bluuebunny/crossref_metadata_2025 huggingface dataset:
Lyme neuroborreliosis
Authors: Halperin John J.
Published: March 2019

Purpose of review

To review the recent evidence clarifying the symptomatology and diagnosis of nervous system Lyme disease.

Recent findings

Two-tier testing combining pairs of ELISAs, using C6 or VlsE assays to replace second tier Western blots, may eliminate confusion about test interpretation. Cerebrospinal fluid (CSF) can be informative in diagnosing central nervous system (CNS) Lyme disease, not peripheral nervous system (PNS) disorders. CSF CXCL13 may provide useful adjunctive information in CNS infection; its specificity remains to be defined. Lyme encephalopathy is not indicative of CNS infection. Post treatment Lyme disease symptoms do not occur in patients who have had definite CNS Lyme infection. Whether post treatment Lyme disease symptom (PTLDS) is an actual entity, or reflects anchoring bias when commonly occurring symptoms arise in patients previously treated for Lyme disease, remains to be determined. Regardless, these symptoms do not reflect CNS infection and do not respond to additional antimicrobial therapy.

Serologic testing is robust in individuals with a priori likelihood of infection of greater than 2–6 weeks duration. Western blots provide useful confirmation of screening ELISAs, but may be replaced by second ELISAs. CSF testing, including CXCL13, may be informative in CNS Lyme, not PNS, and is generally normal in Lyme encephalopathy. PTLDS does not occur following CNS infection, and may not be a distinct entity.
Herpes simplex virus encephalitis update
Authors: Stahl Jean Paul , Mailles Alexandra
Published: March 2019

Purpose of review

HSV is the most frequently identified cause of infectious encephalitis, in Western countries. This article is an update on the topic based on a review of recent studies from 2017 to 2018.

Recent findings

Acyclovir is still the first line treatment, and no new drugs are currently available for clinical use. The major considerations for HSV encephalitis are as follows: point one, clinical evaluation remains the most important factor, as though CSF HSV PCR has a good sensitivity, in a small proportion of patients the initial testing might be negative. MRI brain is the first line imaging test, and mesial temporal lobe involvement and other typical findings are important for diagnosis; point 2, there should be emphasis on sequela, short-term, and long-term outcomes, and not just case fatality rated in future studies and clinical management. Auto-immune encephalitis can be triggered by HSV, and should be considered in patients who are not responding to treatment; point 3, future studies should be on better management of sequela, and better treatment regimens including those targeting the immune response.

Autoimmune encephalitis is a clearly identified complication of HSV encephalitis. Inflammatory mechanisms are linked to the clinical presentation as well as severity and poor outcome. Initial corticosteroid therapy has to be evaluated in order to prevent complications.
Hospital Responses to Mortality Measures: A Survey of Hospital Administrative Leaders
Authors: Soelch Luke A. , Repp Allen B.
Published: March 2019

Background:

Standardized hospital mortality ratios (SHMRs) are widely used for quality improvement, hospital ratings, and health care payment.

Objectives:

(1) To characterize the programs implemented at hospitals in response to SHMRs.

(2) To describe hospital leaders' perceptions of SHMRs as indicators of care quality.

Methods:

Electronic survey of administrative leaders at US academic medical centers who subscribed to Vizient leadership networks.

Results:

Forty-seven administrative leaders from 37 US academic medical centers completed the survey. Respondents reported that SHMRs had the largest role in the decision to implement inpatient hospice programs, electronic early warning systems, and clinical documentation specialist programs at their institution. Respondents perceived clinical documentation specialist programs and condition-specific care pathways as the most effective programs to improve performance on SHMRs. Only 29% of respondents agreed that SHMRs accurately reflect the number of preventable deaths in hospitals, but 78% agreed that SHMRs have helped their hospital reduce preventable deaths.

Conclusions:

Hospitals have employed various strategies in response to SHMRs—including clinical programs that focus on reducing preventable deaths and other programs that target improvement in SHMR performance without reducing preventable deaths. Hospital administrative leaders identify significant benefits and flaws of SHMRs as quality indicators.
Unusual Intraventricular Tumor Mimicker; Choroid Plexus Arteriovenous Malformation
Authors: Izgi Emine , Ogul Hayri
Published: March 2019

Arteriovenous malformations (AVMs) are basically abnormal vessel networks consisting of one or more feeding arteries, central nidus, and dilated drainage veins. They are divided into subtypes as fistulose, mixed (fistulose-plexiform), or plexiform. Intraventricular location of AVMs is unusual. In this location, the lesion may mimic neoplastic processes. Here the authors reported uncommon case of an AVM located in the right choroid plexus presenting with intraventricular hemorrhage.
Best Buy in Public Health or Luxury Expense?
Authors: Yap Ava , Cheung Maija , Muzira Arlene , Healy James , Kakembo Nasser , Kisa Phyllis , Cunningham David , Youngson George , Sekabira John , Yaesoubi Reza , Ozgediz Doruk
Published: March 2019

Objective:

To determine the cost-effectiveness of building and maintaining a dedicated pediatric operating room (OR) in Uganda from the societal perspective.

