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Despite advances in bioinformatics, custom scripts remain a source of difficulty, slowing workflow development and hampering reproducibility. Here, we introduce Vectools, a command-line tool-suite to reduce reliance on custom scripts and improve reproducibility by offering a wide range of common easy-to-use functions for table and vector manipulation. Vectools also offers a number of vector related functions to speed up workflow development, such as simple machine learning and common statistics functions.
Despite advances in bioinformatics, custom scripts remain a source of difficulty, slowing workflow development and hampering reproducibility. Here, we introduce Vectools, a command-line tool-suite to reduce reliance on custom scripts and improve reproducibility by offering a wide range of common easy-to-use functions for table and vector manipulation. Vectools also offers a number of vector related functions to speed up workflow development, such as simple machine learning and common statistics functions.
LSTMVoter : chemical named entity recognition using a conglomerate of sequence labeling tools
(2019)
Background: Chemical and biomedical named entity recognition (NER) is an essential preprocessing task in natural language processing. The identification and extraction of named entities from scientific articles is also attracting increasing interest in many scientific disciplines. Locating chemical named entities in the literature is an essential step in chemical text mining pipelines for identifying chemical mentions, their properties, and relations as discussed in the literature. In this work, we describe an approach to the BioCreative V.5 challenge regarding the recognition and classification of chemical named entities. For this purpose, we transform the task of NER into a sequence labeling problem. We present a series of sequence labeling systems that we used, adapted and optimized in our experiments for solving this task. To this end, we experiment with hyperparameter optimization. Finally, we present LSTMVoter, a two-stage application of recurrent neural networks that integrates the optimized sequence labelers from our study into a single ensemble classifier.
Results: We introduce LSTMVoter, a bidirectional long short-term memory (LSTM) tagger that utilizes a conditional random field layer in conjunction with attention-based feature modeling. Our approach explores information about features that is modeled by means of an attention mechanism. LSTMVoter outperforms each extractor integrated by it in a series of experiments. On the BioCreative IV chemical compound and drug name recognition (CHEMDNER) corpus, LSTMVoter achieves an F1-score of 90.04%; on the BioCreative V.5 chemical entity mention in patents corpus, it achieves an F1-score of 89.01%.
Availability and implementation: Data and code are available at https://github.com/texttechnologylab/LSTMVoter.
Adjuvanted influenza vaccines constitute a key element towards inducing neutralizing antibody responses in populations with reduced responsiveness, such as infants and elderly subjects, as well as in devising antigen-sparing strategies. In particular, squalene-containing adjuvants have been observed to induce enhanced antibody responses, as well as having an influence on cross-reactive immunity. To explore the effects of adjuvanted vaccine formulations on antibody response and their relation to protein-specific immunity, we propose different mathematical models of antibody production dynamics in response to influenza vaccination. Data from ferrets immunized with commercial H1N1pdm09 vaccine antigen alone or formulated with different adjuvants was instrumental to adjust model parameters. While the affinity maturation process complexity is abridged, the proposed model is able to recapitulate the essential features of the observed dynamics. Our numerical results suggest that there exists a qualitative shift in protein-specific antibody response, with enhanced production of antibodies targeting the NA protein in adjuvanted versus non-adjuvanted formulations, in conjunction with a protein-independent boost that is over one order of magnitude larger for squalene-containing adjuvants. Furthermore, simulations predict that vaccines formulated with squalene-containing adjuvants are able to induce sustained antibody titers in a robust way, with little impact of the time interval between immunizations.
