bluuebunny/crossref_metadata_2025 huggingface dataset:
Bladder pressure encoding by near-independent fibre subpopulations — implications for decoding
Authors: Lubba Carl H. , Ouyang Zhonghua , Jones Nick S. , Bruns Tim M. , Schultz Simon R.
Published: November 2019

Objective

We aim at characterising the encoding of bladder pressure (intravesical pressure) by a population of sensory fibres. This research is motivated by the possibility to restore bladder function in elderly patients or after spinal cord injury using implanted devices, so called bioelectronic medicines. For these devices, nerve-based estimation of intravesical pressure can enable a personalized and on-demand stimulation paradigm, which will be more effective and efficient. In this context, a better understanding of the encoding strategies employed by the body might in the future be exploited by informed decoding algorithms that enable a precise and robust bladderpressure estimation.

Approach

To this end, we apply information theory to microelectrode-array recordings from the cat sacral dorsal root ganglion while filling the bladder, conduct surrogate data studies to augment the data we have, and finally decode pressure in a simple informed approach.

Main results

We find an encoding scheme by different main bladder neuron types that we divide into three response types (slow tonic, phasic, and derivative fibres). We show that an encoding by different bladder neuron types, each represented by multiple cells, offers reliability through within-type redundancy and high information rates through near-independence of different types. Our subsequent decoding study shows a potentially more robust decoding from mean responses of homogeneous cell pools.

Significance

We have here, for the first time, analysed the encoding of intravesical pressure by a population of sensory neurons in a principled way using information theory. We show that even a simple adapted decoder can exploit the redundancy in the population to be more robust against cell loss. This work thus paves the way towards principled encoding studies in the periphery and towards a new generation of informed peripheral nerve decoders for bioelectronic medicines.
Brain structural connectivity predicts brain functional complexity: DTI derived centrality accounts for variance in fractal properties of fMRI signal
Authors: Neudorf Josh , Ekstrand Chelsea , Kress Shaylyn , Borowsky Ron
Published: November 2019

The complexity of brain activity has recently been investigated using the Hurst (H) exponent, which describes the extent to which functional magnetic resonance imaging (fMRI) blood oxygen-level dependent (BOLD) activity is self-similar vs. complex. For example, research has demonstrated that fMRI activity is more complex before than after consumption of alcohol and during task than resting state. The measurement of H in fMRI is a novel method that requires the investigation of additional factors contributing to complexity. Graph theory metrics of centrality can assess how centrally important to the brain network each region is, based on diffusion tensor imaging (DTI) counts of probabilistic white matter (WM) tracts. DTI derived centrality was hypothesized to account for the complexity of functional activity, based on the supposition that more sources of information to integrate should result in more complex activity. FMRI BOLD complexity as measured by H was associated with five brain region centrality measures: degree, eigenvector, PageRank, current flow betweenness, and current flow closeness centrality. Multiple regression analyses demonstrated that degree centrality was the most robust predictor of complexity, whereby greater centrality was associated with increased complexity (lower H). Regions known to be highly connected, including the thalamus and hippocampus, notably were among the highest in centrality and complexity. This research has led to a greater understanding of how brain region characteristics such as DTI centrality relate to the novel Hurst exponent approach for assessing brain activity complexity, and implications for future research that employ these measures are discussed.
Modeling Abiotic Niches of Crops and Wild Ancestors Using Deep Learning: A Generalized Approach
Authors: Hulleman W. G. , Vos R. A.
Published: November 2019

Abstract

Introduction

Understanding what interactions and environmental factors shape the geographic distribution of species is one of the fundamental questions in ecology and evolution. Insofar as the focus is on agriculturally important species, insight into this is also of applied importance. Species Distribution Modeling (SDM) comprises a spectrum of approaches for establishing correlative models of species (co-)occurrences and geospatial patterns of abiotic environmental variables.

Methods

Here, we contribute to this field by presenting a generalized approach for SDM that utilizes deep learning, which offers some improvements over current methods, and by presenting a case study on the habitat suitability of staple crops and their wild ancestors. The approach we present is implemented in a reusable software toolkit, which we apply to an extensive data set of geo-referenced occurrence records for 52 species and 59 GIS layers. We compare the habitat suitability projections for selected, major crop species with the actual extent of their current cultivation.

