bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduction or expansion? A bit of both
Authors: Neels Jakob , Hartmann Stefan
Published: May 2018

This paper presents a diachronic analysis of the German quantifier/degree-modifier constructions ein bisschen (‘a bitDIM’) and ein wenig (‘a little’). On the basis of data from two historical corpora, we examine to what extent these constructions followed a grammaticalization path comparable to the one Traugott (e.g. 2008a) observed for their English counterparts. Quantitative analyses on their gradual context expansion are combined with qualitative analyses on potential bridging contexts for reanalysis. Their combined histories suggest that the older German modifiers may have served as attractor sets for an increasingly strengthened mid-level quantifier/degree-modifier schema, promoting the emergence of younger modifiers. These observations stress the crucial role that network links between constructions can play in grammaticalization.
Type frequency, productivity and schematicity in the evolution of the Latin secundum NP construction
Authors: Guardamagna Caterina
Published: May 2018

This paper adopts a constructional approach as a heuristic to explore the changes undergone by Latin secundum NP ‘according to NP’, considering both its frequency and its network organisation. My data demonstrate a significant syntactic and host-class expansion of secundum NP between the years BC 106 – AD 17 and a support to Barðdal’s (2008) model of productivity. The vocabulary growth curve for the construction also suggests that the productivity of secundum NP remains high in all the periods considered. Finally, the discussion highlights the role played by the social context in stimulating some of the changes observed, which is crucial in order to interpret the quantitative data.
Words of Crisis as Words of Power
Authors: Neüff Marta
Published: May 2018

The volume explores crisis rhetoric in contemporary U.S. American presidential speechmaking. Rhetorical leadership constitutes an inherent feature of the modern presidency. Particularly during times of critical events, the president is expected to react and address the nation. However, the power of the office also allows him or her to direct attention to particular topics and thus rhetorically create or exploit the notion of crisis. This monograph examines the verbal responses of George W. Bush and Barack Obama to pressing issues during their terms in office. Assuming an interdisciplinary approach, it illuminates the characteristics of modern crisis rhetoric. The aim of the book is to show that elements of Puritan rhetoric, and specifically the tradition of the jeremiad, although taken out of their original context and modified to suit a modern multiethnic society, can still be detected in contemporary political communication. It will be of interest to students and scholars of presidential rhetoric, political communication, sociolinguistics, and cultural studies.
Nominal referential values of semantic classifiers and role shift in signed narratives
Authors: Barberà Gemma , Quer Josep
Published: May 2018

Bringing together the areas of dynamic semantics and signed discourse, this article focuses on the dynamic potential of referring expressions, such as semantic and limb classifiers, and role shift constructions. On the basis of the Catalan Sign Language version of the Aesop’s fables, a qualitative analysis is presented, which focuses on the interaction between referring expressions and the accessibility scale. While the incorporation of semantic and limb classifiers constructions into the accessibility hierarchy leads to a more fine-grained analysis, role shift also reveals itself as an essential mechanism to associate the classifier handshape to the corresponding discourse referent. Dynamic operations are taken into account with the main aim of offering a novel proposal on discourse accessibility structure in signed narrative discourse.
Directional Particles in Cantonese
Authors: Chor Winnie
Published: May 2018

This book is the first on Cantonese that deals with the grammaticalization phenomenon systematically. Focusing on a group of twelve directional particles, this book tracks their grammaticalization pathways from full-fledged directional verbs, to directional particles indicating meanings relating to tense-aspect, modality, and quantification, in the post-verbal position. Some of these particles have undergone further grammaticalization to convey speaker’s subjective as well as intersubjective stances.
This book is also unique in its diachronic component. Examples in the book are drawn from various sources including early Cantonese pedagogical texts, Cantonese films, and contemporary Cantonese corpora, with data ranging from the mid-nineteenth century to the present. This book will be a valuable resource not only for all linguists interested in the development of grammatical forms, but also for teachers and students in conversation/discourse analysis, psychology, and anthropology interested in deepening their understanding of the interaction between language structure and use.
Suppressive effects of the peel of Citrus kawachiensis (Kawachi Bankan) on astroglial activation, tau phosphorylation, and inhibition of neurogenesis in the hippocampus of type 2 diabetic db/db mice
Authors: Okuyama Satoshi , Shinoka Wakana , Nakamura Kumi , Kotani Maho , Sawamoto Atsushi , Sugawara Kuniaki , Sudo Masahiko , Nakajima Mitsunari , Furukawa Yoshiko
Published: May 2018

We previously reported that the dried peel powder of Citrus kawachiensis exerted anti-inflammatory effects in the brain in several animal models. Hyperglycemia induces inflammation and oxidative stress and causes massive damage in the brain; therefore, we herein examined the anti-inflammatory and other effects of the dried peel powder of C. kawachiensis in the streptozotocin-induced hyperglycemia mice model and in the type 2 diabetic db/db mice model. The C. kawachiensis administration inhibited microglial activation in the hippocampus in the streptozotocin-injected mice. Moreover, The C. kawachiensis treatment inhibited astroglial activation in the hippocampus and the hyperphosphorylation of tau at 231 of threonine and 396 of serine in hippocampal neurons, and also relieved the suppression of neurogenesis in the dentate gyrus of the hippocampus in the db/db mice. It was suggested that the dried peel powder of C. kawachiensis exerts anti-inflammatory and neuroprotective effects in the brain.
Breakthrough Fungal Infections in Patients With Leukemia Receiving Isavuconazole
Authors: Rausch Caitlin R , DiPippo Adam J , Bose Prithviraj , Kontoyiannis Dimitrios P
Published: May 2018