Regular exercise has widespread health benefits. Fundamental to these beneficial effects is the ability of the heart to intermittently and substantially increase its performance without incurring damage, but the underlying homeostatic mechanisms are unclear. We identify the ROS-generating NADPH oxidase-4 (Nox4) as an essential regulator of exercise performance in mice. Myocardial Nox4 levels increase during acute exercise and trigger activation of the transcription factor Nrf2, with the induction of multiple endogenous antioxidants. Cardiomyocyte-specific Nox4-deficient (csNox4KO) mice display a loss of exercise-induced Nrf2 activation, cardiac oxidative stress and reduced exercise performance. Cardiomyocyte-specific Nrf2-deficient (csNrf2KO) mice exhibit similar compromised exercise capacity, with mitochondrial and cardiac dysfunction. Supplementation with an Nrf2 activator or a mitochondria-targeted antioxidant effectively restores cardiac performance and exercise capacity in csNox4KO and csNrf2KO mice respectively. The Nox4/Nrf2 axis therefore drives a hormetic response that is required for optimal cardiac mitochondrial and contractile function during physiological exercise.
Aim of the study: Hepatocyte transplantation has been discussed as an alternative to liver transplantation in selected cases of acute and chronic liver failure and metabolic diseases. Immediately after infusion of hepatocytes, hypoxia-related cell injury is inevitable. N-acetylcysteine (NAC) has been suggested to attenuate hypoxic damage. This study’s objective was to evaluate NAC’s protective effect in a model of hypoxia-related hepatocyte injury.
Material and methods: HepG2 cells were used as a model for hepatocytes and were cultured under standardized hypoxia or normoxia for 24 hours with or without NAC. Growth kinetics were monitored using trypan blue staining. The activation of apoptotic pathways was measured using quantitative real-time PCR for Bcl-2/Bax and p53. The proportions of vital, apoptotic and necrotic cells were verified by fluorescence activated cell sorting using annexin V-labelling. The expression of hypoxia inducible factor 1 (HIF-1) was measured indirectly using its downstream target vascular endothelial growth factor A (VEGF-A).
Results: After NAC, cell proliferation increased under both hypoxia and normoxia by 528% and 320% (p < 0.05), while VEGF-A expression decreased under normoxia by 67% and 37% (p < 0.05). Compared to cells treated without NAC under hypoxia, the Bcl-2/Bax ratio increased significantly in cells treated with NAC. This finding was confirmed by an increased number of vital cells in FACS analysis.
Conclusions: NAC protects hepatocytes from hypoxic injury and ultimately activates anti-apoptotic pathways.
Neuropogonoid species in the lichen-forming fungal genus Usnea exhibit great morphological variation that can be misleading for delimitation of species. We specifically focused on the species delimitation of two closely-related, predominantly Antarctic species differing in the reproductive mode and representing a so-called species pair: the asexual U. antarctica and the sexual U. aurantiacoatra. Previous studies have revealed contradicting results. While multi-locus studies based on DNA sequence data provided evidence that these two taxa might be conspecific, microsatellite data suggested they represent distinct lineages. By using RADseq, we generated thousands of homologous markers to build a robust phylogeny of the two species. Furthermore, we successfully implemented these data in fine-scale population genomic analyses such as DAPC and fineRADstructure. Both Usnea species are readily delimited in phylogenetic inferences and, therefore, the hypothesis that both species are conspecific was rejected. Population genomic analyses also strongly confirmed separated genomes and, additionally, showed different levels of co-ancestry and substructure within each species. Lower co-ancestry in the asexual U. antarctica than in the sexual U. aurantiacoatra may be derived from a wider distributional range of the former species. Our results demonstrate the utility of this RADseq method in tracing population dynamics of lichens in future analyses.
An oroantral fistula (OAF) is a pathological abnormal communication between the oral cavity and the maxillary sinus which may arise as a result of failure of primary healing of an OAF, dental infections, osteomyelitis, radiation therapy, trauma, or iatrogenic complications. With the presence of a fistula, the maxillary sinus is permanently open. Microbial flora passes from the oral cavity into the maxillary sinus, and the inflammation of the sinus occurs with all potential consequences. In literature, various techniques have been proposed for closure of OAFs. Due to the heterogeneity of the data and techniques found, we opted for a narrative review to highlight the variety of techniques discussed in the literature. Techniques of particular interest include the bone sandwich with resorbable guided tissue regeneration (GTR) membrane and platelet-rich fibrin (PRF) used alone as both a clot and a membrane. The great advantage of these techniques is that no donor site surgery is necessary, making the outcome valuable in terms of time savings, cost and, more importantly, less discomfort to the patient. Additionally, both bony and soft tissue closure is performed for OAF, in contrast to flaps, which are typically used for procedures in the sinus area. The reconstructed bony tissue regenerated from these techniques will also be appropriate for endosseous dental implantation.