Results

Our results show that the approach yields especially plausible projections for species with large numbers of occurrences (>500). For the analysis of such data sets, the toolkit provides a convenient interface for using deep neural networks in SDM, a relatively novel application of deep learning. The toolkit, the data, and the results are available as open source / open access packages.

Conclusions

Species Distribution Modeling with deep learning is a promising avenue for method development. The niche projections that can be produced are plausible, and the general approach provides great flexibility for incorporating additional data such as species interactions.
Amperometric measurements of cocaine cue and novel context-evoked glutamate and nitric oxide release in the nucleus accumbens core
Authors: Siemsen BM , McFaddin JA , Haigh K , Brock AG , Leath MN , Hooker KN , McGonegal LK , Scofield MD
Published: November 2019

Cue-induced reinstatement of cocaine seeking after self-administration (SA) and extinction relies on glutamate release in the nucleus accumbens core (NAcore), which in turn activates neuronal nitric oxide synthase (nNOS) interneurons. Nitric oxide (NO) is required for structural plasticity in NAcore medium spiny neurons (MSNs), as well as cued cocaine seeking. However, NO release in the NAcore during reinstatement has yet to be directly measured. Further, the temporal relationship between glutamate release, and the induction of a NO response also remains unknown. Using wireless amperometric recordings in awake behaving rat, we quantified the magnitude and temporal dynamics of novel context- and cue-induced reinstatement-evoked glutamate and NO release in the NAcore. We found that re-exposure to cocaine-conditioned stimuli following SA and extinction increased extracellular glutamate, leading to release of NO in the NAcore. In contrast, exposing drug-naïve rats to a novel context led to a lower magnitude rise in glutamate in the NAcore relative to cue-induced reinstatement. Interestingly, novel context exposure evoked a higher magnitude NO response relative to cue-induced reinstatement. Despite differences in magnitude, novel context evoked-NO release in the NAcore was also temporally delayed when compared to glutamate. These results demonstrate a dissociation between the magnitude of cocaine cue- and novel context-evoked glutamate and NO release in the NAcore, yet similarity in the temporal dynamics of their release. Together, these data contribute to a greater understanding of the relationship between glutamate and NO, two neurotransmitters implicated in encoding the valence of distinct contextual stimuli.
Repetition Attenuates the Influence of Recency on Recognition Memory: Behavioral and Electrophysiological Evidence
Authors: Scofield John E. , Price Mason H. , Flores Angélica , Merkle Edgar C. , Johnson Jeffrey D.
Published: November 2019

Studies of recognition memory often demonstrate a recency effect on behavioral performance, whereby response times (RTs) are faster for stimuli that were previously presented recently as opposed to more remotely in the past. This relationship between performance and presentation lag has been taken to reflect that memories are accessed by serially searching backwards in time, such that RT indicates the self-terminating moment of such a process. Here, we investigated the conditions under which this serial search gives way to more efficient means of retrieving memories. Event-related potentials (ERPs) were recorded during a continuous recognition task in which subjects made binary old/new judgments to stimuli that were each presented up to four times across a range of lags. Stimulus repetition and shorter presentation lag both gave rise to speeded RTs, consistent with previous findings, and we novelly extend these effects to a robust latency measure of the left parietal ERP effect associated with retrieval success. Importantly, the relationship between repetition and recency was further elucidated, such that repetition attenuated lag-related differences that were initially present in both the behavioral and neural latency data. These findings are consistent with the idea that a serial search through recent memory can quickly be abandoned in favor of relying on more efficient ‘time-independent’ cognitive processes or neural signals.
Widespread presence of direction-reversing neurons in the mouse visual system
Authors: Billeh Yazan N. , Iyer Ramakrishnan , Wahle Iman A. , Caldejon Shiella , Durand Séverine , Groblewski Peter A. , Larkin Josh D , Lecoq Jerome , Williford Ali , Mihalas Stefan , Arkhipov Anton , de Vries Saskia E. J.
Published: November 2019