We retrospectively assessed breakthrough invasive fungal infections (b-IFIs) in 100 consecutive patients with leukemia receiving single-agent isavuconazole; 13 had documented b-IFIs (candidiasis in 6, mucormycosis in 4). All b-IFIs were observed in patients with prolonged neutropenia and active leukemia.
Chipping to Destroy Egg Masses of the Spotted Lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae)
Authors: Cooperband Miriam F , Mack Ron , Spichiger Sven-Erik
Published: May 2018

A chipping study was conducted during the winter of 2015 in Berks County, Pennsylvania, to determine efficacy against field collected egg masses of the spotted lanternfly, Lycorma delicatula (White) (Hemiptera: Fulgoridae). Infested Ailanthus altissima Swingle (Sapindales: Simaroubaceae) trees in eastern Pennsylvania were felled and egg masses were counted. Sections were either chipped or allowed to remain intact as controls. Chipped material and intact wood controls were placed in screened barrels and monitored for emergence. No L. delicatula nymphs were found in the chipped treatment, as opposed to hundreds of nymphs per barrel in the intact control treatment. We conclude that mid-winter chipping, using the standard 1-inch in 2-dimension chip size, is a quarantine safe mitigation method suitable for treating wood infested with L. delicatula egg masses.
MiRNA-181d Expression Significantly Affects Treatment Responses to Carmustine Wafer Implantation
Authors: Sippl Christoph , Ketter Ralf , Bohr Lisa , Kim Yoo Jin , List Markus , Oertel Joachim , Urbschat Steffi
Published: May 2018

BACKGROUND

Standard therapeutic protocols for glioblastoma, the most aggressive type of brain cancer, include surgery followed by chemoradiotherapy. Additionally, carmustine-eluting wafers can be implanted locally into the resection cavity.

OBJECTIVE

To evaluate microRNA (miRNA)-181d as a prognostic marker of responses to carmustine wafer implantation.

METHODS

A total of 80 glioblastoma patients (40/group) were included in a matched pair analysis. One group (carmustine wafer group) received concomitant chemoradiotherapy with carmustine wafer implantation (Stupp protocol). The second group (control group) received only concomitant chemoradiotherapy. All tumor specimens were subjected to evaluations of miRNA-181d expression, results were correlated with further individual clinical data. The Cancer Genome Atlas (TCGA) dataset of 149 patients was used as an independent cohort to validate the results.

RESULTS

Patients in the carmustine wafer group with low miRNA-181d expression had significantly longer overall (hazard ratio [HR], 35.03, [95% confidence interval (CI): 3.50-350.23], P = .002) and progression-free survival (HR, 20.23, [95% CI: 2.19-186.86], P = .008) than patients of the same group with a high miRNA-181d expression. These correlations were not observed in the control group. The nonsignificance in the control group was confirmed in the independent TCGA dataset. The carmustine wafer group patients with low miRNA-181d expression also had a significantly longer progression-free (P = .049) and overall survival (OS) (P = .034), compared with control group patients. Gross total resection correlated significantly with longer OS (P = .023).

CONCLUSION

MiRNA-181d expression significantly affects treatment responses to carmustine wafer implantation.
Performance milestones in postoperative physical therapy after total hip arthroplasty: impact on length of stay and discharge destination
Authors: Vaudreuil Nicholas J. , McGlaston Timothy J. , Gulledge Catarina D. , Bove Allyn M. , Klatt Brian A.
Published: May 2018

Background:

Early postoperative physical therapy (PT) regimens after total hip arthroplasty (THA) have become the standard of care at most institutions. Initiating PT on postoperative day (POD) 0 after THA has been shown to shorten hospital length of stay (LOS). However, objective performance milestones for early therapy are not well established.

Methods:

This study retrospectively reviewed 277 patients who underwent primary THA. Specific data assessed included demographic information, number of feet walked at the POD 0 and POD 1 PT evaluations, LOS, and discharge destination. The primary outcome assessed was the relationship between performance in PT with both LOS and discharge destination. For those patients who could not participate in therapy, reasons cited by therapy documentation were recorded.

Results:

Patients who received POD 0 PT had a shorter LOS (P=0.032), decreased discharge to extended care facility (ECF) (P<0.001), and walked farther in PT on POD 1 (P<0.001). Ambulating farther than 10 feet on POD 0 or 100 feet on POD 1 resulted in significant decreases in LOS (P=0.005, P<0.001) and in the percentage of patients discharged to an ECF (P=0.027, P<0.001). The most common reason for inability to participate in therapy was late arrival to the inpatient floor.

Conclusions:

Achieving mobility milestones is a key factor in the determination of a patient’s discharge timing and destination after THA. Limited data exist validating objective performance milestones for patients receiving early PT after THA. This study suggests that achieving mobility milestones on POD 0 and 1 can significantly improve short-term outcomes.
The hidden cost of training orthopaedic surgery residents to perform an open carpal tunnel release
Authors: Daley Dane N. , Patterson Travis M. , Peterson Ann M. , Kokko Kyle P.
Published: May 2018

Background:

Training orthopaedic surgery residents is time consuming and expensive. The objective of the current study was to determine the time and costs associated with teaching orthopaedic residents to perform an open carpal tunnel release (CTR).