Background:

Despite the heavy burden of pediatric surgical disease in low-income countries, definitive treatment is limited as surgical infrastructure is inadequate to meet the need, leading to preventable morbidity and mortality in children.

Methods:

In this economic model, we used a decision tree template to compare the intervention of a dedicated pediatric OR in Uganda for a year versus the absence of a pediatric OR. Costs were included from the government, charity, and patient perspectives. OR and ward case-log informed epidemiological and patient outcomes data, and measured cost per disability adjusted life year averted and cost per life saved. The incremental cost-effectiveness ratio (ICER) was calculated between the intervention and counterfactual scenario. Costs are reported in 2015 US$ and inflated by 5.5%.

Findings:

In Uganda, the implementation of a dedicated pediatric OR has an ICER of $37.25 per disability adjusted life year averted or $3321 per life saved, compared with no existing operating room. The ICER is well below multiple cost-effectiveness thresholds including one times the country's gross domestic product per capita ($694). The ICER remained robust under 1-way and probabilistic sensitivity analyses.

Conclusion:

Our model ICER suggests that the construction and maintenance of a dedicated pediatric operating room in sub-Saharan Africa is very-cost effective if hospital space and personnel pre-exist to staff the facility. This supports infrastructure implementation for surgery in sub-Saharan Africa as a worthwhile investment.
Prognostic Factors of Survival After Neoadjuvant Treatment and Resection for Initially Unresectable Pancreatic Cancer
Authors: Klaiber Ulla , Schnaidt Eva S. , Hinz Ulf , Gaida Matthias M. , Heger Ulrike , Hank Thomas , Strobel Oliver , Neoptolemos John P. , Mihaljevic André L. , Büchler Markus W. , Hackert Thilo
Published: March 2019

Objective:

To evaluate the impact of clinical and pathological parameters, including resection margin (R) status, on survival in patients undergoing pancreatic surgery after neoadjuvant treatment for initially unresectable pancreatic ductal adenocarcinoma (PDAC).

Background:

Prognostic factors are well documented for patients with resectable PDAC, but have not been described in detail for patients with initially unresectable PDAC undergoing resection after neoadjuvant therapy.

Methods:

Prospectively collected data of consecutive patients with initially unresectable pancreatic cancer treated by neoadjuvant treatment and resection were analyzed. The R status was categorized as R0 (tumor-free margin >1 mm), R1 ≤1 mm (tumor-free margin ≤1 mm), and R1 direct (microscopic tumor infiltration at margin). Clinicopathological characteristics and outcomes were compared among these groups and tested for survival prediction.

Results:

Between January, 2006 and February, 2017, 280 patients with borderline resectable (n = 18), locally advanced (n = 190), or oligometastatic (n = 72) disease underwent tumor resection after neoadjuvant treatment. Median overall survival from the time of surgery was 25.1 months for R0 (n = 82), 15.3 months for R1 ≤1 mm (n = 99), and 16.1 months for R1 direct (n = 99), with 3-year overall survival rates of 35.0%, 20.7%, and 18.5%, respectively (P = 0.0076). The median duration of the neoadjuvant treatment period was 5.1 months. In multivariable analysis, preoperative CA 19–9 levels, lymph node status, metastasis category, and vascular involvement were all significant prognostic factors for overall survival. The R status was not an independent prognostic factor.

Conclusions:

In patients undergoing resection after neoadjuvant therapy for initially unresectable PDAC, preoperative CA 19–9 levels, lymph node involvement, metastasis category, and vascular involvement, but not the R status, were independent prognostic factors of overall survival.
Practice Patterns Regarding Apical Support Procedures at Time of Hysterectomy for Pelvic Organ Prolapse
Authors: Hill Austin M. , Pauls Rachel N. , Crisp Catrina C.
Published: March 2019

Objectives

We sought to understand practice patterns of non–female pelvic medicine and reconstructive surgery (FPMRS) clinicians regarding concurrent apical support procedures during hysterectomies when primarily performed for the treatment of pelvic organ prolapse. We also sought to describe differences between those receiving and not receiving apical support.

Methods

This retrospective study analyzed medical records of individuals undergoing hysterectomy for the primary indication of pelvic organ prolapse between 2012 and 2017 at all locations within the TriHealth system. Surgeries performed by board-certified FPMRS physicians were excluded. Comparisons were drawn between those who did and did not receive apical support.

Results

A total of 236 charts met the inclusion criteria. Of these, 66 (28%) received concurrent apical suspension, and 94 (39.8%) underwent no reconstructive procedures. The annual proportion of those receiving apical suspension did not differ over the course of the study period. On average, the addition of apical support added 39.9 minutes (P < 0.001) to the length of surgery. There was, however, no difference noted in estimated blood loss. Risk factors for recurrent prolapse including chronic constipation, pulmonary disease, and connective tissue disorders were similar between groups.

