bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of a 3-Arm Randomized Trial for Posthysterectomy Vault Prolapse Involving Sacral Colpopexy, Transvaginal Mesh, and Native Tissue Apical Repair: The Apical Suspension Repair for Vault Prolapse in a Three-Arm Randomized Trial
Authors: Menefee Shawn , Richter Holly E. , Myers Deborah , Weidner Alison , Moalli Pamela , Harvie Heidi , Rahn David , Jeppson Peter , Paraiso Marie , Thomas Sonia , Mazloomdoost Donna
Published: December 2019

Objective

The objective of this study was to present the design of the Apical Suspension Repair for Vault Prolapse in a Three-Arm Randomized Trial (ASPIRe), which compares the efficacy and safety of 3 apical repairs: native tissue (NT) transvaginal repair, transvaginal mesh, and sacral colpopexy.

Methods

Patient selection criteria, primary and secondary outcome measures including patient-reported outcome questionnaires, masking, surgeon certification, procedure standardization, adverse events collection and adjudication, and cost analysis will be described for this multi-centered randomized trial. Given the unique risks/benefits of each technique, a noninferiority design will be used to compare apical transvaginal mesh to mesh sacral colpopexy. A superiority design will be used to compare the 2 mesh repairs to NT transvaginal apical repair. Survival analysis will be used to assess a composite primary outcome for success composed of a subjective measure (no prolapse symptoms), objective measure (no prolapse beyond the hymen), and no prolapse retreatment, with a minimum follow-up of 36 months. Secondary outcome measures collected every 6 months include assessment of validated general and condition-specific quality of life measures, global impression of improvement, satisfaction and regret, body image, and sexual function.

Results

Randomization and surgical treatment of 360 participants are complete, and the study is in the follow-up phase.

Conclusions

This report will provide valuable insight on the design of a novel 3-arm surgical trial using mesh versus NT to repair vaginal vault prolapse. This trial will provide level 1 evidence on the risks and benefits of mesh augmented versus NT apical repairs.
Effect of Cooking Classes on Healthy Eating Behavior Among College Students
Authors: Barr Anna , Hanson Andrea , Kattelmann Kendra
Published: December 2019

Many college students lack the ability to choose and/or prepare healthy meals, with consequences of convenient, but unhealthy food choices. The objective of this feasibility project was to determine whether cooking classes for college students would improve knowledge and behavior to eat healthfully and practice food safety. A series of 3 cooking classes was provided to students, focusing on simple, healthy recipes with inclusion of food safety education and nutrition instruction. Pre- and posttest surveys assessed nutrition knowledge; frequency of healthy eating; confidence, ability, and cooking frequency; and food safety knowledge. The classes were effective in increasing nutrition knowledge, cooking confidence, and ability, according to posttest surveys.
Developing the Expanded Food Security Screener and Pilot Testing It for Prioritization of Applicants to the Home-Delivered Meal Program
Authors: Vaudin Anna , Simon Judy R. , Sahyoun Nadine R.
Published: December 2019

Food insecurity is multidimensional and may be an outcome not only of economic need but also of inability to prepare meals and shop for food, especially in older adults. As the prevalence of waiting lists for the Older Americans Act home-delivered meal program is increasing, we expanded the 6-item US Department of Agriculture Household Food Security Survey Module, named it the Expanded Food Security Screener, and used it to develop a 5-level prioritization system to assess need for a meal based on economic access and ability to shop and cook, with or without help. We pilot-tested the tool and its prioritization system on older adults who applied for the program. The tool effectively distributes applicants into 5 different levels of need. The priority levels were generally appropriate (75%), based on follow-up assessment by programs. The tool is useful to set priorities for a waiting list and/or to identify need in the community.
Beltrania sinensis sp. nov., an endophytic fungus from China and a key to species of the genus
Authors: Zheng Hua , Yang Xiao-Qian , Deng Jing-Shi , Xu Jian-Ping , Yu Ze-Fen
Published: December 2019

During a survey of endophytic fungi in plant roots in secondary forests in Yunnan, China, a novel ascomyceteous taxon,Beltrania sinensis, was isolated fromQuercus cocciferoidesHand.-Mazz. andFraxinus malacophyllaHemsl. This novel species is characterized by having oval or obovoid conidiogenous cells with several apical, flat-tipped denticles, and biconic, aseptate, smooth, pale brown conidia with a hyaline to subhyaline equatorial transverse band and apical tubular appendage. Phylogenetic analysis of the combined sequences of the internal transcribed spacer and the LSU rRNA gene confirmed its novel species status within the genusBeltrania. Here, the novel species is described and illustrated, and a taxonomic key to species in the genusBeltraniais provided.
The rise of diversity in metabolic platforms across the Candidate Phyla Radiation
Authors: Jaffe Alexander L. , Castelle Cindy J. , Matheus Carnevali Paula B. , Gribaldo Simonetta , Banfield Jillian F.
Published: December 2019