Methods:

A retrospective chart review of a single orthopaedic hand surgeon’s outpatient surgical cases over 18 mo was performed. One hundred-six isolated open carpal tunnel releases were identified. Seventy-seven were performed while training orthopaedic surgery residents, and 29 were performed by the attending surgeon alone. Standard demographics, post-graduate year (PGY) of training, and surgical times were abstracted from the charts.

Results:

The time (minutes) required to perform a CTR for PGY-2, 3, and 4 when compared to the attending surgeon was 13.8±3.5 (P=0.012), 16.4±4.9 (P<0.001) and 13.1±4.2 (P=0.044), respectively, with a resident average of 13.7±4.2 min. The attending surgeon required 10.4±4.2 min, which is 3.3 min less than the average resident time (P<0.001). There was no statistically significant difference when comparing surgical times between resident years of training.

Conclusions:

Orthopaedic surgical residents on average required 32% more surgical time to perform an open CTR. Total ambulatory operating room and anesthesia charge was approximately $137/min at our institution with a collection rate of 27% resulting in a per minute cost equal to $37/min. The 77 cases performed while training residents added an additional $34,811.70 in charges with a resultant $9,401.70 in reimbursement.

Level of Evidence:

Level IV, retrospective review.
Time Course of Radiologic Changes After Lumbar Total Disc Replacement
Authors: Hur Jung-Woo , Kim Jin-Sung , Ryu Kyeong-Sik , Shin Myeong-Hoon , Park Chun-Kun
Published: May 2018

Study Design:

This was a retrospective observatory analysis study.

Objective:

The purpose of this study was to evaluate long-term safety and therapeutic effectiveness of the lumbar total disc replacement (TDR) using ProDisc-L by analyzing the radiologic changes at the index and adjacent levels in minimum 5-year follow-up.

Summary of Background Data:

Early successful clinical results of lumbar TDR have been reported. However, few reports have published its therapeutic effectiveness and radiologic degenerative changes at the index and adjacent segments in the long term.

Materials and Methods:

Forty-three patients were followed-up for at least 60 months. Radiologic changes were assessed by segmental range of motion (ROM) at the index and adjacent levels, global lumbar lordosis, and disc space height (DSH). The magnetic resonance imaging and computed tomographic scans were used to determine the facet arthrosis and intervertebral disc degeneration at the index and adjacent levels.

Results:

Gradual decrements of DSH restoration were observed until the last follow-up. Mean global and segmental ROM of index segments were significantly reduced (P=0.044, 0.00) at the last visit. There were 21 patients (48.8%) with no motion at index segment (ROM<0.5 degrees) at the last visit. Among the 56 segments operated on, progression of facet arthrosis was observed in 30.3% of index segments and 10.9% of adjacent segments. None of the postoperative radiologic parameters included in the present study presented significant correlation with clinical outcome.

Conclusions:

The study demonstrates that only half of the lumbar TDR patients can maintain segmental motion at the index level >5-year after surgery and TDR provides a good clinical outcome postoperatively regardless of motion preservation or DSH height preservation at the last follow-up. After TDR, the degenerative changes in the index and adjacent segments advanced as compared with our previous report of 2-year follow-up, however, these changes did not appear to exert negative influence upon clinical outcomes.
Exercise for Preventing Hospitalization and Readmission in Adults With Congestive Heart Failure
Authors: Aronow Wilbert S. , Shamliyan Tatyana A.
Published: May 2018

We critically appraised all available evidence regarding exercise interventions for improving patient survival and reducing hospital admissions in adults with chronic heart failure (HF). We searched 4 databases up to April 2018 and graded the quality of evidence according to the Grading of Recommendations Assessment, Development and Evaluation working group approach. We reviewed 7 meta-analyses and the publications of 48 randomized controlled trials (RCTs). In HF with reduced ejection fraction, low-quality evidence suggests that exercise prevents all-cause hospitalizations [Relative risk (RR), 0.77; 95% confidence interval (CI), 0.63 to 0.93; 1328 patients in 15 RCTs] and hospitalizations due to HF (RR, 0.57; 95% CI, 0.37 to 0.88; 1073 patients in 13 RCTs) and improves quality of life (standardized mean difference, −0.37; 95% CI, −0.60 to −0.14; 1270 patients in 25 RCTs) but has no effect on mortality. In HF with preserved ejection fraction, low-quality evidence suggests that exercise improves peak oxygen uptake (mean difference, 2.36; 95% CI, 1.16 to 3.57; 171 patients in 3 RCTs) and quality of life (mean difference, −4.65; 95% CI, −8.46 to −0.83; 203 patients in 4 RCTs). In patients after heart transplantation, low-quality evidence suggests that exercise improves peak oxygen uptake (standardized mean difference, 0.68; 95% CI, 0.43 to 0.93; 284 patients in 9 RCTs) but does not improve quality of life. In order to reduce hospitalization and improve quality of life for adults with HF and reduced ejection fraction, clinicians should recommend exercise interventions. For adults with HF and preserved ejection fraction and in those undergoing heart transplantation, clinicians may recommend exercise interventions in order to improve peak oxygen uptake.
Effectiveness of Multi-strain Versus Single-strain Probiotics
Authors: Ouwehand Arthur C. , Invernici Marcos M. , Furlaneto Flávia A.C. , Messora Michel R.
Published: May 2018

