Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection, identification and geographical distribution of European corn borer larval parasitoids using molecular markers

Biological control requires specific tools for the accurate detection and identification of natural enemies, and to detect unusual variations in their density, which may follow changes in agricultural practices. Here we have developed specific molecular markers to detect Lydella thompsoni (Herting) and Pseudoperichaeta nigrolineata (Walker) (Diptera: Tachinidae) within the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). Primers amplifying fragments of the mitochondrial COI gene were designed following alignment of comparable sequences for a range of parasitoid and host species. Each of the primer pairs proved to be species specific to a tachinid species, amplifying DNA fragments of 191 and 91 bp in length for L. thompsoni and P. nigrolineata, respectively. This DNA‐based technique allowed molecular evaluation of parasitism in O. nubilalis natural populations. In order to study the geographical distribution of both species in France, O. nubilalis diapausing larvae in maize stalks were collected from 12 locations over the whole country. The molecular evaluation of parasitism was compared with the traditional method of maintaining O. nubilalis populations in controlled conditions before breaking off the diapause. The percentage parasitism found in both species of tachinids was higher — approximately three times — using the molecular method, suggesting an underestimation by the traditional rearing protocol. Tachinid parasitism on O. nubilalis was not significantly different between geographical areas (south, central and north France) for both species. This study shows that molecular methods are very promising for the correct detection and identification of tachinid parasitoids in natural field populations.
In-stent stenosis after stent-assisted coiling: incidence, predictors and clinical outcomes of 435 cases.

BACKGROUND Neuroform and Enterprise are widely used self-expanding stents designed to treat wide-necked intracranial aneurysms. OBJECTIVE To assess the incidence, clinical significance, predictors, and outcomes of in-stent stenosis (ISS). METHODS Angiographic studies and hospital records were retrospectively reviewed for 435 patients treated between 2005 and 2011 in our institution. A multivariable regression analysis was conducted to determine the predictors of ISS. RESULTS The Neuroform stent was used in 264 patients (60.7%) and the Enterprise in 171 patients (39.3%). A total of 11 patients (2.5%) demonstrated some degree of ISS during the follow-up period at a mean time point of 4.2 months (range, 2-12 months). The stenosis was mild (< 50%) in 8 patients (1.8%), moderate (50-75%) in 2 patients (0.5%), and severe (> 75%) in 1 patient (0.2%). No patients were symptomatic or required further intervention. There was complete ISS resolution in 2 patients, partial resolution in 2 patients, and no change in 5 patients on follow-up angiography. Patients developing ISS were significantly younger than those without ISS (40.3 vs. 54.9 years; P < .001). ISS rates were 2.7% with the Neuroform and 2.3% with the Enterprise stent (P = .6). In multivariable analysis, younger patient age (odds ratio = 0.92; P = .008), carotid ophthalmic aneurysm location (odds ratio = 7.7; P =0.01), and carotid terminus aneurysm location (odds ratio = 8.1; P = .009) were strong independent predictors of ISS. The type of stent was not a predictive factor. CONCLUSION Neuroform and Enterprise ISS is an uncommon, often transient, and clinically benign complication. Younger patients and those harboring anterior circulation aneurysms located at ophthalmic and carotid terminus locations are more likely to develop ISS.
Sesquiterpene lactones: Adverse health effects and toxicity mechanisms

Abstract Sesquiterpene lactones (STLs) present a wide range of biological activities, mostly based on their alkylating capabilities, which underlie their therapeutic potential. These compounds are the active constituents of a variety of plants, frequently used as herbal remedies. STLs such as artemisinin and its derivatives are in use as first-line antimalarials while others, such as parthenolide, have recently reached cancer clinical trials. However, the toxicological profile of these compounds must be thoroughly characterized, since the same properties that make STL useful medicines can also cause severe toxicity. STL-containing plants have long been known to induce a contact dermatitis in exposed farm workers, and also to cause several toxic syndromes in farm animals. More recently, concerns are been raised regarding the genotoxic potential of these compounds and the embryotoxicity of artemisinins. A growing number of STLs are being reported to be mutagenic in different in vitro and in vivo assays. As yet no systematic studies have been published, but the genotoxicity of STLs seems to depend not so much on direct DNA alkylation as on oxidative DNA damage and other partially elucidated mechanisms. As the medicinal use of these compounds increases, further studies of their toxic potential are needed, especially those focusing on the structural determinants of genotoxicity and embryotoxicity.
Donor-antigen Inoculation in the Testis Promotes Skin Allograft Acceptance Induced by Conventional Costimulatory Blockade via Induction of CD8 + CD122+ and CD4 + CD25+ Regulatory T Cells

