Leveraging the partition selection bias to achieve a high-quality clustering of mass spectra.

In proteomics, the identification of peptides from mass spectral data can be mathematically described as the partitioning of mass spectra into clusters (i.e., groups of spectra derived from the same peptide). The way partitions are validated is just as important, having evolved side by side with the clustering algorithms themselves and given rise to many partition assessment measures. An assessment measure is said to have a selection bias if, and only if, the probability that a randomly chosen partition scoring a high value depends on the number of clusters in the partition. In the context of clustering mass spectra, this might mislead the validation process to favor clustering algorithms that generate too many (or few) spectral clusters, regardless of the underlying peptide sequence. A selection bias toward the number of peptides is desirable for proteomics as it estimates the number of peptides in a complex protein mixture. Here, we introduce an assessment measure that is purposely biased toward the number of peptide ion species. We also introduce a partition assessment framework for proteomics, called the Partition Assessment Tool, and demonstrate its importance by evaluating the performance of eight clustering algorithms on seven proteomics datasets while discussing the trade-offs involved. SIGNIFICANCE: Clustering algorithms are widely adopted in proteomics for undertaking several tasks such as speeding up search engines, generating consensus mass spectra, and to aid in the classification of proteomic profiles. Choosing which algorithm is most fit for the task at hand is not simple as each algorithm has advantages and disadvantages; furthermore, specifying clustering parameters is also a necessary and fundamental step. For example, deciding on whether to generate "pure clusters" or fewer clusters but accepting noise. With this as motivation, we verify the performance of several widely adopted algorithms on proteomic datasets and introduce a theoretical framework for drawing conclusions on which approach is suitable for the task at hand.

A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics.

We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.

Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra.

MOTIVATION: We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates. RESULTS: We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable. AVAILABILITY AND IMPLEMENTATION: http://patternlabforproteomics.org/tdgc, freely available for academic use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Before it is too late: description of a new genus and species of butterfly from a highly threatened Brazilian biome

Abstract A new genus, Nhambikuara Freitas, Barbosa & Zacca gen. nov., and species, Nhambikuara cerradensis Freitas, Barbosa & Zacca sp. nov., of the highly diverse Neotropical butterfly subtribe Euptychiina are described. Nhambikuara cerradensis sp. nov. is the type species for the genus, and Euptychia mima Butler, 1867 is also transferred to the new genus, as Nhambikuara mima (Butler, 1867) comb. nov., from the genus Zischkaia Forster, 1964. The taxonomy, phylogenetic relationships, geographic distribution and natural history of species of the genus are also discussed.http://zoobank.org/urn:lsid:zoobank.org:pub:41AD7568-3490-4F63-A019-32D5592A8C44

The Global Alliance for Infections in Surgery: defining a model for antimicrobial stewardship-results from an international cross-sectional survey.

BACKGROUND: Antimicrobial Stewardship Programs (ASPs) have been promoted to optimize antimicrobial usage and patient outcomes, and to reduce the emergence of antimicrobial-resistant organisms. However, the best strategies for an ASP are not definitively established and are likely to vary based on local culture, policy, and routine clinical practice, and probably limited resources in middle-income countries. The aim of this study is to evaluate structures and resources of antimicrobial stewardship teams (ASTs) in surgical departments from different regions of the world. METHODS: A cross-sectional web-based survey was conducted in 2016 on 173 physicians who participated in the AGORA (Antimicrobials: A Global Alliance for Optimizing their Rational Use in Intra-Abdominal Infections) project and on 658 international experts in the fields of ASPs, infection control, and infections in surgery. RESULTS: The response rate was 19.4%. One hundred fifty-six (98.7%) participants stated their hospital had a multidisciplinary AST. The median number of physicians working inside the team was five [interquartile range 4-6]. An infectious disease specialist, a microbiologist and an infection control specialist were, respectively, present in 80.1, 76.3, and 67.9% of the ASTs. A surgeon was a component in 59.0% of cases and was significantly more likely to be present in university hospitals (89.5%, p < 0.05) compared to community teaching (83.3%) and community hospitals (66.7%). Protocols for pre-operative prophylaxis and for antimicrobial treatment of surgical infections were respectively implemented in 96.2 and 82.3% of the hospitals. The majority of the surgical departments implemented both persuasive and restrictive interventions (72.8%). The most common types of interventions in surgical departments were dissemination of educational materials (62.5%), expert approval (61.0%), audit and feedback (55.1%), educational outreach (53.7%), and compulsory order forms (51.5%). CONCLUSION: The survey showed a heterogeneous organization of ASPs worldwide, demonstrating the necessity of a multidisciplinary and collaborative approach in the battle against antimicrobial resistance in surgical infections, and the importance of educational efforts towards this goal.