Probiotics are investigated as single-strain and multistrain products. In the market, however, there is an increasing tendency to work with multistrain probiotics, in particular, products with a high number of different strains. There are some thoughts behind this: more strains imply more chances of success; it can mean a broader spectrum of efficacy, and there is often the hope that there are at least additive and, potentially, even synergistic effects. The present review did not find convincing evidence that these assumptions are valid. There is, however, also no strong evidence that the assumptions are incorrect and/or that there is antagonistic activity between strains in a combination. We suggest that, to answer these questions, structured research is conducted. Starting with a systematic review of meta-analyses that have compared single-strain and multistrain probiotic efficacy, dedicated human studies need to be performed, comparing single-strain and multistrain probiotics to each other and placebo. In vitro and animal studies can provide indications and may help understand mechanisms. For human, animal, and in vitro studies, it is recommended to work with the simple setup of 2 single strains, a 2-strain combination, and placebo. It is also important in such research to take into consideration the doses, as a combination product will have a higher total dose.
Alleviation of Cyclophosphamide-induced Hemorrhagic Cystitis by Dietary Pomegranate: A Comparative Experimental Study With Mesna
Authors: Mahmoudi Negin , Eftekharzadeh Sahar , Golmohammadi Marzieh , Khorramirouz Reza , Hashemi Javad , Kashani Zeinab , Alijani Maryam , Hamidieh Amir Ali , Kajbafzadeh Abdol-Mohammad
Published: May 2018

In this study, we investigated the effects of pomegranate on alleviating cyclophosphamide-induced hemorrhagic cystitis (HC). Initially, 16 Sprague-Dawley rats were allocated into 4 groups: group 1 (control), group 2 (CP) in which HC was induced by cyclophosphamide; group 3 (CP+M), HC-induced rats that received Mesna regimen, and group 4 (CP+P), which compromised rats that had been on a 14-day diet of pomegranate juice before HC induction. Cystometry was performed a few hours before euthanasia; after euthanasia, aortic blood samples and bladder tissue samples were obtained to perform TUNEL assay, and histopathologic and biochemical assessments. Urodynamic findings revealed that mean detrusor pressure in CP+P was significantly lower compared with that in CP and CP+M (P<0.05). Histopathologically, urothelium destruction and inflammation were lower in CP+P and CP+M compared with that in CP. Collagen destruction was less prominent in CP+P compared with that in CP and CP+M. Tissue and plasma levels of malondialdehyde were significantly lower in CP+P versus CP (P<0.05). Catalase activity and total protein thiol group levels in plasma and bladder tissue were higher in CP+P versus CP (P<0.05). The TUNEL positivity in CP+P was significantly weaker than that in CP, indicating less DNA fragmentation and apoptosis. Pomegranate’s characteristics could significantly affect the inflammatory and destructive process of hemorrhagic cystitis.
Abundance of the Organic Anion-transporting Polypeptide OATP4A1 in Early-Stage Colorectal Cancer Patients: Association With Disease Relapse
Authors: Buxhofer-Ausch Veronika , Sheikh Maidah , Ausch Christoph , Zotter Simone , Bauer Heike , Mollik Marina , Reiner Angelika , Gleiss Andreas , Jäger Walter , Sebesta Christian , Kriwanek Stephan , Thalhammer Theresia
Published: May 2018

The abundance of OATP4A1 in colorectal cancer (CRC) might be related to tumor progression. This was studied by immunohistochemistry on paraffin-embedded samples obtained from 178 patients (43 patients with a relapse within 5 y) with early-stage CRC. Positivity for OATP4A1 in tumor cells and noncancerous mucosal cells was proved by double-immunofluorescence staining with antibodies against OATP4A1 and keratin 8, whereas antibodies against appropriate CD markers were used to identify immune cells. Automated microscopic image analysis was used to measure the percentage of OATP4A1-positive cells and OATP4A1 staining intensity in tumor, immune, and adjacent normal-looking mucosal cells separately, as well as in the mucosal and immune cells of 14 nonmalignant tissue samples. In CRC the percentage of OATP4A1-positive cells, but not staining intensity, was significantly higher in tumor and mucosal cells adjacent to the tumor compared to the mucosa of nonmalignant samples (P<0.001 each). No difference was registered between immune cells in malignant and nonmalignant samples. Importantly, high levels of OATP4A1 in immune (odds ratio, 0.73; confidence interval, 0.63-0.85; P<0.001), and tumor cells (odds ratio, 0.79; confidence interval, 0.69-0.91; P<0.001) are significantly associated with a low risk of recurrence and also significantly enhance the discriminative power of other clinical parameters [such as International Union Against Cancer (UICC), adjuvant therapy, localization of the primary tumor] of the risk of relapse (receiver operating characteristics analysis; P=0.002). Using an advanced digital microscopic quantification procedure, we showed that OATP4A1 abundance is negatively associated with tumor recurrence in early-stage CRC. This digital scoring procedure may serve as a novel tool for the assessment of potential prognostic markers in early-stage CRC.
Ensemble allosteric model: energetic frustration within the intrinsically disordered glucocorticoid receptor
Authors: White Jordan T. , Li Jing , Grasso Emily , Wrabl James O. , Hilser Vincent J.
Published: May 2018