A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. Here, we selected ∼1,000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer. Overall, patterns of gene gain and loss, including acquisition of accessory traits in independent transfer events, may have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.
Universal brain signature of emerging reading in two contrasting languages
Authors: Chyl Katarzyna , Kossowski Bartosz , Wang Shuai , Dębska Agnieszka , Łuniewska Magdalena , Marchewka Artur , Wypych Marek , van den Bunt Mark , Mencl William , Pugh Kenneth , Jednoróg Katarzyna
Published: December 2019

Despite dissimilarities among scripts, a universal hallmark of literacy in adults is the convergent brain activity for print and speech. Little is known, however, how early it emerges. Here we compare speech and orthographic processing systems in two contrasting languages, Polish and English, in 100 7-year-old children performing identical fMRI tasks. Results show limited language variation, with speech-print convergence evident mostly in left fronto-temporal perisylvian regions. Correlational and intersect analyses revealed subtle differences in the strength of this coupling in several regions of interest. Specifically, speech-print convergence was higher for transparent Polish than opaque English in right temporal area, associated with phonological processing. Conversely, speech-print convergence was higher for English than Polish in left fusiform, associated with visual reading. We conclude that speech-print convergence is a universal marker of reading even at the beginning of reading acquisition while minor variations can be explained by the differences in the orthographic transparency.
Mismatch responses mediated by adaptation and deviance detection have complementary functional profiles that point to different auditory short-term memory systems
Authors: Teichert Tobias , Jedema Hank , Shen Zhijun , Gurnsey Kate
Published: December 2019

Mismatch negativity (MMN) is a macroscopic EEG deflection in response to rare or unexpected sounds. It has provided important insights into auditory short-term memory, pre-attentive guidance of attention, and their alteration in conditions such as schizophrenia. It remains unclear if MMN is caused by passive adaptation, active memory-comparison processes (deviance detection; DD), or a mix of both. To answer this question, macaque monkeys listened to a new paradigm that quantified both components of MMN. Micro- and macroscopic mismatch responses in the rhesus were dominated by adaptation at short latencies but included a smaller contribution of deviance detection at longer latencies. Most importantly, we show that mismatch responses mediated by adaptation have a short temporal scope and narrow frequency tuning while mismatch responses mediated by deviance detection have a longer temporal scope but broader frequency tuning. The different functional profiles point to the involvement of two distinct auditory short-term memory systems and complementary roles in the pre-attentive guidance of attention.
Visual experience instructs dendrite orientation but is not required for asymmetric wiring of the retinal direction selective circuit
Authors: El-Quessny Malak , Maanum Kayla , Feller Marla B.
Published: December 2019

Changes in dendritic morphology in response to activity have long been thought to be a critical component of how neural circuits develop to properly encode sensory information. Here we report the impact of dark-rearing on the dendritic morphology and function of a retinal ganglion cell type, a ventral-preferring direction-selective ganglion cell (vDSGC). vDSGCs have asymmetric dendrites oriented along their preferred direction. We found that, at eye opening, vDSGC dendrites are not yet ventrally oriented, and that, surprisingly, dark-rearing prevents ventral orientation of vDSGC dendrites. Despite their dramatic change in dendritic morphology, vDSGCs in dark-reared mice maintain ventral directional preference. Direction selective tuning in dark-reared mice is mediated by asymmetric inhibition, as observed in vDSGCs of normally reared animals. Hence, we postulate that dendritic form follows proper circuit function, where dendritic orientation is refined over the course of development and is dependent on structured visual experience following eye opening.
Enhanced canonical Wnt signaling during early zebrafish development perturbs the interaction of cardiac mesoderm and pharyngeal endoderm and causes thyroid specification defects
Authors: Vandernoot Isabelle , Haerlingen Benoît , Trubiroha Achim , Gillotay Pierre , Janssens Véronique , Opitz Robert , Costagliola Sabine
Published: December 2019

Background

Congenital hypothyroidism (CH) due to thyroid dysgenesis is a frequent congenital endocrine disorder for which the molecular mechanisms remain unresolved in the far majority of cases. This situation reflects in part our still limited knowledge about the mechanisms involved in the early steps of thyroid specification from the endoderm, in particular the extrinsic signaling cues that regulate foregut endoderm patterning. In this study, we used small molecules and genetic zebrafish models to characterize the role of various signaling pathways in thyroid specification.

Methods

We treated zebrafish embryos during different developmental periods with small molecule compounds known to modulate the activity of Wnt signaling pathway and observed effects in thyroid, endoderm and cardiovascular development using whole mountin situhybridization and transgenic fluorescent reporter models. We used an antisense morpholino to create a zebrafish acardiac model. For thyroid rescue experiments, BMP pathway induction in zebrafish embryos was obtained by using heatshock inducible transgenic lines.