In this study, a portable electronic nose (E-nose) prototype is developed using metal oxide semiconductor (MOS) sensors to detect odors of different wines. Odor detection facilitates the distinction of wines with different properties, including areas of production, vintage years, fermentation processes, and varietals. Four popular machine learning algorithms—extreme gradient boosting (XGBoost), random forest (RF), support vector machine (SVM), and backpropagation neural network (BPNN)—were used to build identification models for different classification tasks. Experimental results show that BPNN achieved the best performance, with accuracies of 94% and 92.5% in identifying production areas and varietals, respectively; and SVM achieved the best performance in identifying vintages and fermentation processes, with accuracies of 67.3% and 60.5%, respectively. Results demonstrate the effectiveness of the developed E-nose, which could be used to distinguish different wines based on their properties following selection of an optimal algorithm.
An individualized and coherent life story has been described as the form of identity that is required by highly mobile individualistic Western societies, whereas more family-oriented, traditional societies require more role-based, synchronic identities. Therefore in individualistic cultures entire life narratives can be expected to be more coherent and to contain more autobiographical arguments that contribute to life narrative coherence. This cultural group difference is expected to be mediated by individuals’ conformity to their respective cultural normative concept of biography, such that more conformity leads to less life narrative coherence and fewer autobiographical arguments. We tested these expectations by eliciting entire life narratives and cultural life scripts from four different cultural groups of students of technical universities: from provincial Karabük and from metropolitan Istanbul in Turkey, as well as from students with a Turkish migrant and with a native German background from urban Frankfurt am Main, Germany (N = 96). Expectations were confirmed for global life narrative coherence and autobiographical arguments with self-event connections. Conformity with a normative concept of biography indeed partially mediated cultural influences on life narrative coherence. Life narratives from Turkey also contained more family-related events and, unexpectedly, were more negative. Thus creating a coherent life narrative is more typical for cultures that require autonomous, individualized selves rather than for cultures requiring more related selves, reflecting the life story’s suitability for expressing individualized identities and its lesser suitability for expressing interdependent identities.
Aim: To evaluate the occurrence and severity of enterostomy complications in newborns suffering from different intestinal disorders.
Methods: A 10-year retrospective cohort study (2008-2017) investigated newborns that underwent enterostomy formation and reversal for different intestinal disorders. Only infants less than 28 d old at the time of enterostomy creation were included in the study (corrected age was applied in the cases of preterm neonates). The patients were divided into two groups according to their underlying diseases. Group 1 included infants suffering from necrotizing enterocolitis (NEC), whereas Group 2 included newborns diagnosed with intestinal disorders other than NEC, such as meconium obstruction, anorectal malformation, focal intestinal perforation, ileus, intestinal atresia and volvulus. The primary outcome measure was enterostomy-related morbidity. The data were analyzed statistically using Pearson’s χ2 test or Fisher’s exact test for categorical variables and the Wilcoxon-Mann-Whitney U-Test for continuous variables.