Allostery is an important regulatory phenomenon enabling precise control of biological function. Initial understanding of allostery was gained from seminal work on conformational changes exhibited by structured proteins. Within the last decade, protein allostery has also been demonstrated to occur within intrinsically disordered proteins. This emerging concept of disorder-mediated allostery can be usefully understood in the context of a thermodynamic ensemble. The advantage of this ensemble allosteric model is that it unifies the explanations of allostery occurring within both structured and disordered proteins. One central finding from this model is that energetic coupling, the transmission of a signal between separate regions (or domains) of a protein, is maximized when one or more domains are disordered. This is due to a disorder–order transition that contributes additional coupling energy to the allosteric system through formation of a molecular interaction surface or interface. A second key finding is that multiple interfaces may constructively or destructively interfere with each other, resulting in a new form of allosteric regulation called ‘energetic frustration’. Articulating protein allostery in terms of the thermodynamic ensemble permits formulation of experimentally testable hypotheses which can increase fundamental understanding and direct drug-design efforts. These ideas are illustrated here with the specific case of human glucocorticoid receptor, a medically important multi-domain allosteric protein that contains both structured and disordered regions and exemplifies ‘energetic frustration’.

This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization
Authors: Ponzoni Luca , Zhang She , Cheng Mary Hongying , Bahar Ivet
Published: May 2018

The LeuT-fold superfamily includes secondary active transporters from different functional families, which share a common tertiary structure, despite having a remarkably low sequence similarity. By identifying the common structural and dynamical features upon principal component analysis of a comprehensive ensemble of 90 experimentally resolved structures and anisotropic network model evaluation of collective motions, we provide a unified point of view for understanding the reasons why this particular fold has been selected by evolution to accomplish such a broad spectrum of functions. The parallel identification of conserved sequence features, localized at specific sites of transmembrane helices, sheds light on the role of broken helices (TM1 and TM6 in LeuT) in promoting ion/substrate binding and allosteric interconversion between the outward- and inward-facing conformations of transporters. Finally, the determination of the dynamics landscape for the structural ensemble provides a promising framework for the classification of transporters based on their dynamics, and the characterization of the collective movements that favour multimerization.

This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
Markov models for the elucidation of allosteric regulation
Authors: Sengupta Ushnish , Strodel Birgit
Published: May 2018

Allosteric regulation refers to the process where the effect of binding of a ligand at one site of a protein is transmitted to another, often distant, functional site. In recent years, it has been demonstrated that allosteric mechanisms can be understood by the conformational ensembles of a protein. Molecular dynamics (MD) simulations are often used for the study of protein allostery as they provide an atomistic view of the dynamics of a protein. However, given the wealth of detailed information hidden in MD data, one has to apply a method that allows extraction of the conformational ensembles underlying allosteric regulation from these data. Markov state models are one of the most promising methods for this purpose. We provide a short introduction to the theory of Markov state models and review their application to various examples of protein allostery studied by MD simulations. We also include a discussion of studies where Markov modelling has been employed to analyse experimental data on allosteric regulation. We conclude our review by advertising the wider application of Markov state models to elucidate allosteric mechanisms, especially since in recent years it has become straightforward to construct such models thanks to software programs like PyEMMA and MSMBuilder.

This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
The ‘allosteron’ model for entropic allostery of self-assembly
Authors: McLeish Tom , Schaefer C. , von der Heydt A. C.
Published: May 2018

Using the simple ‘allosteron’ model, we show that it is possible, in principle, to elicit pathways by which fluctuation allostery affects self-assembly of protein complexes. We treat the cases of (i) protein fibrils and nucleation, (ii)
n
-mer protein complexes, and (iii) weakly attractive allosteric interactions in protein-like soft nanoscale objects that can be tuned to define exclusive self-associating families.

This article is part of a discussion meeting issue ‘Allostery and molecular machines’.
Synthesis of oxyfunctionalized NSAID metabolites by microbial biocatalysts
Authors: Klenk Jan M. , Kontny Lisa , Nebel Bernd A. , Hauer Bernhard
Published: May 2018

The synthesis of valuable metabolites and degradation intermediates of drugs, like non-steroidal anti-inflammatory drugs (NSAIDs), are substantially for toxicological and environmental studies, but efficient synthesis strategies and the metabolite availability are still challenging aspects. To overcome these bottlenecks filamentous fungi as microbial biocatalysts were applied. Different NSAIDs like diclofenac, ibuprofen, naproxen and mefenamic acid could be oxyfunctionalized to produce human metabolites in isolated yields of up to 99% using 1 g L−1 of substrate. Thereby the biotransformations using Beauveria bassiana, Clitocybe nebularis or Mucor hiemalis surpass previous reported chemical, microbial and P450-based routes in terms of efficiency. In addition to different hydroxylated compounds of diclofenac, a novel metabolite, 3’,4’-dihydroxydiclofenac, has been catalyzed by B. bassiana and the responsible P450s were identified by proteome analysis. The applied filamentous fungi present an interesting alternative, microbial biocatalysts platform for the production of valuable oxyfunctionalized drug metabolites.