Direction selectivity – the preference of motion in one direction over the opposite – is a fundamental property of visual neurons across species. We find that a substantial proportion of direction selective neurons in the mouse visual system reverse their preferred direction of motion in response to drifting gratings at different spatiotemporal parameters. A spatiotemporally asymmetric filter model recapitulates our experimental observations.
GluD1 knockout mice with a pure C57BL/6N background show impaired fear memory, social interaction, and enhanced depressive-like behavior
Authors: Nakamoto Chihiro , Kawamura Meiko , Nakatsukasa Ena , Natsume Rie , Takao Keizo , Watanabe Masahiko , Abe Manabu , Takeuchi Tomonori , Sakimura Kenji
Published: November 2019

The GluD1 gene is associated with susceptibility for schizophrenia, autism, depression, and bipolar disorder. However, the function of GluD1 and how it is involved in these conditions remain elusive. In this study, we generated a GluD1-knockout (GluD1-KO) mouse line with a pure C57BL/6N genetic background and performed several behavioral analyses. Compared to a control group, GluD1-KO mice showed no significant anxiety-related behavioral differences, evaluated using behavior in an open field, elevated plus maze, a light-dark transition test, the resident-intruder test of aggression and sensorimotor gating evaluated by the prepulse inhibition test. However, GluD1-KO mice showed (1) hyper locomotor activity in the open field, (2) decreased sociability and social novelty preference in the three-chambered social interaction test, (3) impaired memory in contextual, but not cued fear conditioning tests, and (4) enhanced depressive-like behavior in a forced swim test. Pharmacological studies revealed that enhanced depressive-like behavior in GluD1-KO mice was restored by the serotonin reuptake inhibitors imipramine and fluoxetine, but not the norepinephrine transporter inhibitor desipramine. In addition, biochemical analysis revealed no significant difference in protein expression levels, such as other glutamate receptors in the synaptosome and postsynaptic densities prepared from the frontal cortex and the hippocampus. These results suggest that GluD1 plays critical roles in fear memory, sociability, and depressive-like behavior.
Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs
Authors: Gemenet Dorcus C , Kitavi Mercy N , David Maria , Ndege Dorcah , Ssali Reuben T , Swanckaert Jolien , Makunde Godwill , Craig Yencho G , Gruneberg Wolfgang , Carey Edward , Mwanga Robert O , Andrade Maria I , Heck Simon , Campos Hugo
Published: November 2019

Quality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.

Key Message

A 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence.
Protein Arginine Deiminase 4 Antagonizes Methylglyoxal-induced Histone Glycation
Authors: Zheng Qingfei , Osunsade Adewola , David Yael
Published: November 2019

Protein arginine deiminase 4 (PAD4) facilitates the post-translational citrullination of the core histones H3 and H4. While the precise epigenetic function of this modification has not been resolved, it was shown to associate with general chromatin decompaction and to compete with arginine methylation. Recently, we showed that histones are subjected to methylglyoxal (MGO)-induced glycation on nucleophilic side chains, particularly arginines, under metabolic stress conditions. These non-enzymatic adducts change chromatin architecture and the epigenetic landscape by competing with enzymatic modifications. Here we report that PAD4 antagonizes histone MGO-glycation by protecting the reactive sites with oxygen substitution, as well as by converting already-glycated arginine residues into citrulline. Moreover, we show that similar to the deglycase DJ-1, PAD4 is overexpressed and histone citrullination is upregulated in breast cancer tumors, suggesting an additional mechanistic link to PAD4’s oncogenic properties.