Conclusion

When excluding FPMRS surgeons, data from our institution showed that most patients undergoing hysterectomy for prolapse did not receive concurrent apical support. This suggests areas of potential improvement for adopting into clinical practice the new American College of Obstetricians and Gynecologists recommendations regarding the treatment of prolapse. Furthermore, this may represent an important opportunity for peer outreach and education by FPMRS surgeons.
Complement-mediated Damage to the Glycocalyx Plays a Role in Renal Ischemia-reperfusion Injury in Mice
Authors: Bongoni Anjan K. , Lu Bo , McRae Jennifer L. , Salvaris Evelyn J. , Toonen Erik J. M. , Vikstrom Ingela , Baz Morelli Adriana , Pearse Martin J. , Cowan Peter J.
Published: March 2019

Background

Complement activation plays an important role in the pathogenesis of renal ischemia-reperfusion (IR) injury (IRI), but whether this involves damage to the vasculoprotective endothelial glycocalyx is not clear. We investigated the impact of complement activation on glycocalyx integrity and renal dysfunction in a mouse model of renal IRI.

Methods

Right nephrectomized male C57BL/6 mice were subjected to 22 minutes left renal ischemia and sacrificed 24 hours after reperfusion to analyze renal function, complement activation, glycocalyx damage, endothelial cell activation, inflammation, and infiltration of neutrophils and macrophages.

Results

Ischemia-reperfusion induced severe renal injury, manifested by significantly increased serum creatinine and urea, complement activation and deposition, loss of glycocalyx, endothelial activation, inflammation, and innate cell infiltration. Treatment with the anti-C5 antibody BB5.1 protected against IRI as indicated by significantly lower serum creatinine (P = 0.04) and urea (P = 0.003), tissue C3b/c and C9 deposition (both P = 0.004), plasma C3b (P = 0.001) and C5a (P = 0.006), endothelial vascular cell adhesion molecule-1 expression (P = 0.003), glycocalyx shedding (tissue heparan sulfate [P = 0.001], plasma syndecan-1 [P = 0.007], and hyaluronan [P = 0.02]), inflammation (high mobility group box-1 [P = 0.0003]), and tissue neutrophil (P = 0.0009) and macrophage (P = 0.004) infiltration.

Conclusions

Together, our data confirm that the terminal pathway of complement activation plays a key role in renal IRI and demonstrate that the mechanism of injury involves shedding of the glycocalyx.
Conformational gating in ammonia lyases
Authors: Lambrughi Matteo , Maršić Željka Sanader , Saez-Jimenez Veronica , Mapelli Valeria , Olsson Lisbeth , Papaleo Elena
Published: March 2019

Ammonia lyases (AL) are enzymes of industrial and biomedical interest. Knowledge of AL structure-dynamics-function relationship would be instrumental for making use of the application potential of these enzymes. We investigated, using microsecond molecular dynamics, the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. In particular, we identified two regulatory elements in the MAL structure, i.e., the β5-α2 loop, and the helix-hairpin-loop subdomain. We showed that they undergo conformational changes switching from ‘occluded’ to ‘open’ states. We observed that these rearrangements are coupled to changes in the accessibility of the active site. The β5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the substrate binding site, making the active site more accessible to the substrate when they are in an open state. We pinpointed a sequential mechanism, in which the helix-hairpin-loop subdomain needs to break a subset of intramolecular interactions first, to then allow the opening of the β5-α2 loop and, as a consequence, make the AL catalytic pocket accessible for the substrate. Our data suggest that protein dynamics need to be considered in the design of new AL variants for protein engineering and therapeutic purposes.
NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly
Authors: Rodríguez-Pérez Héctor , Hernández-Beeftink Tamara , Lorenzo-Salazar José M. , Roda-García José L. , Pérez-González Carlos J. , Colebrook Marcos , Flores Carlos
Published: March 2019

Background

The Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.

Results

We present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly.

Conclusions

With the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aimed to simplify and make more reproducible ONT DNA sequence analysis. The NanoDJ package code, documentation and installation instructions are freely available at https://github.com/genomicsITER/NanoDJ.
The fungal endophyteFusarium solaniprovokes differential effects on the energy balance of twoLotusspecies
Authors: Nieva Amira S. , Vilas Juan M. , Gárriz Andrés , Maiale Santiago J. , Menéndez Ana B. , Erban Alexander , Kopka Joachim , Ruiz Oscar A.
Published: March 2019

Background and aims

The interactions established between plants and endophytic fungi span acontinuumfrom beneficial to pathogenic associations. The aim of this work was to explore the mechanisms underlying the potentially beneficial effects provoked by a fungal strain in legume species of the genusLotus.

Methods

The ability to solubilise phosphorous was evaluated in nine fungal strains isolated from roots ofL. tenuis. A selected strain was further assessed for its ability to colonize plant roots in differentLotusspecies. The effects of the two interactions were assessed by analysis of the photosynthesis, sugar amount, and macronutrient status of leaves and roots.

Results

A fungal isolate identified asFusarium solanishows the highest phosphate-solubilisation activity and grows endophytically in roots ofL. japonicusandL. tenuis. Fungal invasion enhances plant growth inL. japonicusbut provokes a contrasting effect inL. tenuis. Photosynthesis, sugars and K content showed a differential effect in both plant species.