Results

Interestingly, combined analyses of thyroid and cardiovascular development revealed that overactivation of Wnt signaling during early development leads to impaired thyroid specification concurrent with severe defects in the cardiac specification. When using a model of morpholino-induced blockage of cardiomyocyte differentiation, a similar correlation was observed, suggesting that defective signaling between cardiac mesoderm and endodermal thyroid precursors contributes to thyroid specification impairment. Rescue experiments through transient overactivation of BMP signaling could partially restore thyroid specification in models with defective cardiac development.

Conclusion

Collectively, our results indicate that BMP signaling is critically required for thyroid cell specification and identify cardiac mesoderm as a likely source of BMP signals.
Mechanism underlying autoinducer recognition in theVibrio choleraeDPO-VqmA quorum-sensing pathway
Authors: Huang Xiuliang , Duddy Olivia P. , Silpe Justin E. , Paczkowski Jon E. , Cong Jianping , Henke Brad R. , Bassler Bonnie L.
Published: December 2019

Quorum sensing is a bacterial communication process whereby bacteria produce, release and detect the accumulation of extracellular signaling molecules called autoinducers to coordinate collective behaviors. InVibrio cholerae, the quorum-sensing autoinducer, DPO (3,5-dimethyl-pyrazin-2-ol), binds the receptor-transcription factor, VqmA. In response, the DPO-VqmA complex activates transcription of thevqmRgene encoding the VqmR small RNA. VqmR represses genes required for biofilm formation and virulence factor production. Here, we show that VqmA has DPO-dependent and DPO-independent activity. We solved the DPO-VqmA crystal structure and compared it to existing structures to understand the conformational changes the protein undergoes upon DNA binding. Analysis of DPO analogs reveals that a hydroxyl or carbonyl group at the 2’ position is critical for binding. The proposed DPO precursor, a linear molecule, Ala-AA (N-alanyl-aminoacetone), also binds and activates VqmA. DPO and Ala-AA occupy the same binding site as judged by site-directed mutagenesis and competitive ligand binding analyses.
Transient CRISPR immunity leads to coexistence with phages
Authors: Meaden Sean , Capria Loris , Alseth Ellinor , Biswas Ambarish , Lenzi Luca , Buckling Angus , van Houte Stineke , Westra Edze R
Published: December 2019

Phages play a major role in shaping the composition, evolution and function of bacterial communities. While bacteria and phages coexist in many natural environments, their coexistence is often short-lived in the lab due to the evolution of phage resistance. However, fitness costs associated with resistance and mutational loss of resistance alleles may limit the durability of acquired resistances, potentially allowing phages to re-invade the population. Here, we explore this idea in the context of bacteria that evolve CRISPR-based immunity against their phages. Consistent with previous studies, we found that the bacterium Pseudomonas aeruginosa PA14 evolved high levels of CRISPR-based immunity and low levels of surface-based resistance following infection with phage DMS3vir, which led to rapid phage extinction. However, when these pre-immunized bacterial populations were subsequently challenged with the same phage, they failed to clear the infection and instead stably coexisted with the phage. Analysis of bacterial genotypes and phenotypes over time explained why CRISPR-Cas immunity provides only a transient advantage: in the absence of phage (i.e. following the initial phage extinction) formerly CRISPR-immune bacteria regain sensitivity due to evolutionary loss of spacers, whereas in the presence of phage (i.e. upon reinfection) selection favours surface-based resistance over CRISPR immunity. The latter results from an infection-induced fitness cost of CRISPR-immunity that is due to phage gene expression prior to target DNA cleavage by the immune system. Together, these results show that CRISPR-Cas immune systems provide only a transient benefit to bacteria upon phage infection and help to explain why bacteria and phages can coexist in natural environments even when bacteria carry CRISPR-Cas adaptive immune systems that allow for rapid acquisition of immunity against phages.
Robust Stability of Multicomponent Membranes: the Role of Glycolipids
Authors: Chen Yuan , Doelman Arjen , Promislow Keith , Veerman Frits
Published: December 2019

We present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each connecting orbits we associate a manifold of low energy membrane-type configurations parameterized by a large class of admissible interfaces. The normal coercivity of the manifolds is established through criteria depending solely on the structure of the associated connecting orbit. We present a class of examples that arise naturally from geometric singular perturbation techniques, focusing on a model that characterizes the stabilizing role of cholesterol-like glycolipids within phospholipid membranes.
Mycorrhiza Co-Association withAspilia prulisetaSchweif and Phosphorus Uptake Effects on Growth Attributes of Gadam Sorghum in Selected Sites in Kenya
Authors: Muchoka J.P. , Mugendi D.N , Njiruh P.N , Onyari C.N. , Mbugua P.K. , Njeru E.M.
Published: December 2019