Importance

The occurrence of pharmaceutically active compounds, such as diclofenac and its metabolites, in the environment, in particular in aquatic systems, is of increasing concern because of the increased application of drugs. Standards of putative metabolites are therefore necessary for environmental studies. Moreover, pharmaceutical research and development requires assessment of the bioavailability, toxicity and metabolic fate of potential new drugs to ensure its safety for users and the environment. Since most of the reactions in the early pharmacokinetics of drugs are oxyfunctionalizations catalysed by P450s, oxyfunctionalized metabolites are of major interest. However, to assess these metabolites chemical synthesis often suffer from multistep reactions, toxic substances, polluting conditions and achieve only low regioselectivity. Biocatalysis can contribute to this by using microbial cell factories. The significance of our research is to complement or even exceed synthetic methods for the production of oxyfunctionalized drug metabolites.
Operationalizing ecological connectivity in spatial conservation planning with Marxan Connect
Authors: Daigle Remi M , Metaxas Anna , Balbar Arieanna , McGowan Jennifer , Treml Eric A , Kuempel Caitlin D , Possingham Hugh P , Beger Maria
Published: May 2018

Globally, protected areas are being established to protect biodiversity and to promote ecosystem resilience. The typical spatial conservation planning process leading to the creation of these protected areas focuses on representation and replication of ecological features, often using decision support systems such as Marxan. Unfortunately, Marxan currently requires manual input or specialised scripts to explicitly consider ecological connectivity, a property critical to metapopulation persistence and resilience. "Marxan Connect" is a new open source, open access Graphical User Interface (GUI) designed to assist conservation planners in the systematic operationalization of ecological connectivity in protected area network planning. Marxan Connect is able to incorporate estimates of demographic connectivity (e.g. derived from tracking data, dispersal models, or genetics) or structural landscape connectivity (e.g. isolation by resistance). This is accomplished by calculating metapopulation-relevant connectivity metrics (e.g. eigenvector centrality) and treating those as conservation features, or using the connectivity data as a spatial dependency amongst sites to be included in the prioritization process. Marxan Connect allows a wide group of users to incorporate directional ecological connectivity into conservation plans. The least-cost conservation solutions provided by Marxan Connect, combined with ecologically relevant post-hoc testing, are more likely to support persistent and resilient metapopulations (e.g. fish stocks) and provide better protection for biodiversity than if connectivity is ignored.
A constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria)
Authors: Cornet Luc , Wilmotte Annick , Javaux Emmanuelle J. , Baurain Denis
Published: May 2018

Objectives

Cyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria, the unique bacterial group able to perform oxygenic photosynthesis. This group has been extensively studied by phylogenomics during the last decade, notably because it is widely accepted that Cyanobacteria were responsible for the spread of photosynthesis to the eukaryotic domain. The aim of this study was to evaluate the fraction of the oxyphotobacterial diversity for which sequenced genomes are available for genomic studies. For this, we built a phylogenomic-constrained SSU rRNA (16S) tree to pinpoint unexploited clusters of Oxyphotobacteria that should be targeted for future genome sequencing, so as to improve our understanding of Oxyphotobacteria evolution.

Results

We show that only a little fraction the oxyphotobacterial diversity has been sequenced so far. Indeed 31 rRNA clusters on the 60 composing the photosynthetic Cyanobacteria have a fraction of sequenced genomes <1%. This fraction remains low (min = 1%, median = 11.1 %, IQR = 7.3) within the remaining “‘sequenced” clusters that already contain some representative genomes. The “unsequenced” clusters are scattered across the whole Oxyphotobacteria tree, at the exception of very basal clades (G, F, E) and the Oscillatoriales clade (A), which have higher fractions of representative genomes. Yet, the very basal clades still feature some (sub)clusters without any representative genome. This last result is especially important, as these basal clades are prime candidate for plastid emergence.
Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies
Authors: Schiza Christina , Korbakis Dimitrios , Panteleli Efstratia , Jarvi Keith , Drabovich Andrei P. , Diamandis Eleftherios P.
Published: May 2018

TEX101 is a testis-specific protein expressed exclusively in male germ cells and is a validated biomarker of male infertility. Studies in mice suggest that TEX101 is a cell-surface chaperone which regulates, through protein-protein interactions, the maturation of proteins involved in spermatozoa transit and oocyte binding. Male TEX101-null mice are sterile. Here, we identified by co-immunoprecipitation-mass spectrometry the interactome of human TEX101 in testicular tissues and spermatozoa. The testis-specific cell-surface dipeptidase 3 (DPEP3) emerged as the top hit. We further validated the TEX101-DPEP3 complex by using hybrid immunoassays. Combinations of antibodies recognizing different epitopes of TEX101 and DPEP3 facilitated development of a simple immunoassay to screen for disruptors of TEX101-DPEP3 complex. As a proof-of-a-concept, we demonstrated that anti-TEX101 antibody T4 disrupted the native TEX101-DPEP3 complex. Disrupting antibodies may be used to study the human TEX101-DPEP3 complex, and to develop modulators for male fertility.