Conclusions

Our results indicate neither of the plant species evaluated in this work were significantly stressed byF. solani. Thus, the differential responses observed are due to distinct mechanisms involving photosynthesis, potassium homeostasis, and carbohydrate metabolism that are employed by plants to maintain fitness during the endophytic interaction.
The haploinsufficient tumor suppressor Tip60 negatively regulates the oncogenic Aurora B kinase
Authors: Bose Arnab , Sudevan Surabhi , Rao Vinay J. , Shima Hiroki , Igarashi Kazuhiko , Kundu Tapas K.
Published: March 2019

The Aurora kinases represent a group of serine/threonine kinases which are crucial regulators of mitosis. Dysregulated Aurora kinase B (AurkB) expression, stemming from genomic amplification, increased gene transcription or overexpression of its allosteric activators, is capable of initiating and sustaining malignant phenotypes. Although AurkB level in cells is well-orchestrated, studies that relate to its stability or activity, independent of mitosis, are lacking. We report that AurkB undergoes acetylation in vitro by lysine acetyltransferases (KATs) belonging to different families, namely by p300 and Tip60. The haploinsufficient tumor suppressor Tip60 acetylates two highly conserved lysine residues within the kinase domain of AurkB which not only impinges the protein stability but also its kinase activity. These results signify a probable outcome on the increase in “overall activity” of AurkB upon Tip60 downregulation, as observed under cancerous conditions. The present work, therefore, uncovers an important functional interplay between AurkB and Tip60, frailty of which may be an initial event in carcinogenesis.
The transcriptional regulator Id2 is critical for adipose-resident regulatory T cell differentiation, survival and function
Authors: Frias Adolfo B. , Hyzny Eric J. , Buechel Heather M. , Beppu Lisa , Xie Bingxian , Jurczak Michael J. , D’Cruz Louise M.
Published: March 2019

Adipose regulatory T cells (aTregs) have emerged as critical cells for the control of local and systemic inflammation. In this study, we show a distinctive role for the transcriptional regulator Id2 in the differentiation, survival and function of aTregs. Id2 was highly expressed in aTregs compared with high Id3 expression in lymphoid Tregs. Treg-specific deletion of Id2 resulted in a substantial decrease in aTregs, while Tregs in the spleen and lymph nodes were unaffected. Additionally, loss of Id2 resulted in decreased expression of aTreg associated markers including ST2, CCR2, KLRG1 and GATA3. Gene expression analysis revealed that Id2 expression was essential for the survival of aTregs and loss of Id2 increased cell death in aTregs due to increased Fas expression. Id2-mediated aTreg depletion resulted in increased systemic inflammation, increased inflammatory macrophages and CD8+ effector T cells and loss of glucose tolerance under standard diet conditions. Thus, we reveal an unexpected and novel function for Id2 in mediating differentiation, survival and function of adipose-resident Tregs, that when lost resulting in increased metabolic perturbation.
Evolutionary dynamics and diversification in changing environments
Authors: Alekseeva Evgeniia , Doebeli Michael , Ispolatov Iaroslav
Published: March 2019

We use adaptive dynamics models to study how changes in the abiotic environment affect patterns of evolutionary dynamics and diversity in evolving communities of organisms with complex phenotypes. The models are based on the logistic competition model and environmental changes are implemented as a temporal change of the carrying capacity as a function of phenotype. In general we observe that environmental changes cause a reduction in the number of species, in total population size, and in phenotypic diversity. The rate of environmental change is crucial for determining whether a community survives or undergoes extinction. Until some critical rate of environmental changes, species are able to follow evolutionarily the shifting phenotypic optimum of the carrying capacity, and many communities adapt to the changing conditions and converge to new stationary states. When environmental changes stop, such communities gradually restore their initial phenotypic diversity.
The Degree of Polymerization and Sulfation Patterns in Heparan Sulfate are Critical Determinants of Cytomegalovirus Entry into Host Cells
Authors: Hasan Mohammad H. , Mitra Dipanwita , Parmar Rinkuben C. , Fassero Lauren A. , Liang Quntao , Qiu Hong , Tiwari Vaibhav , Sharp Joshua S. , Wang Lianchun , Tandon Ritesh
Published: March 2019

Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been known to result in significant reduction in virus infectivity indicating that HS play important roles in initiating virus entry. In this study, we provide a series of evidence to prove that specific sulfations as well as the degree of polymerization (dp) of HS govern human cytomegalovirus (CMV) binding and infection. First, purified CMV extracellular virions preferentially bind to sulfated longer chain HS on a glycoarray compared to a variety of unsulfated glycosaminoglycans including unsulfated shorter chain HS. Second, the fraction of glycosaminoglycans (GAG) displaying higherdpand sulfation has a larger impact on CMV titers compared to other fractions. Third, cell lines deficient in specific glucosaminyl sulfotransferases produce significantly reduced CMV titers compared to wild-type cells and virus entry is compromised in these mutant cells. Finally, cells pretreated with a peptide that specifically binds sulfated-HS produce significantly reduced virus titers compared to the control peptide treated cells. Taken together, these results highlight the significance of HS chain length and sulfation patterns in CMV attachment and infectivity.