Background Immune responses are somewhat suppressed in immune privileged sites, including the testes, which provide a preexisting opportunity to prolong allograft survival. Previous studies have shown that intratesticular islet allografts enjoy extended survival even without any immunosuppression. However, it is unknown if testicular immune privilege can be exploited to prolong the survival of a solid allograft, including the skin, because it is impractical to implant a solid tissue in human testes. Methods To immunize recipient mice, splenocytes from BALB/c mice were injected into the testis of C57BL/6 recipients 1 week before skin transplantation. CD8 + CD122+ and CD4 + FoxP3+ regulatory T [Treg] cells were quantified by fluorescence-activated cell sorting. Results Although donor-antigen inoculation alone did not delay skin allograft rejection, it significantly extended the allograft survival when combined with CD40/CD40L or B7/CD28 costimulatory blockade and further induced long-term skin allograft acceptance when both costimulatory pathways were blocked. Similarly, donor-antigen inoculation suppressed alloreactive T cell proliferation in draining lymph nodes of skin recipients in the presence of the same costimulatory blockade. Interestingly, donor-antigen inoculation via intratesticular injection increased CD8 + CD122+, but not CD4 + FoxP3+, Treg numbers after transplantation. However, both CD8 + CD122+ and CD4 + CD25+ Treg cells induced by donor-antigen inoculation and the costimulatory blockade were more potent in suppression than that induced without the inoculation. Depletion of CD8+ or CD25+ T cells largely abrogated long-term skin allograft survival induced by donor-antigen inoculation and the costimulatory blockade. Conclusions Intratesticular inoculation with donor antigens promotes long-term skin allograft survival induced by conventional costimulatory blockade via the induction of both CD8 + CD122+ and CD4 + CD25+ Treg cells.
The DARPA TIPSTER project

This note is the first of four papers in this issue describing the ongoing work connected with the DARPA TIPSTER Project. The note provides an overview of the project, and the next papers by three of the contractors involved in the project provide some details on the systems involved, and some of the initial results.The TIPSTER project is sponsored by the Software and Intelligent Systems Technology Office of the Defense Advanced Research Projects Agency (DARPA/SISTO) in an effort to significantly advance the state of the art in effective document detection (information retrieval) and data extraction from large, real-world data collections. The first two-year phase of the program is concerned with the development of algorithms for document retrieval, document routing, and data extraction that are both domain and language independent. A call for proposals was made in June of 1990, and contracts for the six participating groups were let in the fall of 1991. Three meetings have been held so far, with the first results presented in September of 1992.There are two separate, but connected parts of TIPSTER. The first part of the project, document detection, is concerned with retrieving relevant documents" from very large (3 gigabyte) collections of documents, both in a routing environment, and in an adhoc retrieval environment. The routing environment is similar to the document filtering or profile searches currently done in libraries, where a query topic is constant, and the documents are viewed as the incoming stream of publications. The adhoc part of the project is similar to the standard search done against static collections.The second part of the TIPSTER project is concerned with data extraction. Here it is assumed that there is a much smaller set of documents, presumed to be mostly relevant to a topic, and the goal is to extract information to fill a database. This database could then be used for many applications, such as question-answering systems, report writing, or data analysis. The data extraction part of TIPSTER is being done by groups using natural language understanding techniques, and this part will not be described in this issue.
Effects of Modifying Triglycerides and Triglyceride-rich Lipoproteins on Cardiovascular Outcomes

