An annotated catalog of the primary type material of Myriapoda deposited in the Florida State Collection of Arthropods in Gainesville, FL, USA.

The Florida State Collection of Arthropods (FSCA) is one of the top insect collections in the United States with in excess of eight million curated specimens and significant amounts of materials in bulk collections and other unprocessed samples. The subphylum Myriapoda currently comprises approximately 17,500 species in the four classes Diplopoda, Chilopoda, Symphyla, and Pauropoda. The FSCA houses type material in the Diplopoda orders Callipodida, Chordeumatida, Glomeridesmida, Julida, Polydesmida, Polyzoniida, Siphonophorida, Spirobolida, and Spirostreptida. This catalog documents the FSCA primary type material for 74 species in 45 genera in 25 families and nine orders within Diplopoda.

An annotated and illustrated catalog of the primary type material of Hemiptera deposited in the Florida State Collection of Arthropods.

The Florida State Collection of Arthropods (FSCA) is one of the largest and most diverse insect collections in North America and the largest in the southeastern United States with over twelve million curated specimens and significant amounts of materials in bulk collections and other unprocessed samples. The order Hemiptera currently comprises approximately 95,000 species in three suborders. The FSCA houses type material in the auchenorrhynchan families Cicadidae, Cicadellidae, Cixiidae, Delphacidae, Derbidae, and Membracidae; the heteropteran families Coreidae, Corixidae, Curaliidae, Lygaeidae, Miridae, Pentatomidae, Reduviidae, Schizopteridae, Scutelleridae, and Tingidae; the sternorrhynchan families Aleyrodidae, Aphalaridae, Aphididae, Coccidae, Diaspididae, Matsucoccidae, Pseudococcidae, Phacopteronidae, and Triozidae. This catalog documents the FSCA primary type material for 167 species in 79 genera in 24 families across the three suborders.

An annotated catalog of the type material of Mecoptera deposited in the Florida State Collection of Arthropods in Gainesville, Florida, USA.

The Florida State Collection of Arthropods (FSCA) is one of the largest and most valuable insect collections in the United States with more than twelve million curated specimens. The order Mecoptera currently comprises over 800 extant described species in nine extant families. The FSCA houses type material in the families Bittacidae, Panorpidae, and Panorpodidae. This catalog documents the FSCA type material for 23 species in five genera in Mecoptera.

Descriptions of New Species of Chespirito Ferreira, Keller amp; Branham (Coleoptera: Lampyridae: Chespiritoinae) and the First Record for the Subfamily in the United States.

Three new species of Chespirito Ferreira, Keller and Branham 2020 are described from North America, including the first species from the United States: Chespirito milleri new species from Arizona, USA, Chespirito hintoni new species from Mexico state, Mexico and Chespirito costae new species from Morelo state, Mexico. An updated distribution map and key to males of Chespirito is provided along with illustrations of diagnostic characters of the newly described species.

Rhagophthalmidae Olivier, 1907 (Coleoptera, Elateroidea): described genera and species, current problems, and prospects for the bioluminescent and paedomorphic beetle lineage.

Rhagophthalmidae are a small beetle family known from the eastern Palaearctic and Oriental realms. Rhagophthalmidae are closely related to railroad worms (Phengodidae) and fireflies (Lampyridae) with which they share highly modified paedomorphic females and the ability to emit light. Currently, Rhagophthalmidae include 66 species classified in the following 12 genera: Bicladodrilus Pic, 1921 (two spp.), Bicladum Pic, 1921 (two spp.), Dioptoma Pascoe, 1860 (two spp.), Diplocladon Gorham, 1883 (two spp.), Dodecatoma Westwood, 1849 (eight spp.), Falsophrixothrix Pic, 1937 (six spp.), Haplocladon Gorham, 1883 (two spp.), Menghuoius Kawashima, 2000 (three spp.), Mimoochotyra Pic, 1937 (one sp.), Monodrilus Pic, 1921 (two spp. in two subgenera), Pseudothilmanus Pic, 1918 (two spp.), and Rhagophthalmus Motschulsky, 1854 (34 spp.). The replacement name Haplocladongorhami Kundrata, nom. nov. is proposed for Diplocladonhasseltii Gorham, 1883b (described in subgenus Haplocladon) which is preoccupied by Diplocladonhasseltii Gorham, 1883a. The genus Reductodrilus Pic, 1943 is tentatively placed in Lampyridae: Ototretinae. Lectotypes are designated for Pseudothilmanusalatus Pic, 1918 and P.marginalis Pic, 1918. Interestingly, in the eastern part of their distribution, Rhagophthalmidae have remained within the boundaries of the Sunda Shelf and the Philippines demarcated by the Wallace Line, which separates the Oriental and Australasian realms. This study is intended to be a first step towards a comprehensive revision of the group on both genus and species levels. Additionally, critical problems and prospects for rhagophthalmid research are briefly discussed.

A catalog of the Lampyridae (Coleoptera) of the West Indies.