IMPORTANCE

Heparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It binds to a variety of protein ligands, including cytokines, chemokines, growth factors and morphogens and regulates a wide range of biological activities, including developmental processes, angiogenesis, blood coagulation, and tumor metastasis. The molecular diversity in HS chains generates unique binding sites for specific ligands and can offer preferential binding for a specific virus over other viruses or cellular ligands. In the current study human cytomegalovirus (CMV) was found to bind preferentially to uniquely sulfated and polymerized HS. The HS mimics designed with these properties inhibited CMV infection. The results were corroborated by parallel studies in mutant mouse cells as well as using peptide inhibition. Combined together, the data suggests that CMV preferentially attaches to uniquely modified HS and thus this virus-host interaction is amenable to targeting by specifically designed HS mimics or peptides.
TreeCluster: clustering biological sequences using phylogenetic trees
Authors: Balaban Metin , Moshiri Niema , Mai Uyen , Mirarab Siavash
Published: March 2019

Clustering homologous sequences based on their similarity is a problem that appears in many bioinformatics applications. The fact that sequences cluster is ultimately the result of their phylogenetic relationships. Despite this observation and the natural ways in which a tree can define clusters, most applications of sequence clustering do not use a phylogenetic tree and instead operate on pairwise sequence distances. Due to advances in large-scale phylogenetic inference, we argue that tree-based clustering is under-utilized. We define a family of optimization problems that, given a (not necessarily ultrametric) tree, return the minimum number of clusters such that all clusters adhere to constraints on their heterogeneity. We study three specific constraints that limit the diameter of each cluster, the sum of its branch lengths, or chains of pairwise distances. These three versions of the problem can be solved in time that increases linearly with the size of the tree, a fact that has been known by computer scientists for two of these three criteria for decades. We implement these algorithms in a tool called TreeCluster, which we test on three applications: OTU picking for microbiome data, HIV transmission clustering, and divide-and-conquer multiple sequence alignment. We show that, by using tree-based distances, TreeCluster generates more internally consistent clusters than alternatives and improves the effectiveness of downstream applications. TreeCluster is available athttps://github.com/niemasd/TreeCluster.
Substrate structure and computation guided engineering of a Lipase for Omega-3 fatty acid selectivity
Authors: Moharana Tushar Ranjan , Rao Nalam Madhusudhana
Published: March 2019

Optimum health benefits of omega-3 fatty acids (ω-3 FAs) require it to be concentrated in its natural sources. Fatty acid selectivity of lipase governs the efficacy of the production of lipase-mediated ω-3 FAs concentrates. We attempted to improve the fatty acid selectivity of a lipase from thermophilic bacteriumGeobacillus thermoleovorans(GTL) by two approaches. In a semi-rational approach, six amino acid positions of GTL interacting with the substrate, were identified by docking and were subjected to site-saturation mutagenesis. Three best substitutions were incorporated into GTL(CM-GTL). Hydrolysis of oil by lipase was monitored in a pH-Stat and the fatty acids released at various time points were analyzed by GC-MS.CM-GTL showed a significant improvement in discrimination against DHA during hydrolysis. In the second approach based on rational design, the active site was narrowed by incorporating heavier amino acids in the lining of acyl-binding pocket to hinder access to bulky ω-3 FAs. For this purpose, two amino acids surrounding the opening of the acyl pocket were replaced with the next heavier amino acids and the affinities were evaluatedin silico.The double mutant, thus deigned, was found to be excellent in discriminating the ω-3 FAs during hydrolysis of triglycerides. Engineering the binding pocket of a complex substrate, such as a triglyceride, with the supportive information on substrate structure and its binding modes with the enzyme provided by computational methods, has resulted in designing two efficient lipase variants with improved substrate selectivity.
A simple adaptation to a protein crystallography station to facilitate difference X-ray scattering studies
Authors: Sharma Amit , Berntsen Peter , Harimoorthy Rajiv , Appio Roberto , Sjöhamn Jennie , Järvå Michael , Björling Alexander , Hammarin Greger , Westenhoff Sebastian , Brändén Gisela , Neutze Richard
Published: March 2019

The X-ray crystallography station I911-2 at MAXLab II (Lund, Sweden) has been adapted to enable difference small- and wide-angle X-ray scattering (SAXS/WAXS) data to be recorded. Modifications to the beamline included a customized flow cell, a motorized flow cell holder, a helium cone, a beam stop, a sample stage and a sample delivery system. This setup incorporated external devices such as infrared lasers, LEDs and reaction mixers to induce conformational changes in macromolecules. This platform was evaluated through proof-of-principle experiments capturing light-induced conformational changes in phytochromes. A difference WAXS signature of conformational changes in a plant aquaporin was also demonstrated using caged calcium.
Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data
Authors: Paissoni Cristina , Jussupow Alexander , Camilloni Carlo
Published: March 2019