Elevated levels of triglycerides (and triglyceride-rich lipoproteins) are increasingly being recognized as treatment targets to lower cardiovascular risk in certain patient subgroups, including individuals receiving HMG-CoA reductase inhibitors (statins). Evidence suggests that these agents reduce the risk of coronary events more markedly in patients with elevated triglycerides and low levels of high-density lipoprotein cholesterol (HDL-C). Further, intensive long-term statin therapy that reduces both low-density lipoprotein cholesterol (LDL-C) to <70 mg/dL and triglycerides to <150 mg/dL results in a decreased risk of cardiovascular events compared with more moderate statin treatment. Long-term therapy with fibric-acid derivatives, which lower triglycerides and raise HDL-C, appears to reduce mortality in patients with elevated triglycerides and/or those experiencing the most marked reductions in triglycerides on therapy. However, randomized clinical trials involving fibrates have not shown consistent benefit. Niacin (nicotinic acid), which is the most effective available medication for raising HDL-C and also lowers triglycerides, has not been as extensively studied as fibrates in long-term randomized controlled trials. Initial reports (eg, Coronary Drug Project) demonstrated a reduction in coronary disease but not total mortality in patients randomized to niacin. However, a 15-year follow-up demonstrated that all-cause mortality was significantly reduced in those initially randomized to niacin. At the pathophysiologic level, elevated triglycerides and triglyceride-rich lipoproteins are recognized as potential factors in driving atherosclerotic progression, particularly in mild-to-moderate lesions. Elevated triglycerides also constitute a plausible therapeutic target in certain patients with coronary heart disease (and/or insulin resistance) but without profound LDL-C elevations. The foregoing and other evidence has led consensus panels to lower the upper limit for “normal” triglycerides to 150 mg/dL. Adequately powered randomized controlled trials that specifically assess the effects of lowering triglycerides and raising HDL-C, and trials that target individuals with high triglycerides and low HDL-C, may provide data for recommending specific treatment targets for triglycerides and HDL-C, as well as effective and well-tolerated therapies to achieve these goals.
Assisting students in online experimentation

With the advancement of technology and universities' aspiration to reach more students including students studying in distance mode, remote laboratories are gaining popularity and becoming a common feature of STEM programs. Remote laboratories make laboratory equipment more accessible to both on-campus and off-campus students. However, assistance to students experimenting outside the scheduled supervised classes is hard to provide and therefore usually not available in remote laboratories. With the advancements in software engineering and intelligent systems, it is a natural step forward to develop intelligent tutoring systems that will assist students in online experimentation when a human tutor is not available. In this article, we present our work in this direction.
A revisionist replicon model for higher eukaryotic genomes

The replicon model devised to explain replication control in bacteria has served as the guiding paradigm in the search for origins of replication in the more complex genomes of eukaryotes. In Saccharomyces cerevisiae, this model has proved to be extremely useful, leading to the identification of specific genetic elements (replicators) and the interacting initiator proteins that activate them. However, replication control in organisms ranging from Schizosaccharomyces pombe to mammals is far more fluid: only a small number of origins seem to represent classic replicators, while the majority correspond to zones of inefficient, closely spaced start sites none of which are indispensable for origin activity. In addition, it is apparent that the epigenetic state of a given sequence largely determines its ability to be used as a replication initiation site. These conclusions were arrived at over a period of three decades, and required the development of several novel replicon mapping techniques, as well as new ways of examining the chromatin architecture of any sequence of interest. Recently, methods have been elaborated for isolating all of the active origins in the genomes of higher eukaryotes en masse. Microarray analyses and more recent high‐throughput sequencing technology will allow all the origins to be mapped onto the chromosomes of any organism whose genome has been sequenced. With the advent of whole‐genome studies on gene expression and chromatin composition, the field is now positioned to define both the genetic and epigenetic rules that govern origin activity. J. Cell. Biochem. 105: 321–329, 2008. © 2008 Wiley‐Liss, Inc.
[Fluorine-18]Fluorodeoxyglucose Positron Emission Tomography, DNA Ploidy and Growth Fraction in Squamous-Cell Carcinomas of the Head and Neck