Results: In total, 76 infants met the inclusion criteria and were evaluated for enterostomy-related complications. Neither group showed significant differences regarding gender, gestational age, weight at birth or weight at enterostomy formation. Infants suffering from NEC (Group 1) were significantly older at enterostomy formation than the neonates of Group 2 [median (range), 11 (2-75) d vs 4 (1-101) d, P = 0.004)]. Significantly more ileostomies were created in Group 1 [47 (92.2%) vs 16 (64.0%), P = 0.007], whereas colostomies were performed significantly more often in Group 2 [2 (3.9%) vs 8 (32.0%), P = 0.002]. The initiation of enteral nutrition after enterostomy was significantly later in Group 1 infants than in Group 2 infants [median (range), 5 (3-13) vs 3 (1-9), P < 0.001]. The overall rate of one or more complications in patients of both groups after enterostomy formation was 80.3%, with rates of 86.3% in Group 1 and 68.0% in Group 2 (P = 0.073). Most patients suffered from two complications (23.7%). Four or more complications occurred in 21.6% of the infants in Group 1 and in 12.0% of the infants in Group 2 (P = 0.365). Following enterostomy closure, at least one complication was observed in 26.0% of the patients (30.6% in Group 1 and 16.7% in Group 2, P = 0.321). The occurrence of complications was not significantly different between neonates with NEC and infants with other intestinal disorders. 48 (65.8%) patients required no treatment or only pharmacological treatment for the complications that occurred [Clavien-Dindo-Classification (CDC) < III], while 25 (34.2%) required surgery to address the complications (CDC ≥ III). Early reversal of the enterostomy was performed significantly more often (P = 0.003) and the time to full enteral nutrition after closure was significantly longer [median (range), 7 (3-87) d vs 12 (5-93) d, P = 0.006] in infants with a CDC grading ≥ III than in infants with a CDC grading < III.
Conclusion: Complications occur in almost all infants with enterostomies. The majority of these complications are minor and do not require surgical treatment. There is a clear trend that neonates with NEC have a higher risk for developing complications than those without NEC.
Background: Arthropod-borne diseases remain a major health-threat for humans and animals worldwide. To estimate the distribution of pathogenic agents and especially Bartonella spp., we conducted tick microbiome analysis and determination of the infection status of wild animals, pets and pet owners in the state of Hesse, Germany.
Results: In total, 189 engorged ticks collected from 163 animals were tested. Selected ticks were analyzed by next generation sequencing (NGS) and confirmatory PCRs, blood specimens of 48 wild animals were analyzed by PCR to confirm pathogen presence and sera of 54 dogs, one cat and 11 dog owners were analyzed by serology. Bartonella spp. were detected in 9.5% of all ticks and in the blood of 17 roe deer. Further data reveal the presence of the human and animal pathogenic species of genera in the family Spirochaetaceae (including Borrelia miyamotoi and Borrelia garinii), Bartonella spp. (mainly Bartonella schoenbuchensis), Rickettsia helvetica, Francisella tularensis and Anaplasma phagocytophilum in ticks. Co-infections with species of several genera were detected in nine ticks. One dog and five dog owners were seropositive for anti-Bartonella henselae-antibodies and one dog had antibodies against Rickettsia conorii.
Conclusions: This study provides a snapshot of pathogens circulating in ticks in central Germany. A broad range of tick-borne pathogens are present in ticks, and especially in wild animals, with possible implications for animal and human health. However, a low incidence of Bartonella spp., especially Bartonella henselae, was detected. The high number of various detected pathogens suggests that ticks might serve as an excellent sentinel to detect and monitor zoonotic human pathogens.
Effects of seasonal or daily temperature variation on fitness and physiology of ectothermic organisms and their ways to cope with such variations have been widely studied. However, the way multivoltines organisms cope with temperature variations from one generation to the next is still not well understood. The aim of this study was to investigate whether the multivoltine midge Chironomus riparius Meigen (1803) responds mainly via acclimation as predicted by current theories or whether rapid genetic adaptation is involved. To investigate this issue, a common garden approach has been applied. A mix of larvae from five European populations was raised in the laboratory at three different pre‐exposure temperatures (PET): 14, 20, and 26°C. After three and five generations, respectively, larvae were exposed to three treatment temperatures (TT): 14, 20, and 26°C. Mortality was monitored for the first 48 hr and after emergence. After three generations, significant mortality rate differences depended on an interaction of PET and TT. This finding supports the hypothesis that chironomids respond rapidly to climatic variation via adaptive mechanisms and to a lesser extent via phenotypic plasticity. The result of the experiment indicates that three generations were sufficient to adapt to warm temperature, decreasing the mortality rate, highlighting the potential for chironomids to rapidly respond to seasonally changing conditions.