The use of small-angle X-ray scattering (SAXS) in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speeded up by using a coarse-grain representation of the structure. Following the work of Niebling, Björling & Westenhoff [J. Appl. Cryst. (2014), 47, 1190–1198], the Martini bead form factors for nucleic acids have been derived and then implemented, together with those previously determined for proteins, in the publicly available PLUMED library. A hybrid multi-resolution strategy has also been implemented to perform SAXS restrained simulations at atomic resolution by calculating the virtual positions of the Martini beads on the fly and using them for the calculation of SAXS. The accuracy and efficiency of the method are demonstrated by refining the structure of two protein–nucleic acid complexes. Instrumental for this result is the use of metainference, which allows the consideration and alleviation of the approximations at play in the present SAXS calculations.
Influence of the elastic deformations on the form factor of polyhedral nanocrystals: the illustrative example of the pseudomorphic inclusion
Authors: Croset Bernard
Published: March 2019

Using an analytically tractable example, the pseudomorphic inclusion, this article examines the influence of elastic deformations on the form factor of polyhedral nanocrystals. A control parameter, the total amplitude of the variation of the complex density phase, is identified and it is shown that for low enough deformations the characteristic asymptotic behaviours as a function of the scattering vector associated with the polyhedral crystal shape are preserved, leading to a strong contrast in the dependence of the form factor on orientation. Using the sections method, it is explained why these results can be generalized to more realistic elastic situations.
Crystal structure solution for the A
6
B
2O17 (A = Zr, Hf; B = Nb, Ta) superstructure
Authors: McCormack Scott J. , Kriven Waltraud M.
Published: March 2019

Zr6Ta2O17, Hf6Nb2O17 and Hf6Ta2O17 crystal structure solutions have been solved using synchrotron X-ray powder diffraction and neutron powder diffraction in conjunction with simulated annealing, charge flipping and Rietveld refinement. These structures have been shown to be isomorphous with the Zr6Nb2O17 superstructure, leading to the classification of the A
6
B
2O17 (A = Zr, Hf; B = Nb, Ta) orthorhombic compound family with symmetry Ima2 (No. 46). The asymmetrical structural units of cation-centred oxygen polyhedra used to build the structure are as follows: (i) one set of symmetry-equivalent six-coordinated polyhedra, (ii) three sets of symmetry-equivalent seven-coordinated polyhedra and (iii) one set of symmetry-equivalent eight-coordinated polyhedra. The potential for cation order and disorder was discussed in terms of cation atomic number contrast in X-ray and neutron powder diffraction as well as the bond valence method. In addition, the structural mechanisms for experimentally observed compositional variations within the solid solution range can be attributed to the addition or removal of a set of symmetry-equivalent seven-coordinated polyhedra accompanied by corresponding oxygen tilts within the A
6
B
2O17 structure.
Operation of networked multi-carrier microgrid considering demand response
Authors: Amir Vahid , Jadid Shahram , Ehsan Mehdi
Published: March 2019

Purpose

Microgrids are inclined to use renewable energy resources within the availability limits. In conventional studies, energy interchange among microgrids was not considered because of one-directional power flows. Hence, this paper aims to study the optimal day-ahead energy scheduling of a centralized networked multi-carrier microgrid (NMCMG). The energy scheduling faces new challenges by inclusion of responsive loads, integration of renewable sources (wind and solar) and interaction of multi-carrier microgrids (MCMGs).

Design/methodology/approach

The optimization model is formulated as a mixed integer nonlinear programing and is solved using GAMS software. Numerical simulations are performed on a system with three MCMGs, including combined heat and power, photovoltaic arrays, wind turbines and energy storages to fulfill the required electrical and thermal load demands. In the proposed system, the MCMGs are in grid-connected mode to exchange power when required.

Findings

The proposed model is capable of minimizing the system costs by using a novel demand side management model and integrating the multiple-energy infrastructure, as well as handling the energy management of the network. Furthermore, the novel demand side management model gives more accurate optimal results. The operational performance and total cost of the NMCMG in simultaneous operation of multiple carriers has been effectively improved.

Originality/value

Introduction and modeling of the multiple energy demands within the MCMG. A novel time- and incentive-based demand side management, characterized by shifting techniques, is applied to reshape the load curve, as well as for preventing the excessive use of energy in peak hours. This paper analyzes the need to study how inclusion of multiple energy infrastructure integration and responsive load can impact the future distribution network costs.
The new talent management challenges of Industry 4.0
Authors: Whysall Zara , Owtram Mike , Brittain Simon
Published: March 2019

Purpose

The transformational changes to business environments brought about by the fourth industrial revolution create a perfect storm for strategic human resource management, prompting a need to explore the implications of this context for talent management theory and practice. The paper aims to discuss these issues.

Design/methodology/approach

In-depth interviews were conducted with HR directors and senior leaders within engineering-led organisations to explore current challenges experienced across each stage of the talent pipeline: attraction and recruitment, training and development, career development, talent mobility and succession planning.

Findings

The speed of technological change brought about by Industry 4.0 had created a significant gap between current capability of employees and the rapidly evolving requirements of their roles, prompting a need to consider new and more effective approaches to talent development. Middle managers are increasingly recognised as overlooked critical talent within this context of unprecedented change, given their essential role in change management. In addition, whilst lateral hiring remains a common talent management practice, in the case of Industry 4.0 this equates to fighting a war for talent that does not exist.