Mycorrhiza fungi are important components of soil microbiota in the rhizosphere and greatly influence uptake of mineral elements to plants. A green house experiment was conducted at the University of Embu. The experiment involved use of sterilized polythene potting material sized 30 cm by 40 cm. The pots were filled two thirds the height of the potting material with soil from a predetermined source in Gakurungu, Tunyai and Kanyuombora in the upper eastern region in Kenya. The soil used in the pots was collected from the rhizosphere ofAspilia prulisetaSchweif vegetation as well as adjacent areas without this vegetation as a control at 0-20 cm, 21-40 cm and 41-60 cm for each of the soil types (silty clay, silt loam and sandy loam) used in the experiment. Two sorghum seeds inoculated with mycorrhiza fungi were planted in each pot and a similar number of pots planted with un inoculated sorghum seeds as a control. Each of the 4 treatments mentioned above, was replicated four times giving n=144. Each pot was watered after every two days using a two-litre watering can for the first one week. Thereafter, watering regime was reduced to once a week but ensuring the pots remained moist. Watering was done uniformly to all the pots. This was maintained for a period of thirty five days. Data was analysed using SAS edition 8.2. Seed emergence, hypocotyl development and stand count were enhanced at P≤0.05 in both mycorrhiza fungi inoculated gadam sorghum seeds and in pots whose soils were taken from the rhizosphere ofAspilia prulisetaplants. The growth attributes had a positive correlation to yield at 95% confidence. Soil phosphate level was enhanced in both cases of gadam seed inoculation with mycorrhiza and in soils previously grownAspilia prulisetavegetation.
Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization
Authors: Vera Andrés Manuel , Galera-Prat Albert , Wojciechowski Michał , Różycki Bartosz , Laurents Douglas Vinson , Carrión-Vázquez Mariano , Cieplak Marek , Tinnefeld Philip
Published: December 2019

Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule Fluorescence Resonance Energy Transfer, molecular dynamics simulations and NMR measurements on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.
Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation
Authors: Pony Pauline , Rapisarda Chiara , Terradot Laurent , Marza Esther , Fronzes Rémi
Published: December 2019

Acetaldehyde – alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanolviaan acetaldehyde intermediate during ethanol fermentation in anaerobic environment. This two-step reaction is associated to NAD+regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. In synthetic biology and biotechnology, because of its central role in bacterial alcoholic fermentation, AdhE raised a lot of attention as a key enzyme to produce ethanol from bacterial cultures.

AdhE is commonly found as an oligomeric form called spirosomes. While these helical macromolecular assemblies are conserved, their function remains elusive. We used cryo-electron microscopy to obtain structures ofEscherichia colispirosomes in different conformational states. We confirm that spirosomes contain active AdhE monomers and show that AdhE filamentation is essential for its activityin vitroand functionin vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity. These new data will help to design molecules or mutations that control AdhE activity to fight bacterial pathogens or to optimize ethanol production in biotechnology.
Modelling the role of LHCII-LHCII, PSII-LHCII and PSI-LHCII interactions in state transitions
Authors: Wood W. H. J. , Johnson M. P.
Published: December 2019

The light-dependent reactions of photosynthesis take place in the plant chloroplast thylakoid membrane, a complex three-dimensional structure divided into the stacked grana and unstacked stromal lamellae domains. Plants regulate the macro-organization of photosynthetic complexes within the thylakoid membrane to adapt to changing environmental conditions and avoid oxidative stress. One such mechanism is the state transition which regulates photosynthetic light harvesting and electron transfer. State transitions are driven by changes in the phosphorylation of light harvesting antenna complex II (LHCII), which cause a decrease in grana diameter and stacking, a decreased energetic connectivity between photosystem II (PSII) reaction centres and an increase in the relative LHCII antenna size of photosystem I (PSI) compared to PSII. Phosphorylation is believed to drive these changes by weakening the intra-membrane lateral PSII-LHCII and LHCII-LHCII interactions and the inter-membrane stacking interactions between these complexes, while simultaneously increasing the affinity of LHCII for PSI. We investigated the relative roles and contributions of these three types of interaction to state transitions using a lattice-based model of the thylakoid membrane based on existing structural data, developing a novel algorithm to simulate protein complex dynamics. Monte Carlo simulations revealed that state transitions are unlikely to lead to a large-scale migration of LHCII from the grana to the stromal lamellae. Instead, the increased light harvesting capacity of PSI is largely due to the more efficient recruitment of LHCII already residing in the stromal lamellae into PSI-LHCII supercomplexes upon its phosphorylation. Likewise, the increased light harvesting capacity of PSII upon dephosphorylation was found to be driven by a more efficient recruitment of LHCII already residing in the grana into functional PSII-LHCII clusters, primarily driven by lateral interactions.