Significance

Metabolic syndromes and diabetes increase the risk for certain diseases such as cancer. However, the mechanism behind this correlation is poorly understood. Methylglyoxal (MGO), a reactive dicarbonyl sugar metabolite found in cells under metabolic stress, can non-enzymatically modify arginine and lysine residues in histone proteins, making it a new epigenetic marker linking metabolism and disease. Histone MGO-glycation induces changes in chromatin architecture and the epigenetic landscape, and abrogates gene transcription. In this study, we found that protein arginine deiminase 4 (PAD4) exhibits dual functions to antagonize histone MGO-glycation: removing glycation adducts from arginines and converting the unmodified side chains into citrulline, which protects them from undergoing glycation. This unprecedented biochemical mechanism demonstrates a potential function of PAD4 in cancer cells.
Secondary metabolism in the gill microbiota of shipworms (Teredinidae) as revealed by comparison of metagenomes and nearly complete symbiont genomes
Authors: Altamia Marvin A. , Lin Zhenjian , Trindade-Silva Amaro E. , Uy Iris Diana , Shipway J. Reuben , Wilke Diego Veras , Concepcion Gisela P. , Distel Daniel L. , Schmidt Eric W. , Haygood Margo G.
Published: November 2019

Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil, and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria encode many biosynthetic gene cluster families (GCFs) for bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts, and sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 out of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species, and collectively constitute an immense resource for the discovery of new biosynthetic pathways to bioactive secondary metabolites.

Importance

We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs, and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.
Correction of missing-wedge artifacts in filamentous tomograms by template-based constrained deconvolution
Authors: Kovacs Julio , Song Jun Ha , Auer Manfred , He Jing , Wriggers Willy
Published: November 2019

Cryo-electron tomography maps often exhibit considerable noise and anisotropic resolution, due to the low-dose requirements and the missing wedge in Fourier space. These spurious features are visually unappealing and, more importantly, prevent an automated segmentation of geometric shapes, requiring a highly subjective, labor-intensive manual tracing. We developed a novel computational strategy for objectively denoising and correcting missing-wedge artifacts in the special but important case of repetitive basic shapes, such as filamentous structures. In this approach, we use the template and a non-negative “location map” to constrain the deconvolution scheme, allowing us to recover, to a considerable degree, the information lost in the missing wedge. We applied our method to data of actin-filament bundles of inner-ear stereocilia, which are critical in hearing transduction processes, and found a good overlap with the experimental map and with manual tracing. In addition, we demonstrate that our method can also be used for membrane detection.
Entorhinal and ventromedial prefrontal cortices abstract and generalise the structure of reinforcement learning problems
Authors: Baram Alon B , Muller Timothy H , Nili Hamed , Garvert Mona , Behrens Timothy E J
Published: November 2019

Knowledge of the structure of a problem, such as relationships between stimuli, enables rapid learning and flexible inference. Humans and other animals can abstract this structural knowledge and generalise it to solve new problems. For example, in spatial reasoning, shortest-path inferences are immediate in new environments. Spatial structural transfer is mediated by grid cells in entorhinal and (in humans) medial prefrontal cortices, which maintain their structure across different environments. Here, using fMRI, we show that entorhinal and ventromedial prefrontal cortex (vmPFC) representations perform a much broader role in generalising the structure of problems. We introduce a task-remapping paradigm, where subjects solve multiple reinforcement learning (RL) problems differing in structural or sensory properties. We show that, as with space, entorhinal representations are preserved across different RL problems only if task structure is preserved. In vmPFC, representations of standard RL signals such as prediction error also vary as a function of task structure.
Regulation of apical constriction via microtubule- and Rab11-dependent apical transport during tissue invagination
Authors: Le Thao Phuong , Chung SeYeon
Published: November 2019

The formation of an epithelial tube is a fundamental process for organogenesis. DuringDrosophilaembryonic salivary gland (SG) invagination, Folded gastrulation (Fog)- dependent Rho-associated kinase (Rok) promotes contractile apical myosin formation to drive apical constriction. Microtubules (MTs) are also crucial for this process and are required for forming and maintaining apicomedial myosin. However, the underlying mechanism that coordinates actomyosin and MT networks still remains elusive. Here, we show that MT-dependent intracellular trafficking regulates apical constriction during SG invagination. Key components involved in protein trafficking, such as Rab11 and Nuclear fallout (Nuf), are apically enriched near the SG invagination pit in a MT-dependent manner. Disruption of the MT networks or knockdown ofRab11impairs apicomedial myosin formation and apical constriction. We show that MTs and Rab11 are required for apical enrichment of the Fog ligand and the continuous distribution of the apical determinant protein Crumbs (Crb) and the key adherens junction protein E-Cadherin (E-Cad) along junctions. Targeted knockdown ofcrborE-Cadin the SG disrupts apical myosin networks and results in apical constriction defects. Our data suggest a role of MT- and Rab11-dependent intracellular trafficking in regulating actomyosin networks and cell junctions, to coordinate cell behaviors during tubular organ formation.
Sleep promotes downward firing rate homeostasis
Authors: Pacheco Alejandro Torrado , Bottorff Juliet , Turrigiano Gina G.
Published: November 2019