Practical implications

This study suggests that there is a need for evolution of talent management theory and practice towards a more dynamic, systems-thinking orientation, acknowledging the interrelated nature of different talent management activities.

Originality/value

This paper provides an in-depth insight into the impact of the unprecedented change brought about by Industry 4.0 on contemporary talent management practice, considering how theory and practice might need to evolve to enable individuals and organisations to keep up with the rate of technological change.
Formation of a student managed investment fund: risk management and oversight
Authors: Horstmeyer Derek
Published: March 2019

Purpose

The creation and formation of a student managed investment fund (SMIF) is a risky proposition for all stakeholders involved in the process. These risks include reputational risks for the individuals involved, fiduciary risks for the school’s Board of Trustees and monetary risks for the university itself. The purpose of this paper is to explain and detail how these risks can be mitigated through specific oversight committee (OC) construction, distributional/benchmarking requirements for the fund and detailed trading rules (exit points, short sale constraints, loss provisions, etc.) for fund managers, which can all be codified in the bylaws of the SMIF.

Design/methodology/approach

This investigation is done through a specific case study – the 2017/2018 formation of the George Mason University SMIF. As head of the OC for the fund and lead architect in the creation of the fund for the GMU faculty, the statements below come from firsthand accounts of dealing with all parties of interest and firsthand knowledge of the year-long process of managing all risks, which culminated in being granted endowment capital from the Board of Trustees to officially begin the SMIF on May 1, 2018.

Findings

First, this paper details how a complete investment policy statement can be used to mitigate the fears and concerns of all parties that have a fiduciary duty to the university’s endowment (which the students will now be partially managing). These bylaws include statements on the risk characteristics of the fund, distributions back to the endowment, oversight features and benchmarking. Next, written into the bylaws of the fund can be several benchmarking and distributional requirements to mitigate the risk exposure of the SMIF’s holdings. Finally, aside from benchmarking constraints, another successful risk management technique can be rules written directly into the investment policy statement that define exit points, tracking error, short sale constraints and other rules for trading.

Originality/value

This paper offers a roadmap by which these risks can be mitigated through the content of an investment policy statement/bylaws. The author details several techniques that eventually led to all stakeholders at GMU in signing off on the formation of an SMIF, and endowment capital being given to the fund as a seed investment. This is a firsthand account of this process and the author has not seen it documented in the literature anywhere else.
Parasite sharing in wild ungulates and their predators: Effects of phylogeny, range overlap, and trophic links
Authors: Stephens Patrick R. , Altizer Sonia , Ezenwa Vanessa O. , Gittleman John L. , Moan Emili , Han Barbara , Huang Shan , Pappalardo Paula
Published: March 2019

Understanding factors that facilitate interspecific pathogen transmission is a central issue for conservation, agriculture, and human health. Past work showed that host phylogenetic relatedness and geographical proximity can increase cross‐species transmission, but further work is needed to examine the importance of host traits, and species interactions such as predation, in determining the degree to which parasites are shared between hosts.

Here we consider the factors that predict patterns of parasite sharing across a diverse assemblage of 116 wild ungulates (i.e., hoofed mammals in the Artiodactyla and Perissodactyla) and nearly 900 species of micro‐ and macroparasites, controlling for differences in total parasite richness and host sampling effort. We also consider the effects of trophic links on parasite sharing between ungulates and carnivores.

We tested for the relative influence of range overlap, phylogenetic distance, body mass, and ecological dissimilarity (i.e., the distance separating species in a Euclidean distance matrix based on standardized traits) on parasite sharing. We also tested for the effects of variation in study effort as a potential source of bias in our data, and tested whether carnivores reported to feed on ungulates have more ungulate parasites than those that use other resources.

As in other groups, geographical range overlap and phylogenetic similarity predicted greater parasite community similarity in ungulates. Ecological dissimilarity showed a weak negative relationship with parasite sharing. Counter to our expectations, differences, not similarity, in host body mass predicted greater parasite sharing between pairs of ungulate hosts. Pairs of well‐studied host species showed higher overlap than poorly studied species, although including sampling effort did not reduce the importance of biological traits in our models. Finally, carnivores that feed on ungulates harboured a greater richness of ungulate helminths.