Statement of significance

For photosynthesis to operate at maximum efficiency the activity of the light-driven chlorophyll-protein complexes, photosystems I and II (PSI and PSII) must be fine-tuned to environmental conditions. Plants achieve this balance through a regulatory mechanism known as the state transition, which modulates the relative light-harvesting antenna size and therefore excitation rate of each photosystem. State transitions are driven by changes in the extent of the phosphorylation of light harvesting complex II (LHCII), which modulate the interactions between PSI, PSII and LHCII. Here we developed a novel algorithm to simulate protein complex dynamics and then ran Monte Carlo simulations to understand how these interactions cooperate to affect the organization of the photosynthetic membrane and bring about state transitions.
Calcium channel-dependent induction of long-term synaptic plasticity at excitatory Golgi cell synapses of cerebellum
Authors: Locatelli F. , Soda T. , Montagna I. , Tritto S. , Botta L. , Prestori F. , D’Angelo E.
Published: December 2019

The Golgi cells, together with granule cells and mossy fibers, form a neuronal microcircuit regulating information transfer at the cerebellum input stage. Despite theoretical predictions, little was known about long-term synaptic plasticity at Golgi cell synapses. Here we have used whole-cell patch-clamp recordings and calcium imaging to investigate long-term synaptic plasticity at excitatory synapses impinging on Golgi cells. In acute mouse cerebellar slices, mossy fiber theta-burst stimulation (TBS) could induce either long-term potentiation (LTP) or long-term depression (LTD) at mossy fiber-Golgi cell and granule cell-Golgi cell synapses. This synaptic plasticity showed a peculiar voltage-dependence, with LTD or LTP being favored when TBS induction occurred at depolarized or hyperpolarized potentials, respectively. LTP required, in addition to NMDA channels, activation of T-type Ca2+channels, while LTD required uniquely activation of L-type Ca2+channels. Notably, the voltage-dependence of plasticity at the mossy fiber-Golgi cell synapses was inverted with respect to pure NMDA receptor-dependent plasticity at the neighboring mossy fiber-granule cell synapse, implying that the mossy fiber presynaptic terminal can activate different induction mechanisms depending on the target cell. In aggregate, this result shows that Golgi cells show cell-specific forms of long-term plasticity at their excitatory synapses, that could play a crucial role in sculpting the response patterns of the cerebellar granular layer.

Significance statement

This paper shows for the first time a novel form of Ca2+channel-dependent synaptic plasticity at the excitatory synapses impinging on cerebellar Golgi cells. This plasticity isbidirectionalandinvertedwith respect to NMDA receptor-dependent paradigms, with LTD and LTP being favored at depolarized and hyperpolarized potentials, respectively. Furthermore, LTP and LTD induction requires differential involvement ofT-ype and L-type voltage-gated Ca2+channelsrather than the NMDA receptors alone. These results, along with recent computational predictions, support the idea that Golgi cell plasticity could play a crucial role in controlling information flow through the granular layer along with cerebellar learning and memory.
Including crystallographic symmetry in quantum-based refinement: Q|R#2
Authors: Zheng Min , Biczysko Malgorzata , Xu Yanting , Moriarty Nigel W. , Kruse Holger , Urzhumtsev Alexandre , Waller Mark P. , Afonine Pavel V.
Published: December 2019

Three-dimensional structure models refined using low-resolution data from crystallographic or electron cryo-microscopy experiments can benefit from high-quality restraints derived from quantum-chemical methods. However, nonperiodic atom-centered quantum-chemistry codes do not inherently account for nearest-neighbor interactions of crystallographic symmetry-related copies in a satisfactory way. Here, these nearest-neighbor effects have been included in the model by expanding to a super-cell and then truncating the super-cell to only include residues from neighboring cells that are interacting with the asymmetric unit. In this way, the fragmentation approach can adequately and efficiently include nearest-neighbor effects. It has previously been shown that a moderately sized X-ray structure can be treated using quantum methods if a fragmentation approach is applied. In this study, a target protein (PDB entry 4gif) was partitioned into a number of large fragments. The use of large fragments (typically hundreds of atoms) is tractable when a GPU-based package such as TeraChem is employed or cheaper (semi-empirical) methods are used. The QM calculations were run at the HF-D3/6-31G level. The models refined using a recently developed semi-empirical method (GFN2-xTB) were compared and contrasted. To validate the refinement procedure for a non-P1 structure, a standard set of crystallographic metrics were used. The robustness of the implementation is shown by refining 13 additional protein models across multiple space groups and a summary of the refinement metrics is presented.
Catalytic mechanism and evolutionary characteristics of thioredoxin from Halobacterium salinarum NRC-1
Authors: Arai Shigeki , Shibazaki Chie , Shimizu Rumi , Adachi Motoyasu , Ishibashi Matsujiro , Tokunaga Hiroko , Tokunaga Masao
Published: December 2019