Non-standard abbreviations

TEX101

Testis-expressed sequence 101 protein

DPEP3

Dipeptidase 3

AC-MS

Affinity capture-mass spectrometry

co-IP-MS

Coimmunoprecipitation-mass spectrometry

GPI

Glycosylphosphatidylinositol

LFQ

Label-free quantification

mAb

Monoclonal antibody

NHS

N-hydroxysuccinimide

PRM

Parallel reaction monitoring

PTM

Posttranslational modification

SP

Seminal plasma

SRM

Selected reaction monitoring

FDR

false detection rate
Identification of TEX101 functional interactome through proteomic measurement of human spermatozoa homozygous for the missense variant rs35033974
Authors: Schiza Christina , Korbakis Dimitrios , Jarvi Keith , Diamandis Eleftherios P. , Drabovich Andrei P.
Published: May 2018

TEX101 is a testis-specific cell-surface protein expressed exclusively in the male germ cells and a validated biomarker of male infertility. Mouse TEX101 was found essential for male fertility, and was suggested to function as a cell surface chaperone involved in maturation of proteins required for sperm migration and sperm-oocyte interaction. However, the precise functional role of human TEX101 is not known and cannot be studiedin vitrodue to the lack of human germ cell lines. Here, we genotyped 386 healthy fertile men and sub-fertile patients for a common and potentially deleterious missense variant rs35033974 ofTEX101, and identified 52 heterozygous and 4 homozygous patients. We then discovered by targeted proteomics that the variant allele rs35033974 was associated with near-complete degradation (>97%) of the corresponding G99V TEX101 form, and suggested that spermatozoa of homozygous patients could serve as a knockdown model to study TEX101 function in humans. Differential proteomic profiling with label-free quantification measured 8,046 proteins in spermatozoa of eight men and identified 8 cell-surface and 9 secreted testis-specific proteins significantly down-regulated in four patients homozygous for rs35033974. Substantially reduced levels of testis-specific cell-surface proteins potentially involved in sperm migration and sperm-oocyte fusion (including LY6K and ADAM29) were confirmed by targeted proteomics and western blotting assays. Since recent population-scale genomic data revealed homozygous fathers with biological children, rs35033974 is not a single pathogenic factor of male infertility in humans. However, median TEX101 levels in seminal plasma were found 5-fold lower (P=0.0005) in heterozygous than in wild-type men of European ancestry. We conclude that spermatozoa of rs35033974 homozygous men have substantially reduced levels of TEX101 and could be used as a model to elucidate the precise TEX101 function, which will advance biology of human reproduction.

Non-standard abbreviations

TEX101

Testis-expressed sequence 101 protein

LY6K

Lymphocyte antigen 6 complex locus K

ADAM29

A disintegrin and metalloproteinase domain-containing protein 29

DPEP3

Dipeptidase 3

BH-adjusted t-test

Benjamini-Hochberg-adjusted t-test

FDR

False discovery rate

FWHM

Full width at half maximum

GPI

Glycosylphosphatidylinositol

LC-MS/MS

liquid chromatography - tandem mass spectrometry

LFQ

Label-free quantification

MS

Mass spectrometry

mAb

Monoclonal antibody

MWU

Mann Whitney Unpaired t-test

PRM

Parallel reaction monitoring

ROC AUC

Receiver operating characteristic area under the curve

SCX

strong cation exchange chromatography

SP

seminal plasma

SNV

Single nucleotide variation

SRM

Selected reaction monitoring

WT

wild-type
Improving management strategies of plant diseases using sequential sensitivity analyses
Authors: Rimbaud Loup , Dallot Sylvie , Bruchou Claude , Thoyer Sophie , Jacquot Emmanuel , Soubeyrand Samuel , Thébaud Gaël
Published: May 2018

Improvement of management strategies of epidemics is often hampered by constraints on experiments at large spatiotemporal scales. A promising approach consists of modelling the biological epidemic process and human interventions, which both impact disease spread. However, few methods enable the simultaneous optimisation of the numerous parameters of sophisticated control strategies. To do so, we propose a heuristic approach (i.e., a practical improvement method approximating an optimal solution) based on sequential sensitivity analyses. In addition, we use an economic improvement criterion, based on the net present value, accounting for both the cost of the different control measures and the benefit generated by disease suppression. This work is motivated by sharka (caused by Plum pox virus), a vector-borne disease of prunus trees (especially apricot, peach and plum) whose management in orchards is mainly based on surveillance and tree removal. We identified the key parameters of a spatiotemporal model simulating sharka spread and control, and approximated optimal values for these parameters. The results indicate that the current French management of sharka efficiently controls the disease, but can be economically improved using alternative strategies that are identified and discussed. The general approach should help policymakers to design sustainable and cost-effective strategies for disease management.
Fine-scale resolution and analysis of runs of homozygosity in domestic dogs
Authors: Sams Aaron J. , Boyko Adam R.
Published: May 2018

Abstract/Summary

Inbreeding and consanguinity leave distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (> 5 megabase (Mb)) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long versus short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied.