DiagnoProt: a tool for discovery of new molecules by mass spectrometry.

MOTIVATION: Around 75% of all mass spectra remain unidentified by widely adopted proteomic strategies. We present DiagnoProt, an integrated computational environment that can efficiently cluster millions of spectra and use machine learning to shortlist high-quality unidentified mass spectra that are discriminative of different biological conditions. RESULTS: We exemplify the use of DiagnoProt by shortlisting 4366 high-quality unidentified tandem mass spectra that are discriminative of different types of the Aspergillus fungus. AVAILABILITY AND IMPLEMENTATION: DiagnoProt, a demonstration video and a user tutorial are available at http://patternlabforproteomics.org/diagnoprot . CONTACT: andrerfsilva@gmail.com or paulo@pcarvalho.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Efficacy and effectiveness trials have different goals, use different tools, and generate different messages.

The discussion about the optimal design of clinical trials reflects the perspectives of theory-based scientists and practice-based clinicians. Scientists compare the theory with published results. They observe a continuum from explanatory to pragmatic trials. Clinicians compare the problem they want to solve by completing a clinical trial with the results they can read in the literature. They observe a mixture of what they want and what they get. None of them can solve the problem without the support of the other. Here, we summarize the results of discussions with scientists and clinicians. All participants were interested to understand and analyze the arguments of the other side. As a result of this process, we conclude that scientists tell what they see, a continuum from clear explanatory to clear pragmatic trials. Clinicians tell what they want to see, a clear explanatory trial to describe the expected effects under ideal study conditions and a clear pragmatic trial to describe the observed effects under real-world conditions. Following this discussion, the solution was not too difficult. When we accept what we see, we will not get what we want. If we discuss a necessary change of management, we will end up with the conclusion that two types of studies are necessary to demonstrate efficacy and effectiveness. Efficacy can be demonstrated in an explanatory, ie, a randomized controlled trial (RCT) completed under ideal study conditions. Effectiveness can be demonstrated in an observational, ie, a pragmatic controlled trial (PCT) completed under real-world conditions. It is impossible to design a trial which can detect efficacy and effectiveness simultaneously. The RCTs describe what we may expect in health care, while the PCTs describe what we really observe.

Predatory capability of the nematophagous fungus Arthrobotrys robusta preserved in silica gel on infecting larvae of Haemonchus contortus.

Biological control of gastrointestinal nematodiasis in ruminants is an alternative to reduce the number of infective larvae. The fungal isolates predatory activity preservation is a basic requirement for the success of this control type. The aim of this work is to evaluate the predatory capacity of the fungus Arthrobotrys robusta (isolate I-31), preserved on silica gel on infective larvae of Haemonchus contortus under laboratory conditions on 2 % water agar (2 % WA). In this essay, A. robusta storage on silica gel showed successful predatory activity on H. contortus L3 larvae (p < 0.01) compared to the control group. Nematophagous fungi were not observed in the control group during the experiment. There was a significant reduction (p < 0.01) of 73.84 % in the means of H. contortus (L3) recovered from treatment with isolate I-31 compared to the control without fungi. Results indicate that A. robusta (I-31) could survive stored on silica gel for at least 7 years and keep its predatory activity on H. contortus (L3).

Ovicidal activity of seven Pochonia chlamydosporia fungal isolates on Ascaris suum eggs.