Thioredoxin (TRX) is an important antioxidant against oxidative stress. TRX from the extremely halophilic archaeon Halobacterium salinarum NRC-1 (HsTRX-A), which has the highest acidic residue content [(Asp + Glu)/(Arg + Lys + His) = 9.0] among known TRXs, was chosen to elucidate the catalytic mechanism and evolutionary characteristics associated with haloadaptation. X-ray crystallographic analysis revealed that the main-chain structure of HsTRX-A is similar to those of homologous TRXs; for example, the root-mean-square deviations on Cα atoms were <2.3 Å for extant archaeal TRXs and <1.5 Å for resurrected Precambrian TRXs. A unique water network was located near the active-site residues (Cys45 and Cys48) in HsTRX-A, which may enhance the proton transfer required for the reduction of substrates under a high-salt environment. The high density of negative charges on the molecular surface (3.6 × 10−3 e Å−2) should improve the solubility and haloadaptivity. Moreover, circular-dichroism measurements and enzymatic assays using a mutant HsTRX-A with deletion of the long flexible N-terminal region (Ala2–Pro17) revealed that Ala2–Pro17 improves the structural stability and the enzymatic activity of HsTRX-A under high-salt environments (>2 M NaCl). The elongation of the N-terminal region in HsTRX-A accompanies the increased hydrophilicity and acidic residue content but does not affect the structure of the active site. These observations offer insights into molecular evolution for haloadaptation and potential applications in halophilic protein-related biotechnology.
Using cryo-electron microscopy maps for X-ray structure determination of homologues
Authors: Zeng Lingxiao , Ding Wei , Hao Quan
Published: December 2019

The combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography reflects an important trend in structural biology. In a previously published study, a hybrid method for the determination of X-ray structures using initial phases provided by the corresponding parts of cryo-EM maps was presented. However, if the target structure of X-ray crystallography is not identical but homologous to the corresponding molecular model of the cryo-EM map, then the decrease in the accuracy of the starting phases makes the whole process more difficult. Here, a modified hybrid method is presented to handle such cases. The whole process includes three steps: cryo-EM map replacement, phase extension by NCS averaging and dual-space iterative model building. When the resolution gap between the cryo-EM and X-ray crystallographic data is large and the sequence identity is low, an intermediate stage of model building is necessary. Six test cases have been studied with sequence identity between the corresponding molecules in the cryo-EM and X-ray structures ranging from 34 to 52% and with sequence similarity ranging from 86 to 91%. This hybrid method consistently produced models with reasonable R
work and R
free values which agree well with the previously determined X-ray structures for all test cases, thus indicating the general applicability of the method for X-ray structure determination of homologues using cryo-EM maps as a starting point.
Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data. Corrigendum
Authors: Caldararu Octav , Manzoni Francesco , Oksanen Esko , Logan Derek T. , Ryde Ulf
Published: December 2019

Corrections are published for the article by Caldararu et al. [(2019), Acta Cryst. D75, 368–380].
Performance of the k-kL model for aerodynamics applications
Authors: Kalkote Nikhil , Kumar Ashutosh , Assam Ashwani , Eswaran Vinayak
Published: December 2019

Purpose

The purpose of this paper is to study the predictability of the recently proposed length scale-based two-equation k-kL model for external aerodynamic flows such as those also encountered in the high-lift devices.

Design/methodology/approach

The two-equation k-kL model solves the transport equations of turbulent kinetic energy (TKE) and the product of TKE and the integral length scale to obtain the effect of turbulence on the mean flow field. In theory, the use of governing equation for length scale (kL) along with the TKE promises applicability in a wide range of applications in both free-shear and wall-bounded flows with eddy-resolving capability.

Findings

The model is implemented in the in-house unstructured grid computational fluid dynamics solver to investigate its performance for airfoils in difficult-to-predict situations, including stalling and separation. The numerical findings show the good capability of the model in handling the complex flow physics in the external aerodynamic computations.

Originality/value

The model performance is studied for stationary turbulent external aerodynamic flows, using five different airfoils, including two multi-element airfoils in high-lift configurations which, in the knowledge of the authors, have not been simulated with k-kL model until now.
Examination of cyber aggression by adult consumers: ethical framework and drivers
Authors: Han Mei , Vasquez Arturo Z.
Published: December 2019

Purpose

The widespread use of information and communication technologies enables consumers to obtain and share information whenever they feel the urge. With the advent of review websites and forums, companies and business owners may find themselves victims of consumer cyber aggression, which can hurt a company badly. This study aims to explore why consumers would engage in cyber aggression against companies, and to that end, it examines consumers’ ethical orientation and other possible drivers of cyber aggression.