Overall, we show that the factors that predict parasite sharing in wild ungulates are similar to those known for other mammal groups, and demonstrate the importance of controlling for heterogeneity in host sampling effort in future analyses of parasite sharing. We also show that ecological interactions, in this case trophic links via predation, can allow sharing of some parasite species among distantly related host species.
Athanasian Paganisation of Arius: Unprecedented Application of the Deification Theme
Authors: Kharlamov Vladimir
Published: March 2019

Athanasian contribution to the development of the deification theme and its subsequent influence on Christian spirituality remains significant. Athanasius certainly applied deification in his fight with Arianism. A generally acknowledged application of deification in Athanasius in an anti‐Arian context also finds additional support in a seemingly unexpected place—Athanasian criticism of pagan divinization, mostly concentrated in Against the Pagans. Relying on a traditional Christian apologetic approach for criticism of pagan divinization, Athanasius contextualizes the theology of Arius as the paganization of Christianity as well as proposes necessary prerequisites for Christian understanding of deification. This is an unprecedented application of deification in Christian theology where one Christian author portrays the teaching of another Christian author as pagan divinization.
Wrangling with the Black monster: young Black mixed‐race men and masculinities
Authors: Joseph‐Salisbury Remi
Published: March 2019

In recent times there has been a proliferation of scholarship exploring ‘mixedness’ and mixed‐race people. This is evidenced by the emergence of Critical Mixed Race Studies (CMRS) as a distinct field of academic inquiry. However, despite the growth of CMRS, there remains a scarcity of scholarship that considers mixed‐race experiences from a disaggregated, intersectional perspective. Where CMRS has been attentive to the intersection of gender, the focus has largely been on women and femininity. By way of a response, in this article I draw upon data from semi‐structured interviews with Black mixed‐race men in the UK and the US in order to explore how Black mixed‐race men negotiate their raced and gendered identities, particularly in the context of schooling. Drawing upon George Yancy’s (2017) theorizations of the Black monster, I argue that a sense of double consciousness (and evenmultipleconsciousness) means Black mixed‐race men are acutely aware of how the white gaze threatens to fragment and erase them. Yet rather than being passive victims of racism, I show that, through hybridity, the imposition of the Black monster stereotype is something that Black mixed‐race men are able to resist, modify and manipulate for their own ends.
Gluten‐Free Breads: The Gap Between Research and Commercial Reality
Authors: Roman Laura , Belorio Mayara , Gomez Manuel
Published: March 2019

The market for gluten‐free products is steadily growing and gluten‐free bread (GFB) keeps on being one of the most challenging products to develop. Although numerous research studies have worked on improving the manufacture of GFBs, some have adopted approaches far from commercial reality. This review analyzes the ingredient list and nutrition facts of 228 commercially available GFBs produced by different brands around the world. The results from studying the ingredient list of breads revealed that commercial breads do not tend to use a single starchy source or gluten replacer, but a combination of several ingredients to optimize bread quality. Maize, tuber starches, and rice flour were the main starchy sources. Regarding hydrocolloids, the most often included ingredients were hydroxypropyl methylcellulose, xanthan and guar gum, and psyllium. Proteins and sugars were added, respectively, in 81% and 87% of the commercial breads analyzed. Furthermore, it was found that vegetable oils were preferred over fats. A long list of ingredients was observed in commercial GFBs, with the presence of a wide range of additives, including acidifiers, emulsifiers, leavening agents, preservatives, and aromas or flavorings. Meanwhile, nutrition facts showed a lower protein and higher fat content for GFBs compared to a gluten‐containing counterpart, with small differences for salt and sugar. This research expands the current knowledge on GFB manufacturing, giving a panoramic outlook on the current situation in the GFB market, and helping both scientists and gluten‐free companies unify/identify common trends.
Determination of Vehicle Speed from Recorded Video Using Reverse Projection Photogrammetry and File Metadata
Authors: Epstein Brandon , Westlake Bryce Garreth
Published: March 2019

The prevalence of security and in‐car video has increased the number of motor vehicle accidents captured on digital video. However, inconsistencies in how to accurately determine time and distance for vehicle speed has led to examinations with varying results. A potential solution for calculating time intervals is to use frame timing contained within many digital video file's metadata, recorded with 0.000001 sec precision. This paper examines a fatal motor vehicle accident where frame timing information was used with distance measurements from reverse projection photogrammetry to calculate vehicle speed. A margin of error was then calculated based on the accuracy in performing reverse projection photogrammetry distance measurements. The resulting speed calculation was then compared to event data recorder data and found to be within an average of ±1.43538 MPH. Using specific time intervals may lead investigators to more accurate speed calculations, specifically those involving variable frame rate video.
Does XBRL Adoption Constrain Earnings Management? Early Evidence from Mandated U.S. Filers
Authors: Kim Jeong‐Bon , Kim Joung W. , Lim Jee‐Hae
Published: March 2019

We examine whether the use of eXtensible Business Reporting Language (XBRL) for financial reporting (i.e., interactive data submissions) reduces earnings management during the period of XBRL implementation by the SEC. Using a sample of mandated XBRL filers, we compare the magnitude of absolute discretionary accruals in the XBRL adoption quarters with that in the non‐adopting quarters. We also take advantage of staggered (three‐stage phase‐in) XBRL implementations to perform difference‐in‐differences analyses. Our results show that absolute discretionary accruals decrease significantly from the pre‐ to the post‐XBRL period, suggesting that XBRL adoption constrains earnings management via discretionary accrual choices. Our analyses further reveal that the use of standardized official XBRL elements significantly reduces the levels of discretionary accruals, while the use of customized extension elements does not, suggesting that the former discourages accrual‐based earnings management, while the latter does not. Our results are robust to a variety of sensitivity checks.