The ovicidal effect of the nematophagous fungus Pochonia chlamydosporia on eggs of Ascaris suum was tested under laboratory conditions. A. suum eggs were plated on 2% water-agar with seven fungal isolates (Isol. 5, Isol. 31, Isol. 1, VC1, Isol. 12, Isol. 22 and VC4) and control without fungus. After 5, 7, 10, 14, 15 and 21 days of incubation, approximately 100 eggs were removed from the plates and classified according to the following parameters: type 1, biochemical and physiological effect without morphological damage to the eggshell, type 2, lytic effect with morphological alteration of the eggshell and embryo and type 3, lytic effect with morphological alteration of eggshell and embryo showing hyphal penetration and internal egg colonization. The isolates effectively destroyed A. suum eggs and all types of effects were observed during the experiment. There was no variation in ovicidal capacity (type 3 effect) among the isolates (p>0.05) throughout the experiment. After 21 days, isolate 5 showed the highest percentages of type 3 effect (58.33%). The results indicated that P. chlamydosporia (Isol. 5, Isol. 31, Isol. 1, VC1, Isol. 12, Isol. 22 and VC4) can destroy A. suum eggs and is, therefore, a potential biological control agent of nematodes.

In vitro predatory activity of the fungi Duddingtonia flagrans, Monacrosporium thaumasium, Monacrosporium sinense and Arthrobotrys robusta on Ancylostoma ceylanicum third-stage larvae.

The potential role of companion animals as reservoirs for zoonotic diseases has been recognised as a significant public health problem worldwide. Ancylostoma ceylanicum is the only ancylostomatidae species known for infecting human beings. This article aimed to compare the predatory capacity of predatory fungi isolates Duddingtonia flagrans (AC001), Monacrosporium thaumasium (NF34), Monacrosporium sinense (SF53) and Arthrobotrys robusta (I31) on A. ceylanicum infectious larvae (L(3)) in a 2% water-agar plate. There was no predatory capacity variation among the fungi tested (P>0.05) over the 7-day period experimental assay. When compared to the control (without fungi), there was a significant reduction (P<0.05) of 95.6%, 85.1%, 87.4% and 90.2% on the A. ceylanicum L(3) mean recovered from treatments with isolates AC001, NF34, SF53 and I31, respectively. Regarding linear regression coefficients, negative values were noted for treatments, therefore indicating A. ceylanicum non-predated larvae reduction over 7 days. In this work, all predatory fungi isolates were efficient at capturing and destroying in vitro the A. ceylanicum L(3); therefore being able to be used as biological controllers of such nematode.

Predatory activity of the nematophagous fungus Duddingtonia flagrans on horse cyathostomin infective larvae.

This work was performed to determine the predatory capacity in vitro of the nematophagous fungus Duddingtonia flagrans (isolate AC001) on cyathostomin infective larvae of horse (L(3)). The experimental assay was carried out on plates with 2% water-agar (2% WA). In the treated group, each plate contained 1.000 L(3) and 1.000 conidia of the fungus. The control group without fungus only contained 1.000 L(3) in the plates. Ten random fields (4 mm diameter) were examined per plate of treated and control groups, every 24 h for seven days under an optical microscope (10x and 40x objective lens) for non-predated L(3) counts. After 7 days, the non-predated L(3) were recovered from the Petri dishes using the Baermann method. The interaction there was a significant reduction (p < 0.01) of 93.64% in the cyathostomin L(3) recovered. The results showed that the D. flagrans is a potential candidate to the biological control of horse cyathostomin L(3).

Predatory activity of Pochonia chlamydosporia fungus on Toxocara (syn. Neoascaris) vitulorum eggs.

Toxocara (Neoascaris) vitulorum is a gastrointestinal nematode parasite of young ruminants, responsible for high mortality rates in parasitized cattle and buffalo calves. The objective of this work was to compare the predatory capacity under laboratory conditions of four fungal isolates of the nematophagous fungus Pochonia chlamydosporia (VC1, VC4, VC5 and VC12) on T. vitulorum eggs in 2% water-agar (2% WA). T. vitulorum eggs were plated on 2% WA Petri dishes which contained cultured fungal isolates and control plates without fungi. After 10 and 15 days one hundred eggs were removed and classified according to the following parameters: type 1, biochemical and physiological effect without morphological damage to the eggshell, type 2, lytic effect with morphological alteration of the eggshell and embryo and type 3, lytic effect with morphological alteration of eggshell and embryo in addition to hyphal penetration and internal egg colonization. The fungal isolates were effective in the destruction of T. vitulorum eggs presenting the type 3 effect at 10 and 15 days after contact with the fungus. No nematophagous fungi were observed in the control group during the experiment. There was no variation in the predatory capacity of the fungal isolates (P > 0.01) at the intervals of 10 and 15 days. These results indicate that P. chlamydosporia (VC1, VC4, VC5 and VC12) negatively influenced the development of T. vitulorum eggs and can be considered a potential candidate for the biological control of nematodes.