Design/methodology/approach

To examine how ethical orientation affects consumers’ intention to engage in cyber aggression, a scenario-based 2 × 2 (deontological: moral/immoral × teleological: good result/bad result) between-subject experimental design is used. Moreover, 26 possible drivers in related literature are identified and included in a questionnaire administered to 226 college students.

Findings

The results show that adult consumers’ deontological and teleological evaluations significantly affect their ethical judgment about engaging in cyber aggression, which further impacts their intention to perpetrate an act of cyber aggression. Moreover, the study identifies six factors contributing to cyber aggression engagement as follows: personal aggressiveness, ease of perpetration, internet negativity, personal gains, helping the company and recreation.

Originality/value

Cyber aggression is generally viewed as interpersonal violence among adolescents. This study views cyber aggression from a different perspective and it is one of the few studies to look at adult consumers’ motivations to engage in cyber aggression against companies. The findings of this study can help firms understand why their customers attack them online, and understanding that will enable businesses to formulate more effective responses to attacks.
Industry 4.0: coherent definition framework with technological and organizational interdependencies
Authors: Nosalska Katarzyna , Piątek Zbigniew Michał , Mazurek Grzegorz , Rządca Robert
Published: December 2019

Purpose

The purpose of this paper is to introduce coherent Industry 4.0 definition via a rigorous analysis framework, and provide a holistic view of technological, organizational and other key aspects (variables) of Industry 4.0 along with the identification of interdependencies that co-occur between them.

Design/methodology/approach

The study conducts a systematic literature review using Preferred Reporting Items for Systematic Review and Meta-Analysis methodology, and includes 675 papers analyzed both quantitatively and qualitatively. The former utilizes TIBCO Statistica. Furthermore, to define Industry 4.0, the authors reviewed 52 publications.

Findings

Industry 4.0 is a multidimensional system of value creation that includes 42 groups of terms in management, organizational and business-related variables, 30 technological and manufacturing-related variables – classified into seven categories – and several interdependencies that co-occur between them.

Practical implications

The analyses’ outcomes are of high importance both for academia and industry practitioners, as the findings elucidate the meaning of Industry 4.0 and may be used as the basis of future research in management, production management, industrial organizations and other Industry 4.0-related disciplines. Regarding industrial companies, the publication serves as a compendium, and should support industrial businesses in the transition from traditional manufacturing into the Industry 4.0 era.

Originality/value

This work’s novelty and value is threefold: first, the paper introduces an Industry 4.0 definition framework based on the most popular publications in the field. Second, the paper identifies and presents Industry 4.0’s common technologies and organizational variables via a systematic and current literature review. Finally, the paper extends the ongoing discourse on Industry 4.0. For the first time in this discipline, interdependences between identified Industry 4.0 variables are presented and discussed.
When reciprocal violence turns into mutual acceptance
Authors: Farias Carine
Published: December 2019

Purpose

The purpose of this paper is to identify practices aimed at “passing the test” in fieldwork contexts characterized by reciprocal forms of symbolic violence.

Design/methodology/approach

It is based on an analysis of a fieldwork experience in an intentional community of activists inspired by anarchist ideas.

Findings

This study suggests that in a context of reciprocal violence, the researcher must qualify the specific threat that her presence poses and develop a set of behavioral practices aimed at neutralizing this threat in order to gain acceptance and gather valuable data. Three sets of practices – showing tenacity, disclosing oneself and adjusting while staying consistent – helped the researcher in crafting an acceptable status in the field.

Originality/value

Identifiable moments of hostile challenges should be addressed rather than avoided. They constitute indeed key gateways for understanding the culture and socializing processes of the observed group, and lead to relevant ethical questions regarding the ethnographer’s position.
Does the size and developmental stage of traits at fledging reflect juvenile flight ability among songbirds?
Authors: Jones Todd M. , Benson Thomas J. , Ward Michael P.
Published: December 2019

Morphological traits can influence the ability of animals to perform ecologically relevant tasks that are essential for their growth, survival and fitness. Understanding such links in juvenile animals is of particular importance, as periods of juvenile life are often associated with high rates of mortality and can be critical with respect to evolution of life histories and viability of populations. To study such links, an important first step is to assess relationships between juvenile morphologies and measures of performance.

Altricial songbirds can provide novel insights into morphology–performance relationships owing to the high locomotor demand placed on juveniles after they leave the nest. Therefore, we examined the relationships between the size and developmental stage of juvenile traits and juvenile flight ability among 13 coexisting songbirds in east‐central Illinois. Among potential traits, we focused on relationships between flight ability and four measures of wing development at fledging as well as two body measures thought to reflect an individual's overall quality and musculature.