Homeostatic plasticity is hypothesized to regulate neuronal activity around a stable set point to compensate for learning-related plasticity. This regulation is predicted to be bidirectional but only upward firing rate homeostasis (FRH) has been demonstrated in vivo. We combined chronic electrophysiology in freely behaving animals with a protocol that induces robust plasticity in primary visual cortex (V1) to induce downward FRH and show that neurons bidirectionally regulate firing rates around an individual set point. Downward FRH did not require N-methyl-D-aspartate receptor (NMDAR) signaling and was associated with homeostatic scaling down of synaptic strengths. Like upward FRH, downward FRH was gated by vigilance state, but in the opposite direction: it occurred during sleep and not during wake. In contrast, FR changes associated with Hebbian plasticity happened independently of sleep and wake. Thus, we find that sleep’s impact on neuronal plasticity depends on the particular forms of plasticity that are engaged.
Metabolic dependencies and vulnerabilities in leukemia
Authors: Rashkovan Marissa , Ferrando Adolfo
Published: November 2019

Leukemia cell proliferation requires up-regulation and rewiring of metabolic pathways to feed anabolic cell growth. Oncogenic drivers directly and indirectly regulate metabolic pathways, and aberrant metabolism is central not only for leukemia proliferation and survival, but also mediates oncogene addiction with significant implications for the development of targeted therapies. This review explores leukemia metabolic circuitries feeding anabolism, redox potential, and energy required for tumor propagation with an emphasis on emerging therapeutic opportunities.
Human stem cell models: lessons for pancreatic development and disease
Authors: Gaertner Bjoern , Carrano Andrea C. , Sander Maike
Published: November 2019

A comprehensive understanding of mechanisms that underlie the development and function of human cells requires human cell models. For the pancreatic lineage, protocols have been developed to differentiate human pluripotent stem cells (hPSCs) into pancreatic endocrine and exocrine cells through intermediates resembling in vivo development. In recent years, this differentiation system has been employed to decipher mechanisms of pancreatic development, congenital defects of the pancreas, as well as genetic forms of diabetes and exocrine diseases. In this review, we summarize recent insights gained from studies of pancreatic hPSC models. We discuss how genome-scale analyses of the differentiation system have helped elucidate roles of chromatin state, transcription factors, and noncoding RNAs in pancreatic development and how the analysis of cells with disease-relevant mutations has provided insight into the molecular underpinnings of genetically determined diseases of the pancreas.
Hippo signaling does it again: arbitrating cardiac fibroblast identity and activation
Authors: Johansen Anne Katrine Z. , Molkentin Jeffery D.
Published: November 2019

The Hippo pathway is an evolutionarily conserved kinase cascade that is fundamental for tissue development, homeostasis, and regeneration. In the developing mammalian heart, Hippo signaling regulates cardiomyocyte numbers and organ size. While cardiomyocytes in the adult heart are largely postmitotic, Hippo deficiency can increase proliferation of these cells and affect cardiac regenerative capacity. Recent studies have also shown that resident cardiac fibroblasts play a critical role in disease responsiveness and healing, and in this issue of Genes and Development, Xiao and colleagues (pp. 1491–1505) demonstrate that Hippo signaling also integrates the activity of fibroblasts in the heart. They show that Hippo signaling normally maintains the cardiac fibroblast in a resting state and, conversely, its inactivation during disease-related stress results in a spontaneous transition toward a myofibroblast state that underlies fibrosis and ventricular remodeling. This phenotypic switch is associated with increased cytokine signaling that promotes nonautonomous resident fibroblast and myeloid cell activation.
Small-Scale Isolation of Bacterial Artificial Chromosome (BAC) DNA and Verification by Polymerase Chain Reaction (PCR)
Authors: Heintz Nathaniel , Gong Shiaoching
Published: November 2019