Purpose: To examine whether applying case management in general practices reduces thromboembolic events requiring hospitalization and major bleeding events (combined primary outcome). Secondary endpoints were mortality, frequency and duration of hospitalization, severe treatment interactions, adverse events, quality of anticoagulation, health-related quality of life and intervention costs, patients’ assessment of chronic illness care, self-reported adherence to medication, GP and HCA knowledge, patient knowledge and satisfaction with shared decision-making.
Methods: Cluster-randomized controlled trial undertaken at 52 general practices in Germany with adult patients with a long-term indication for oral anticoagulation. The complex intervention included training for healthcare assistants, information and quality circles for general practitioners and 24 months of case management for patients. Assessment was after 12 and 24 months. The intention-to-treat population included all randomized practices and patients, while the per-protocol analysis included only those that received treatment without major protocol violations.
Results: The mean (SD) age of the 736 patients was 73.5 (9.4) years and 597 (81.1%) had atrial fibrillation. After 24 months, the primary endpoint had occurred in 40 (11.0%) intervention and 48 (12.9%) control patients (hazard ratio 0.83, 95% CI 0.55 to 1.25; P = .37). Patients’ perceived quality of care, their knowledge, and HCAs’ knowledge, had improved significantly at 24 months. The other secondary endpoints did not differ between groups. In the intervention group, hospital admissions were significantly reduced in patients that received treatment without major protocol deviations.
Conclusions: Even though the main outcomes did not differ significantly, the intervention appears to have positively influenced several process parameters under "real-world conditions".
Hier werden bemerkenswerte floristische Funde aus Nordrhein-Westfalen aus dem Jahr 2018 und einige Nachträge aus 2017 zusammengestellt, die aus Sicht der Schriftleitung von landesweiter Bedeutung sind. Die Funde werden im Laufe des Jahres zunächst chronologisch auf die Homepage des Bochumer Botanischen Vereins gestellt und am Ende des Jahres zu einem Artikel zusammengefasst. Bei der Auswahl der Arten für diese Liste ist in der Regel nicht an Bestätigung bereits lange bekannter Vorkommen gedacht, die an Ort und Stelle durchgehend vorkommen, sondern z. B. an Neufunde seltener Arten, Wieder-funde seltener Arten, die zwischendurch verschwunden schienen (wie z. B. Acker-unkräuter) oder auch an bekannte Vorkommen, die erloschen sind oder kurz vor dem Erlöschen stehen. Außerdem nehmen Beobachtungen von neophytischen Arten einen großen Raum ein, die entweder auf dem Wege der Einbürgerung sind, deren Einbürgerung noch nicht allgemein bekannt bzw. anerkannt ist oder deren Vorkommen bisher erst selten für Nordrhein-Westfalen veröffentlicht wurden. Ein wichtiges Kriterium für aufgeführte Arten ist die Seltenheit im Bundesland oder in der betreffenden Großlandschaft bzw. Region. Die Zuordnung der Arten zu Pflanzenfamilien richtet sich nach PAROLLY & ROHWER 2016.
In Aachen konnten an zwei Stellen naturverjüngte Populationen von Corylus ×colurnoides, der Hybride zwischen der heimischen Hasel, C. avellana, und der oft gepflanzten, in Aachen tendenziell etablierten Baum-Hasel, C. colurna, festgestellt werden. Sie wachsen im Siedlungsbereich an Straßen und auf einem Friedhof. Hybrid-pflanzen zeigen morphologisch eine große Spanne zwischen den Eltern. Ihre Merkmale und die der Eltern werden ausführlich beschrieben und abgebildet. Ebenso werden Ökologie und Vorkommen der Elternarten in Aachen kurz angerissen. Die Entstehung der Hybridpopulationen wird diskutiert. Wahrscheinlich sind Hybridpopulationen unter Beteiligung gepflanzter Hybriden entstanden.