Among measures of wing development, wing emergence was the strongest, most consistent predictor of ability within and among species. Relative wing length and wing emergence‐loading were often good predictors of flight ability as well, while relative wing‐loading was rarely a good predictor. Estimates of body mass and body condition were poor, inconsistent predictors of flight ability both within and among species.

Our results highlight the importance of wing development for flight performance of juvenile songbirds. Furthermore, our evaluation of different wing characteristics suggests that the importance of macro‐scale transmissivity and wing/disc loading towards flight ability changes with respect to juvenile ontogeny. Though mass likely interacts with wing characteristics in determining flight ability, our results suggest that body mass and condition are likely reflective of other, non‐flight measures of fledgling performance.

Few studies on altricial songbirds have examined morphology–performance relationships in juveniles. By linking wing emergence with juvenile flight ability, our research has taken a first step in assessing the adaptive significance of variation in wing development for juvenile songbirds.

A free Plain Language Summary can be found within the Supporting Information of this article.
Green's function for three‐dimensional elastic wave equation with a moving point source on the free surface with applications
Authors: Chen Jing‐Bo , Cao Jian
Published: December 2019

High‐speed train seismology has come into being recently. This new kind of seismology uses a high‐speed train as a repeatable moving seismic source. Therefore, Green's function for a moving source is needed to make theoretical studies of the high‐speed train seismology. Green's function for three‐dimensional elastic wave equation with a moving point source on the free surface is derived. It involves a line integral of the Green's function for a fixed point source with different positions and corresponding time delays. We give a rigorous mathematical proof of this Green's function. According to the principle of linear superposition, we have also obtained the Green's function for a group of moving sources which can be regarded as a model of a traveling high‐speed train. Based on a temporal convolution, an analytical formula for other moving sources is also given. In terms of a moving Gaussian source, we deal with the issue of numerical calculations of the analytical formula. Applications to modelling of a traveling high‐speed train are presented. We have considered both the land case and the bridge case for a traveling high‐speed train. The theoretical seismograms show different waveform features for these two cases.
Depression has an impact on disease activity and health‐related quality of life in rheumatoid arthritis: A systematic review and meta‐analysis
Authors: Zhang Lijuan , Cai Pingping , Zhu Weiyi
Published: December 2019

Objective

The aim of this study was to explore the impact of depression on pain, disease activity, functional disability and quality of life in patients with rheumatoid arthritis (RA).

Methods

English (PubMed, the Cochrane Library, Web of Science and PsycINFO) and Chinese (Wan Fang Database and Chinese National Knowledge Infrastructure) databases were systematically and independently searched from their inception until 30 September, 2019. Studies evaluating the impact of depression on pain, disease activity, functional disability and quality of life with the use of the Short Form‐36 questionnaire (SF‐36) scoring system were included. Statistical analyses were performed with Revman5.3. Data were pooled using a fixed or random‐effects model according to heterogeneity.

Results

A total of 7 identified studies matched the inclusion criteria, reporting on a total of 1078 patients with RA in the analysis. The total Disease Activity Score in 28 joints was significantly higher in patients with depression than in patients without depression [standardized mean difference (SMD) =0.47, 95% CI 0.10‐0.85, P = .01]. All SF‐36 dimensions (physical function, role physical function, emotional role function, vitality, mental health, social function, body pain, general health, physical component scale, mental component scale) were lower in patients with depression than in groups without depression. Interestingly, the results of this meta‐analysis showed no significant difference between patients with and without depression in pain (SMD = 0.57, 95% CI − 0.03‐1.17, P = .06) and functional disability (SMD = 0.48, 95% CI − 0.03‐0.99, P = .43).

Conclusion

This meta‐analysis showed that RA patients with depression tended to have higher disease activity and lower quality of life than patients without depression.
Global Standards in the Asian Infrastructure Investment Bank: The Contribution of the European Members
Authors: Gabusi Giuseppe
Published: December 2019

In 2015, seventeen European states joined the Asian Infrastructure Investment Bank (AIIB) as Founding Members. France, Germany, Italy and the United Kingdom, among the group, have the largest share of capital and votes, giving them significant voice in the Bank. The purpose of the European members in joining was mainly twofold: (i) to help increase financial flows available for investment infrastructure in Asia; and (ii) to help ensure that the new Bank would adhere to global financial, environmental and social standards, as established by the existing multilateral development banks (MDBs). It can be said that the Europeans have largely succeeded. Existing MDBs have served as models for the standards which the AIIB is institutionalizing. However, some European‐based civil society organizations are increasingly critical of the operations of the AIIB. Moreover, some developing countries may see the AIIB's standards as an unnecessary burden. It can therefore not be assumed that the AIIB will continue to expand its portfolio by merely complementing the existing MDBs.