In domestic dogs, nearly 200 mutations are known to cause recessive diseases, most of which can be efficiently assayed using SNP arrays. By examining genome-wide data from over 200,000 markers, including 150 recessive disease variants, we built high-resolution ROH density maps for nearly 2,500 dogs, recording ROH down to 500 kilobases. We observed over 500 homozygous deleterious recessive genotypes in the panel, 90% of which overlapped with ROH inferred by GERMLINE. Although most of these genotypes were contained in ROH over 5 Mb in length, 14% were contained in short (0.5 - 2.5 Mb) tracts, a significant enrichment compared to the genetic background, suggesting that even short tracts are useful for computing inbreeding metrics like the coefficient of inbreeding estimated from ROH (FROH).

In our dataset, FROH differed significantly both within and among dog breeds. All breeds harbored some regions of reduced genetic diversity due to drift or selective sweeps, but the degree of inbreeding and the proportion of inbreeding caused by short versus long tracts differed between breeds, reflecting their different population histories. Although only available for a few species, large genome-wide datasets including recessive disease variants hold particular promise not only for disentangling the genetic architecture of inbreeding depression, but also evaluating and improving upon current approaches for detecting ROH.
Prioritizing network communities
Authors: Zitnik Marinka , Sosič Rok , Leskovec Jure
Published: May 2018

Uncovering modular structure in networks is fundamental for systems in biology, physics, and engineering. Community detection identifies candidate modules as hypotheses, which then need to be validated through experiments, such as mutagenesis in a biological laboratory. Only a few communities can typically be validated, and it is thus important to prioritize which communities to select for downstream experimentation. Here we develop CRANK, a mathematically principled approach for prioritizing network communities. CRANKefficiently evaluates robustness and magnitude of structural features of each community and then combines these features into the community prioritization. CRANKcan be used with any community detection method. It needs only information provided by the network structure and does not require any additional metadata or labels. However, when available, CRANKcan incorporate domain-specific information to further boost performance. Experiments on many large networks show that CRANKeffectively prioritizes communities, yielding a nearly 50-fold improvement in community prioritization.
T Cell Activation Triggers Reversible Inosine-5'-Monophosphate Dehydrogenase Assembly
Authors: Duong-Ly Krisna , Kuo Yin-Ming , Johnson Matthew C , Kollman Justin , Soboloff Jonathan , Rall Glenn , Andrews Andrew , Peterson Jeffrey
Published: May 2018

T cell-mediated adaptive immunity requires naïve, unstimulated T cells to transition from a quiescent metabolic state into a highly proliferative state upon T cell receptor engagement. This complex process depends on transcriptional changes mediated by Ca2+-dependent NFAT signaling, mTOR-mediated signaling and increased activity of the guanine nucleotide biosynthetic enzyme inosine-5'-monophosphate (IMP) dehydrogenase (IMPDH). Inhibitors of these pathways serve as potent immunosuppressants. Unexpectedly, we discovered that all three pathways converge to promote the assembly of IMPDH protein into micron-scale macromolecular filamentous structures in response to T cell activation. Assembly is post-transcriptionally controlled by mTOR and the Ca2+ influx regulator STIM1. Furthermore, IMPDH assembly and catalytic activity were negatively regulated by guanine nucleotide levels, suggesting a negative feedback loop that limits biosynthesis of guanine nucleotides. Filamentous IMPDH may be more resistant to this inhibition, facilitating accumulation of the higher GTP levels required for T cell proliferation.
Sequential replay of non-spatial task states in the human hippocampus
Authors: Schuck Nicolas W , Niv Yael
Published: May 2018

Neurophysiological research has found that previously experienced sequences of spatial events are reactivated in the hippocampus of rodents during wakeful rest. This phenomenon has become a cornerstone of modern theories of memory and decision making. Yet, whether hippocampal sequence reactivation at rest is of general importance also for humans and non-spatial tasks has remained unclear. Here, we investigated sequences of fMRI BOLD activation patterns in humans during wakeful rest following a sequential non-spatial decision-making task. We found that pattern reactivations within the human hippocampus reflected the order of previous task state sequences, and that the extent of this offline reactivation was related to the on-task representation of task states in the orbitofrontal cortex. Permutation analyses and fMRI signal simulations confirmed that these results reflected underlying BOLD activity, and showed that our novel statistical analyses are, in principle, sensitive to sequential neural events occurring as fast as one hundred milliseconds apart. Our results support the importance of sequential reactivation in the human hippocampus for decision making, and establish the feasibility of investigating such rapid signals with fMRI, despite its substantial temporal limitations.
A limited number of double-strand DNA breaks are sufficient to delay cell cycle progression
Authors: van den Berg Jeroen , Manjón Anna G. , Kielbassa Karoline , Feringa Femke M. , Freire Raimundo , Medema René H.
Published: May 2018

DNA damaging agents cause a variety of lesions, of which DNA double-strand breaks (DSBs) are the most genotoxic. Unbiased approaches aimed at investigating the relationship between the number of DSBs and outcome of the DNA damage response have been challenging due to the random nature in which damage is induced by classical DNA damaging agents. Here we describe a CRISPR/Cas9-based system that permits us to efficiently introduce DSBs at defined sites in the genome. Using this system, we show that a guide RNA targeting only a single site in the human genome can trigger a checkpoint response that is potent enough to delay cell cycle progression. Abrogation of this checkpoint leads to DNA breaks in mitosis which give rise to micronucleated daughter cells.