The West Indies represents one of the world's hotspots for beetles in the family Lampyridae and includes many endemic taxa. Nine out of 19 genera and 181 out of 186 species of the currently described firefly taxa present in the West Indies are endemic to the region. The objective of this catalog and bibliography is to generate an exhaustive list of firefly taxa present in the West Indies. A short discussion of previous efforts to catalog this fauna is presented, and all published distribution data is herein synthesized. This catalog serves as a starting point for systematic and taxonomic research on the fireflies of this region and provides a full bibliography for each species. The following species were deemed subspecific and unavailable: Callopisma rufa var. humeralis E. Olivier, Lucidota fulvotincta var. flavicollis Mutchler, and Robopus magnus var. turquino (Mutchler).

An annotated catalog of the type material of Adephaga and Myxophaga (Coleoptera) deposited in the Florida State Collection of Arthropods in Gainesville, Florida, United States of America.

The Florida State Collection of Arthropods (FSCA) ranks in the top 10 largest Coleoptera collections in the United States of America with in excess of 1.5 million pinned beetles and significant amounts of materials in bulk collections and other unprocessed samples. The suborder Adephaga currently comprises approximately 34,000 species in 10 extant families and the suborder Myxophaga contains approximately 94 species in four extant families. The FSCA owns type material in the adephagan families Carabidae, Dytiscidae, Gyrinidae, Haliplidae, and Noteridae. The myxophagan holdings in the FSCA include type material from the families Hydroscaphidae and Lepiceridae. There were no holdings of type material in the suborder Archostemata at FSCA. This catalogue documents the FSCA type material for 253 species in 80 genera across the two suborders. A total of 3,528 type specimens are reported, including 60 holotypes, 36 allotypes, 3,426 paratypes, and six syntypes.

A new species of Notaepytus Skelley, 2009 (Coleoptera: Erotylidae: Tritomini) from Dominican amber.

Notaepytus quisqueya sp. nov. (Erotylidae: Erotylinae: Tritomini), is described here from Dominican amber and is the second amber fossil description for the family from the West Indies (Hispaniola). An emended key and a checklist to all known species of Notaepytus are presented.

Smartphone and Tablet-Based Sensing of Environmental Radioactivity: Mobile Low-Cost Measurements for Monitoring, Citizen Science, and Educational Purposes.

Sensors for environmental radioactivity based on two novel setups using photodiodes, on the one hand, and an advanced tablet-based hybrid pixel detector, on the other hand, are presented. Measurements of four kinds of terrestrial and every-day radiation sources are carried out: Airborne radon, a mineral containing traces of uranium, edible potassium salt, and an old radium watch. These measurements permit comparisons between different types of ambient radioactive sources and enable environmental monitoring. Available data comprise discrimination between α - and ß - -particles in an energy range of 33 keV to 8 MeV and under ambient air conditions. The diode-based sensor is particularly useful in portable applications since it is small and sturdy with little power consumption. It can be directly connected to a smartphone via the headset socket. For its development, the low-cost silicon positive-intrinsic-negative (PIN) diodes BPX61 and BPW34 have been characterised with capacitance versus voltage (C-V) curves. Physical detection limits for ionising radiation are discussed based on obtained depletion layer width: ( 50 ± 8 ) µ m at 8 V. The mobile and low-cost character of these sensors, as alternatives to Geiger counters or other advanced equipment, allows for a widespread use by individuals and citizen science groups for environmental and health protection purposes, or in educational settings. Source code and hardware design files are released under open source licenses with this publication.

Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.

Knowledge-analytics synergy in Clinical Decision Support.

Clinical Decision Support (CDS) systems hold tremendous potential for improving patient care. Most existing systems are knowledge-based tools that rely on relatively simple rules. More recent approaches rely on analytics techniques to automatically mine EHR data to reveal meaningful insights. Here, we propose the Knowledge-Analytics Synergy paradigm for CDS, in which we synergistically combine existing relevant knowledge with analytics applied to EHR data. We propose a framework for implementing such a paradigm and demonstrate its principles over real-world clinical and genomic data of hypertensive patients.

Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio.

BACKGROUND: Obtaining transcripts of homologs of closely related organisms and retrieving the reconstructed exon-intron patterns of the genes is a very important process during the analysis of the evolution of a protein family and the comparative analysis of the exon-intron structure of a certain gene from different species. Due to the ever-increasing speed of genome sequencing, the gap to genome annotation is growing. Thus, tools for the correct prediction and reconstruction of genes in related organisms become more and more important. The tool Scipio, which can also be used via the graphical interface WebScipio, performs significant hit processing of the output of the Blat program to account for sequencing errors, missing sequence, and fragmented genome assemblies. However, Scipio has so far been limited to high sequence similarity and unable to reconstruct short exons. RESULTS: Scipio and WebScipio have fundamentally been extended to better reconstruct very short exons and intron splice sites and to be better suited for cross-species gene structure predictions. The Needleman-Wunsch algorithm has been implemented for the search for short parts of the query sequence that were not recognized by Blat. Those regions might either be short exons, divergent sequence at intron splice sites, or very divergent exons. We have shown the benefit and use of new parameters with several protein examples from completely different protein families in searches against species from several kingdoms of the eukaryotes. The performance of the new Scipio version has been tested in comparison with several similar tools. CONCLUSIONS: With the new version of Scipio very short exons, terminal and internal, of even just one amino acid can correctly be reconstructed. Scipio is also able to correctly predict almost all genes in cross-species searches even if the ancestors of the species separated more than 100 Myr ago and if the protein sequence identity is below 80%. For our test cases Scipio outperforms all other software tested. WebScipio has been restructured and provides easy access to the genome assemblies of about 640 eukaryotic species. Scipio and WebScipio are freely accessible at http://www.webscipio.org.