Weit ab von dem einzigen bekannten nordrhein-westfälischen Kleinareal von Ochlopoa supina im Hochsauerland konnte ein Bestand der Art in kolliner Lage in einem Scherrasen und einem Gebüschsaum in Aachen gefunden werden. Ebenfalls nachgewiesen werden konnte eine Pflanze von O. ×nannfeldtii s. l., der Hybride von O. supina mit O. annua s. l. Die Merkmale von O. supina, O. annua s. str. und O. ×nannfeldtii s. l. in Aachen werden ausführlich dargestellt, abgebildet und diskutiert.
Merkmale und Ökologie der im Aachener Stadtgebiet und angrenzenden Gebieten häufigen, nah verwandten Moose Streblotrichum commutatum (= Barbula commutata JUR. = B. sardoa (SCHIMP.) J.-P. FRAHM) und S. convolutum s. str. (= B. convoluta s. str.) werden vorgestellt. Durch stabile Merkmale wie Größe, Habitus, Blattform und -farbe sind sie meist problemlos zu unterscheiden und behalten bei Kultur unter gleichen Bedingungen ihre Unterschiede bei. Ökologisch sind sie im Untersuchungsgebiet euryök bei überlappenden, schwerpunktmäßig aber getrennten Standortbedingungen. S. commutatum wächst hauptsächlich auf Mauern und frischem Schotter sowie auf offenen, meist lehmigen Böden. Die Art hat dabei Pioniercharakter. Weniger belichtete, basenreiche Standorte werden bevorzugt, sind aber nicht notwendig. Demgegenüber zieht S. convolutum eher stabilere Standortbedingungen vor und bildet typischerweise gemeinsam mit anderen Arten geschlossene Moosrasen besonders auf älteren Wegen und übererdetem Teer. Offene bis halbschattige, somit recht lichtreiche Standorte werden bevorzugt. Literaturangaben zur Ökologie von S. commutatum und S. convolutum aus anderen Regionen werden diskutiert. Dabei stellt sich heraus, dass S. commutatum im Untersuchungsgebiet eine breitere Standortpalette besiedelt als für andere Regionen angegeben und anderswo beobachtete ökologische Unterschiede im Untersuchungsgebiet oft nicht oder nur tendenziell zutreffen.
Auf dem Gelände des Dortmunder Flughafens kommen an zwei Stellen Populationen der Knabenkraut-Hybride Dactylorhiza maculata agg. × D. majalis vor: an einer parallel zur Rollbahn verlaufenden nordexponierten Böschung und in der Dachbegrünung neben der Besucherterrasse des Flughafengebäudes. Die Flächen werden von den Flughafenmitarbeitern gepflegt, wodurch ein dauerhafter Schutz der Orchideen-Vorkommen gewähr-leistet ist. Morphologie und Zeichnungen der Blüten und Blätter der Hybriden werden genau beschrieben, ihre Wuchsorte und die Populationsentwicklung an den Wuchsorten geschildert. Auf dem Gelände konnte außerdem eine Reihe von interessanten Pflanzenarten gefunden werden, die auf der Roten Liste stehen. Sie stammen z. T. aus Ansaaten und haben sich durch geeignete Pflegemaßnahmen in Wiesen eingebürgert.
Es wird über den Erstnachweis der sehr seltenen Schachtelhalmhybride Equisetum ×meridionale (E. ramosis-simum × E. variegatum) für Nordrhein-Westfalen in einem ehemaligen Kalksteinbruch bei Hagen berichtet. Die Verbreitung der Hybride für Deutschland wird anhand einer Verbreitungskarte illustriert. Der Steinbruch beher-bergt mit u. a. E. variegatum und E. ×moorei darüber hinaus weitere für das Bundesland sehr bemerkenswerte Equisetum-Sippen. Diese werden vorgestellt und in Hinblick auf ihre Ansiedlung und Verbreitung diskutiert. Alle aus NRW bekannten Vertreter der Untergattung Hippochaete werden in einer Merkmalstabelle gegenübergestellt.