Background: Positron emission tomography (PET) offers an opportunity to examine noninvasively cellular functions with different tracers. [18F]Fluorodeoxyglucose (FDG) is most commonly used in identifying malignant tumors. Several tumor biologic characteristics (tumor cell viability, growth faction, treatment response to radiation, cell membrane dysfunction, recurrence rate) are suggested to be characterized by [18F]FDG PET. The aim of this study was to assess which other tumor biologic characteristics of squamous-cell carcinoma of the head and neck are correlated with [18F]FDG PET. Methods: [18F]FDG PET was performed in 14 patients with squamous-cell carcinomas of the upper digestive tract (TNM classification T2–T4, N1–N3). After attenuation correction, predefined areas of the tumor were semiquantitatively analyzed by the technique of the region of interest and calculated as standard uptake values (SUV). Afterwards, 5 biopsies of different tumor regions were obtained during endoscopy in each patient under general anesthesia, and a correlation between SUV of [18F]FDG PET and tumor biologic parameters was attempted. These parameters included: quantitative DNA measurements (i.e. 2c deviation index, 5c exceeding rate), immunohistochemical assessment of growth fraction (i.e. Ki67-MIB-1, PCNA) along with morphological tumor front grading. Results: The results revealed a marked variation of proliferation and cellular differentiation in various regions of the tumor for all parameters examined. There was a close correlation between [18F]FDG uptake and growth fraction (r = 0.83 for Ki67-MIB-1 and r = 0.8 for PCNA). A poor correlation was found between DNA aneuploidy (r = 0.4) or tumor front grading (r = 0.12) and [18F]FDG uptake. Conclusions: Our results confirm previous clinical and histologic observations that squamous-cell carcinomas of the upper digestive tract are heterogeneous tumors. Ki67 antigen, which has been shown to be of predictive value for proliferation and individual prognosis, correlated with [18F]FDG uptake. Using [18F]FDG PET, the main proliferation centers of inhomogeneous squamous-cell carcinomas could be identified with possible clinical implications for patient management.
Kinetic Bias in Estimates of Coastal Picoplankton Community Structure Obtained by Measurements of Small-Subunit rRNA Gene PCR Amplicon Length Heterogeneity

ABSTRACT Marine bacterioplankton diversity was examined by quantifying natural length variation in the 5′ domain of small-subunit (SSU) rRNA genes (rDNA) amplified by PCR from a DNA sample from the Oregon coast. This new technique, length heterogeneity analysis by PCR (LH-PCR), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. Relationships between the sizes of amplicons and gene phylogeny were predicted by an analysis of 366 SSU rDNA sequences from cultivated marine bacteria and from bacterial genes cloned directly from environmental samples. LH-PCR was used to compare the distribution of bacterioplankton SSU rDNAs from a coastal water sample with that of an SSU rDNA clone library prepared from the same sample and also to examine the distribution of genes in the PCR products from which the clone library was prepared. The analysis revealed that the relative frequencies of genes amplified from natural communities are highly reproducible for replicate sets of PCRs but that a bias possibly caused by the reannealing kinetics of product molecules can skew gene frequencies when PCR product concentrations exceed threshold values.
Dual Ka-band radar experiment for the DPR algorithm development

A dual Ka-band radar system is developed by the Japan Aerospace Exploration Agency (JAXA) for the Global Precipitation Measurement (GPM) dual-wavelength radar (DPR) algorithm development. The usage of the system is to measure backscattering and extinction cross sections by precipitation separately, and to provide testbed data for DPR algorithm. The parameters required in the DPR algorithm are raindrop size distribution for the liquid precipitation, and particle density, shape, and melting ratio for the solid precipitation. When the two Ka-radar systems separated by 10-20 km observe precipitation in between two radars, the specific attenuation can be measured. Along with other radar, a C-band radar, Mie scattering effect which is deviation from Rayleigh scattering could be estimated. A field experiment using the dual Ka-radar system is conducted in Okinawa Island. A C-band polarization Doppler radar is also operated, and preliminary result is presented.
Does a Triplet Birth Pose a Special Risk for Infant Development? Assessing Cognitive Development in Relation to Intrauterine Growth and Mother-Infant Interaction Across the First 2 Years