A novel hybrid gene prediction method employing protein multiple sequence alignments.

MOTIVATION: As improved DNA sequencing techniques have increased enormously the speed of producing new eukaryotic genome assemblies, the further development of automated gene prediction methods continues to be essential. While the classification of proteins into families is a task heavily relying on correct gene predictions, it can at the same time provide a source of additional information for the prediction, complementary to those presently used. RESULTS: We extended the gene prediction software AUGUSTUS by a method that employs block profiles generated from multiple sequence alignments as a protein signature to improve the accuracy of the prediction. Equipped with profiles modelling human dynein heavy chain (DHC) proteins and other families, AUGUSTUS was run on the genomic sequences known to contain members of these families. Compared with AUGUSTUS' ab initio version, the rate of genes predicted with high accuracy showed a dramatic increase. AVAILABILITY: The AUGUSTUS project web page is located at http://augustus.gobics.de, with the executable program as well as the source code available for download.

A phase II study of biweekly pemetrexed and gemcitabine in patients with metastatic breast cancer.

PURPOSE: Pemetrexed (PEM) is a novel folate antimetabolite which inhibits thymidylate synthase, dihydrofolate reductase and glycinamide ribonucleotide formyl transferase. This phase II study was designed to assess the efficacy of Gemcitabine (GEM) and PEM given in a novel schedule in metastatic breast cancer (MBC) patients. METHODS: Eligible patients had MBC and received one prior chemotherapy regimen for metastatic disease; Performance status (PS) 0-2; measurable disease (RECIST criteria). PEM(500 mg/m2) was administered intravenously (IV) over 10 min prior to GEM(1,500 mg/m2) IV given over 30 min on day 1 every 14 days. RESULTS: Median age of the 16 patients in the study was 54 years (range 33-77). Fourteen patients had a PS of 0/1 and were evaluable for response. There were no reported complete or partial responses, seven patients with stable disease, six patients with disease progression and one patient with unknown response. Most common toxicities were skin rash: Grade 1/2(8) and Grade 3/4(1). Grade 3/4 non-hematological toxicities were fatigue(1); anorexia(1); pneumonia(1); peripheral ischemia(1) and elevation of liver transaminases(1). Three patients experienced febrile neutropenia (FN). This study did not meet the predefined criteria to proceed with additional accrual. CONCLUSIONS: This regimen of PEM and GEM showed no clinical activity in the dose and schedule tested.

WebScipio: an online tool for the determination of gene structures using protein sequences.

BACKGROUND: Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. RESULTS: WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. CONCLUSION: WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org.

Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.

BACKGROUND: For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience. RESULTS: Scipio is a tool based on the alignment program BLAT to determine the precise gene structure given a protein sequence and a genome sequence. It identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. Instead of producing a set of hits with varying confidence, Scipio gives the user a coherent summary of locations on the genome that code for the query protein. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in closely related species. Scipio was tested with 979 protein queries against 16 arthropod genomes (intra species search). For cross-species annotation, Scipio was used to annotate 40 genes from Homo sapiens in the primates Pongo pygmaeus abelii and Callithrix jacchus. The prediction quality of Scipio was tested in a comparative study against that of BLAT and the well established program Exonerate. CONCLUSION: Scipio is able to precisely map a protein query onto a genome. Even in cases when there are many sequencing errors, or when incomplete genome assemblies lead to hits that stretch across multiple target sequences, it very often provides the user with the correct determination of intron-exon borders and splice sites, showing an improved prediction accuracy compared to BLAT and Exonerate. Apart from being able to find genes in the genome that encode the query protein, Scipio can also be used to annotate genes in closely related species.

AUGUSTUS: ab initio prediction of alternative transcripts.

AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder that can predict multiple transcripts. In addition, we offer a motif searching facility, where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://augustus.gobics.de.

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

BACKGROUND: Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands. RESULTS: We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU) of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format.It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods. CONCLUSION: SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes.

Gastrointestinal stromal tumours: etiology, pathology and clinical management.

Investigation of the regulation of cell growth, differentiation and death by signalling pathways has led to a greater understanding of how alterations in these pathways play a critical role in the development of some cancers, and has opened new opportunities for their treatment. In the present review, results with the prototype drug of this class, imatinib (Gleevec, Glivec [formerly STI571]; Novartis, Switzerland), in metastatic gastrointestinal stromal tumours are presented. The present review originated from a conference of the authors held in Montreal, Quebec in June 2003, under the sponsorship of Novartis.