[In vitro evaluation of nematode predacious fungus Duddingtonia fagrans on cyathostomes infective larvae of equines (Nematoda: Cyathostominae)]. / Avaliação in vitro do fungo predador de nematoides Duddingtonia flagrans sobre larvas infectantes de ciatostomíneos de equinos (Nematoda: Cyathostominae).

The predatory capacity of one isolate of nematode-trapping fungus Duddingtonia flagrans (AC001) on infective larvae of cyathostomes was evaluated in laboratorial conditions in medium water-agar 2% (WA 2%). There was significant reduction (p<0.01) of 93.64% in the average of infective larvae of cyathostomes recovered of medium WA 2% at seven day. These results show that the isolated AC001 could be used in the biological control of cyathostomes of horses.

Avaliação in vitro do fungo predador de nematoides Duddingtonia flagrans sobre larvas infectantes de ciatostomíneos de equinos (Nematoda: Cyathostominae) / In vitro evaluation of nematode predacious fungus Duddingtonia flagrans on cyathostomes infective larvae of equines (Nematoda: Cyathostominae)

A capacidade predatória de um isolado de fungo predador de nematoides Duddingtonia flagrans (AC001) sobre larvas infectantes de ciatostomíneos foi avaliada em condições laboratoriais em ensaio experimental em meio ágar-água 2% (AA 2%). Houve redução significativa (p < 0,01) de 93,64% na média de larvas infectantes de ciatostomíneos recuperadas do meio AA2%, ao final de sete dias. Os resultados desse ensaio evidenciam que o isolado fúngico AC001 poderia ser utilizado no controle biológico de ciatostomíneos de equinos.

The predatory capacity of one isolate of nematode-trapping fungus Duddingtonia flagrans (AC001) on infective larvae of cyathostomes was evaluated in laboratorial conditions in medium water-agar 2% (WA 2%). There was significant reduction (p < 0. 01) of 93.64% in the average of infective larvae of cyathostomes recovered of medium WA 2% at seven day. These results show that the isolated AC001 could be used in the biological control of cyathostomes of horses.

Biological control of sheep gastrointestinal nematodiasis in a tropical region of the southeast of Brazil with the nematode predatory fungi Duddingtonia flagrans and Monacrosporium thaumasium.

Formulations in matrix of sodium alginate (pellets) of the nematode predatory fungi Duddingtonia flagrans and Monacrosporium thaumasium were evaluated in the biological control of sheep gastrointestinal nematodiasis. Three groups (1, 2, and 3), each one with eight sheep of the Santa Inês breed, at the ages of 15-48 months, were placed in paddocks of Brachiaria decumbens for 5 months. In group 1, each animal received 1 g/10 kg of live weight (l.w.) of pellets of D. flagrans (0.2 g of fungus/10 kg l.w.). In group 2, each animal received 1 g/10 kg of l.w. of pellets of the fungus M. thaumasium (0.2 g of fungus/10 kg l.w.), twice a week, for 5 months. In group 3 (control), the animals received 1 g/10 kg of live weight of pellets without fungus. The monthly averages of the egg countings per gram of feces of the animals of groups 1 and 2 treated were 71.6% and 61.1% smaller, respectively, in comparison to the animals of group 3 (control). The treatment of sheep with pellets containing the nematophagous fungi D. flagrans and M. thaumasium may be used as an alternative for the control of sheep gastrointestinal nematodiasis.

Interaction and ovicidal activity of nematophagous fungus Pochonia chlamydosporia on Taenia saginata eggs.

The ovicidal activity of the nematophagous fungi Pochonia chlamydosporia (isolates VC1 and VC4), Duddingtonia flagrans (isolate AC001) and Monacrosporium thaumasium (isolate NF34) on Taenia saginata eggs was evaluated under laboratory conditions. T. saginata eggs were plated on 2% water-agar with fungal isolates and controls without fungus and examined after 5, 10 and 15 days. At the end of the experiment P. chlamydosporia showed ovicidal activity against T. saginata eggs (p<0.05), mainly for internal egg colonization with results of 12.8% (VC1) and 2.2% (VC4); 18.1% (VC1) and 7.0% (VC4); 9.76% (VC1) and 8.0% (VC4) at 5, 10 and 15 days, respectively. The other fungi showed only lytic effect without morphological damage to the eggshell. Results demonstrated that P. chlamydosporia was effective in vitro against T. saginata eggs unlike the other fungi.