Objective. To examine whether a triplet birth per se poses a risk to the development of infants' cognitive competencies and to the mother-infant relationship. Methods. Twenty-three sets of triplets were matched with 23 sets of twins and 23 singleton infants (n = 138) with respect to gestational age, birth weight, and medical and demographic features. Infants with perinatal asphyxia, intraventricular hemorrhage of grade 3 or 4, periventricular leukomalacia, or central nervous system infection were excluded from the study. At 6, 12, and 24 months of age, mother-infant interaction was observed and infants' cognitive development was tested with the Bayley II test. Results. Mothers of triplets displayed lower levels of sensitivity at 6, 12, and 24 months and infants were less socially involved at 6 and 24 months, compared with singletons and twins. Triplets scored lower than singletons and twins on the Bayley Mental Developmental Index at 6, 12, and 24 months. A weight discordance of >15% was found for 15 triplet sets (65.2%). The discordant triplets showed decreased cognitive skills at 12 and 24 months, compared with their siblings, and received the lowest scores for maternal sensitivity. Hierarchical multivariate regression analysis revealed that greater medical risk at birth, multiple-birth status, lower maternal sensitivity, and reduced infant social involvement in the first 2 years were each predictive of lower cognitive outcomes at 2 years (R2 = 0.33). Conclusions. Triplets appear to be at higher risk for cognitive delays in the first 2 years of life, and discordant infants are at especially high risk. This delay is related in part to the difficulty of providing sensitive mothering to 3 infants at the same time. The findings may assist practitioners in guiding prenatal and postpartum parental care and management.
EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes

MOTIVATION Identification of functionally equivalent genes in different species is essential to understand the evolution of biological pathways and processes. At the same time, identification of strings of conserved orthologous genes helps identify complex genomic rearrangements across different organisms. Such an insight is particularly useful, for example, in the transfer of experimental results between different experimental systems such as Drosophila and mammals. RESULTS Here, we describe the Encapsulated Gene-by-gene Matching (EGM) approach, a method that employs a graph matching strategy to identify gene orthologs and conserved gene segments. Given a pair of genomes, EGM constructs a global gene match for all genes taking into account gene context and family information. The Hungarian method for identifying the maximum weight matching in bipartite graphs is employed, where the resulting matching reveals one-to-one correspondences between nodes (genes) in a manner that maximizes the gene similarity and context. CONCLUSION We tested our approach by performing several comparisons including a detailed Human versus Mouse genome mapping. We find that the algorithm is robust and sensitive in detecting orthologs and conserved gene segments. EGM can sensitively detect rearrangements within large and small chromosomal segments. The EGM tool is fully automated and easy to use compared to other more complex methods that also require extensive manual intervention and input. AVAILABILITY The EGM software, Supplementary information and other tools are available online from http://vbc.med.monash.edu. au/ approximately kmahmood/EGM.
Restriction of DNA Replication to the Reductive Phase of the Metabolic Cycle Protects Genome Integrity

When prototrophic yeast cells are cultured under nutrient-limited conditions that mimic growth in the wild, rather than in the high-glucose solutions used in most laboratory studies, they exhibit a robustly periodic metabolic cycle. Over a cycle of 4 to 5 hours, yeast cells rhythmically alternate between glycolysis and respiration. The cell division cycle is tightly constrained to the reductive phase of this yeast metabolic cycle, with DNA replication taking place only during the glycolytic phase. We show that cell cycle mutants impeded in metabolic cycle–directed restriction of cell division exhibit substantial increases in spontaneous mutation rate. In addition, disruption of the gene encoding a DNA checkpoint kinase that couples the cell division cycle to the circadian cycle abolishes synchrony of the metabolic and cell cycles. Thus, circadian, metabolic, and cell division cycles may be coordinated similarly as an evolutionarily conserved means of preserving genome integrity.