics is to detect and explain landscape effects on genetic diversity and structure. Despite the increasing popularity of landscape genetic approaches, the statistical methods for linking genetic and landscape data remain largely untested. This lack of method evaluation makes it difficult to compare studies utilizing different statistics, and compromises the future development and application of the field. To investigate the suitability and comparability of various statistical approaches used in landscape genetics, we simulated data sets corresponding to five landscape-genetic scenarios. We then analyzed these data with eleven methods, and compared the methods based on their statistical power, type-1 error rates, and their overall ability to lead researchers to accurate conclusions about landscape-genetic relationships. Results suggest that some of the most commonly applied techniques (e.g. Mantel and partial Mantel tests) have high type-1 error rates, and that multivariate, non-linear methods are better suited for landscape genetic data analysis. Furthermore, different methods generally show only moderate levels of agreement. Thus, analyzing a data set with only one method could yield method-dependent results, potentially leading to erroneous conclusions. Based on these findings, we give recommendations for choosing optimal combinations of statistical methods, and identify future research needs for landscape genetic data analyses.     

Assessing the effects of vegetation type on hoverfly (Diptera: Syrphidae) diversity in a Mediterranean landscape: implications for conservation

Understanding the responses of insects to ecological variables provides information that is fundamental for their conservation. The present study took place in three different landscapes (three plots of 10 × 10 km each) in a typical Mediterranean ecosystem of a Spanish national park. Each landscape included three vegetation types, grasslands, scrublands, and woodlands, and was characterised by a dominant vegetation type. Our objectives were: (1) to assess how important the influence of the dominant vegetation type and the vegetation type of sites are on hoverfly (Diptera: Syrphidae) diversity at landscape scale; (2) to assess whether scrublands are contributing to the loss of hoverfly diversity in an ecosystem with a long history of human use. In order to achieve these goals, we compared hoverfly diversity among sampling sites by prospecting all three diversity levels, alpha, beta and gamma, at each landscape. We sampled adult hoverflies at 18 sites located in different vegetation types within the three landscapes. No evidence was found that demonstrated an effect of the dominant vegetation type on alpha or beta diversity of sites, but the vegetation type of sites did have an affect. The highest species richness was found in woodland sites, particularly in the grassland-dominated landscape. At each landscape, beta diversity among sampling sites contributed more to gamma diversity than alpha diversity did. Our results highlight the need to focus on the conservation of woodland remnants of grassland-dominated landscape and scrubland-dominated landscape in order to preserve a large proportion of the biodiversity of Cabañeros hoverflies, as well as on the maintenance of the mosaic landscape, which is linked to high beta diversity, typical in many Mediterranean ecosystems. We emphasise the importance of open clearings in the vast mass of scrubland in the scrubland-dominated landscape in order to provide extra resources for the hoverflies.     

Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data

LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.     

Real-time PCR: approaches to data analysis (a review)

The registration of the accumulation of polymerase chain reaction (PCR) products in the course of amplification (real-time PCR) requires specific equipment, i.e., detecting amplifiers capable of recording the level of fluorescence in the reaction tube during amplicon formation. By the time the reaction is completed, researchers obtain DNA accumulation graphs. The review discusses the most promising algorithms of analysis of real-time PCR curves and possible errors, whether caused by the software used or the operators' mistakes. The data included will assist researchers in understanding the features of the method to obtain more reliable results.     

Zingiber officinale Roscoe (ginger) as an adjuvant in cancer treatment: a review

Despite acquiring a strong understanding of the molecular basis and advances in treatment, cancer is the second major cause of death in the world. In clinics, the stagedependent treatment strategies may include surgery, radiotherapy and systemic treatments like hormonotherapy and chemotherapy, which are associated with side effects. The use of traditional herbal medicine in cancer patients is on a rise, as it is believed that these medications are non toxic and alleviate the symptoms of cancer, boost the immune system, or may tackle the cancer itself. Since antiquity the rhizome of Zingiber officinale Roscoe commonly known as ginger (family Zingiberaceae) have widely been used as a spice and condiment in different societies. Additionally, ginger also has a long history of medicinal use in various cultures for treating common colds, fever, to aid digestion, treat stomach upset, diarrhoea, nausea, rheumatic disorders, gastrointestinal complications and dizziness. Preclinical studies have also shown that ginger possesses chemopreventive and antineoplastic properties. It is also reported to be effective in ameliorating the side effects of γ-radiation and of doxorubicin and cisplatin; to inhibit the efflux of anticancer drugs by P-glycoprotein (P-gp) and to possess chemosensitizing effects in certain neoplastic cells in vitro and in vivo. The objective of this review is to address observations on the role of ginger as adjuvant to treatment modalities of cancer. Emphasis is also placed on the drawbacks and on future directions for research that will have a consequential effect on cancer treatment and cure.     

Evaluating long-term introduction success of the Florida scrub endemic Crotalaria avonensis (Fabaceae) using a decade of demographic data

Introductions are a critical tool in the recovery of many imperiled species, yet adequate evaluation and development of best practices has lagged. Importantly, long-term post-introduction data are typically lacking, as well as suitable comparisons to wild populations to provide a baseline against which to assess performance. Here, we report on three experimental introductions of Crotalaria avonensis (Fabaceae), a federally endangered perennial herb that is narrowly endemic to scrub of the Lake Wales Ridge in peninsular Florida, U.S.A. We synthesize 10 years of post-introduction monitoring at both the introduced and a nearby, protected wild population to (1) develop best practices for conservation, and (2) evaluate the success of the introduction. First, our study identified best practices that included using transplants propagated from stem cuttings, as well as several factors that may increase seed germination such as habitat choice, seed burial, and litter addition. Second, during the 10 years following the introduction, population density in the introduced population was higher than in a nearby protected, wild population, and a comparison of vital rates revealed that this result was due to relatively high clonal and seedling recruitment rates in the introduced population. Furthermore, the source population, which occurred on unprotected lands, precipitously declined during this time period, further highlighting the importance of safeguarding plants from that population. We report that a new, growing population of C. avonensis has been established to date, with important implications for the species' conservation as well as how introductions are evaluated.     

Multiple causes of seedling rarity in scrub plum, Prunus geniculata (Rosaceae), an endangered shrub of the Florida scrub

Conservation of an imperiled plant often requires an understanding of its reproductive ecology. Scrub plum (Prunus geniculata) is an endangered Florida shrub endemic to pyrogenic xeric uplands. Although plants are long-lived and may flower profusely, particularly after burning, fruit yield is sparse and seedlings are rare. We investigated potential causes of seedling rarity in scrub plum by studying its floral sex and breeding systems, fruit development, and germination ecology. We also developed a flow chart based on two time-since-fire scenarios to illustrate the cumulative impact of these factors on seedling recruitment. Breeding system experiments suggested partial gametophytic self-incompatibility in this functionally andromonoecious species, with inbreeding depression in self-compatible individuals. Predispersal seed predation, the major constraint on seedling recruitment, was lower in the first postburn season. In two field experiments, seed germination was <11% irrespective of treatment. These results indicate that seedling recruitment in scrub plum may be limited by multiple factors, including sexual reproductive failure, high predispersal seed predation, and low seed germination. The chance of a bisexual flower producing a seedling ranges from 5 in 1000 to 5 in 100000, depending on the time since fire. Restoration of scrub plum's historical fire regime may mitigate some of these factors.