Observação in vitro da ação dos fungos nematòfagos Duddingtonia flagrans, Monacrosporium thaumasium e Pochonia chlamydosporia sobre ovos de Eurytrema coelomaticum / In vitro evaluation of the action of the nematophagous fungi Duddingtonia flagrans, Monacrosporium thaumasium and Pochonia chlamydosporia on Eurytrema coelomaticum eggs

Objetivou-se a observação in vitro da ação dos fungos nematófagos Duddingtonia flagrans (AC001), Monacrosporium thaumasium (NF 34) e Pochonia chlamydosporia (VC1 e VC4) sobre ovos de Eurytrema coelomaticum. Os ovos foram vertidos em superfície de ágar-água 2 por cento contendo os isolados fúngicos e em AA 2 por cento sem fungo como controle. Ao completarem sete, 10 e 14 dias, aproximadamente os ovos foram removidos e classificados de acordo com os seguintes parâmetros: efeito tipo 1, efeito lítico sem prejuízo morfológico a casca do ovo; tipo 2, efeito lítico com alteração morfológica da casca e embrião e tipo 3, efeito lítico com alteração morfológica do embrião e da casca, além de penetração de hifas e colonização interna do ovo. Os isolados AC001 e NF34 não demonstraram percentuais para o efeito do tipo 3, contudo o isolado VC1 apresentou resultados percentuais para o efeitodo tipo 3 que determinam a atividade ovicida de um fungo: 27,2 por cento aos sete dias, 23,1 por cento aos 10dias e 25,0 por cento aos 14 dias. Da mesma forma que isolado VC4 apresentou: 15,0 por cento aos sete dias, 25,4 por cento aos 10 dias e 21,8 por cento aos 14 dias respectivamente. Pochonia chlamydosporia é um fungo promissor que pode ser usado no controle biológico de E. coelomaticum.

The present study assessed in vitro action of nematophagous fungi species Duddingtonia flagrans (AC 001), Monacrosporium thaumasium (NF 34) and Pochonia chlamydosporia (VC1 and VC4) on eggs of Eurytrema coelomaticum. Eggs were placed on Petri dishes with fungus isolate grown in water- agar 2 percent and in the control (no fungus). After seven, 10 and 14 days, the eggs were removed and classified according to the following parameters: type 1, lytic effect without morphological damage to eggshell; type 2, lytic effect with morphological alteration of embryo and eggshell; and type 3, lytic effect with morphological alteration of embryo and eggshell, besides hyphal penetration and internal egg colonization. The isolate AC001 andNF34 had not demonstrated percentages to type 3 effects, however isolated VC1 presented results percentages for the type 3 effect that it determines the ovicida activity of one fungus: 27.2 percent to the seven days, 23.1 percent to the 10 days and 25.0 percent to the 14 days. The isolated VC4 presented: 15.0 percent to the seven days, 25.4 percent to the 10 days and, 21.8 percentto the 14 days. P. chlamydosporia is a promising fungus can be used in the biological control of E. coelomaticum.

Overspinning a nearly extreme charged black hole via a quantum tunneling process.

We examine a nearly extreme macroscopic Reissner-Nördstrom black hole in the context of semiclassical gravity. The absorption rate associated with the quantum tunneling process of scalar particles whereby this black hole can acquire enough angular momentum to violate the weak cosmic-censorship conjecture is shown to be nonzero.

[In vitro observation of the action of isolates of the fungi Duddingtonia flagrans, Monacrosporium thaumasium and Verticillium chlamydosporium on the eggs of Ascaris lumbricoides (Linnaeus, 1758)]. / Observação in vitro da ação dos isolados fúngicos Duddingtonia flagrans, Monacrosporium thaumasium e Verticillium chlamydosporium sobre ovos de Ascaris lumbricoides (Lineu, 1758).

The in vitro action of the nematophagous fungi Duddingtonia flagrans, Monacrosporium thaumasium and Verticillium chlamydosporium on eggs of Ascaris lumbricoides was observed. After 7, 10 and 14 days of interaction, the fungus showing most promise for use in biologically control over Ascaris lumbricoides was Verticillium chlamydosporium (26-30%). The other fungi did not present satisfactory results.