In this protocol, small amounts of selected bacterial artificial chromosome (BAC) DNAs are prepared from 5-mL cultures of the Escherichia coli host transformed with the BAC clone. DNA is isolated by an adaptation of the alkaline lysis method. The yield is 0.1–0.4 µg, and the BAC DNA is suitable for analysis by polymerase chain reaction (PCR). Considerations for clone selection are also addressed.
Toward the computational design of protein crystals with improved resolution
Authors: Jeliazkov Jeliazko R. , Robinson Aaron C. , García-Moreno E. Bertrand , Berger James M. , Gray Jeffrey J.
Published: November 2019

Substantial advances have been made in the computational design of protein interfaces over the last 20 years. However, the interfaces targeted by design have typically been stable and high-affinity. Here, we report the development of a generic computational design method to stabilize the weak interactions at crystallographic interfaces. Initially, we analyzed structures reported in the Protein Data Bank to determine whether crystals with more stable interfaces result in higher resolution structures. We found that for 22 variants of a single protein crystallized by a single individual, the Rosetta-calculated `crystal score' correlates with the reported diffraction resolution. We next developed and tested a computational design protocol, seeking to identify point mutations that would improve resolution in a highly stable variant of staphylococcal nuclease (SNase). Using a protocol based on fixed protein backbones, only one of the 11 initial designs crystallized, indicating modeling inaccuracies and forcing us to re-evaluate our strategy. To compensate for slight changes in the local backbone and side-chain environment, we subsequently designed on an ensemble of minimally perturbed protein backbones. Using this strategy, four of the seven designed proteins crystallized. By collecting diffraction data from multiple crystals per design and solving crystal structures, we found that the designed crystals improved the resolution modestly and in unpredictable ways, including altering the crystal space group. Post hoc, in silico analysis of the three observed space groups for SNase showed that the native space group was the lowest scoring for four of six variants (including the wild type), but that resolution did not correlate with crystal score, as it did in the preliminary results. Collectively, our results show that calculated crystal scores can correlate with reported resolution, but that the correlation is absent when the problem is inverted. This outcome suggests that more comprehensive modeling of the crystallographic state is necessary to design high-resolution protein crystals from poorly diffracting crystals.
The utilisation of library spaces by postgraduate students at a university in an African country
Authors: Bangani Siviwe , Moyo Mathew , Mashiyane Dina Mokgadi
Published: November 2019

Purpose

The purpose of this paper is to determine the use of library spaces by postgraduate students at the North-West University in South Africa.

Design/methodology/approach

A survey research methodology was used in which both online and print questionnaires were used to gather data.

Findings

The major findings of the study were that postgraduate students frequently visited the libraries to make use of the quite study spaces, which include the research commons and the study carrels. The study further found out that postgraduate students rarely visited the libraries for the purpose of consulting librarians regarding their studies. Challenges expressed by the students include insufficient workstations, poor internet and Wi-Fi connectivity and limited seating capacity. The benefit of the study is that it will help librarians and the university administrators to better understand the postgraduate students space needs, as well as the challenges being encountered.

Research limitations/implications

This biggest limitation of this study was a lack or low response rate by certain faculties, which mitigated against comparing the use of spaces by faculty.

Practical implications

The results of this study re-affirm the need for postgraduate spaces. University libraries that seek to build postgraduate spaces in the future need to ensure that an adequate number of computer workstations are supplied and Wi-Fi and bandwidth are improved. University libraries that already have postgraduate spaces should consider adding more workstations and improving bandwidth and Wi-Fi connectivity in those spaces. These results further point to a need for libraries in Africa and elsewhere to consider having more quiet study spaces for postgraduate students while reducing the number of group study spaces.

Social implications

The results of this study point to a need for libraries and university authorities to periodically review library spaces as a way to ensure their continued optimal usage. They also point to a need for more funds to further enhance the library spaces for postgraduate students’ use.

Originality/value

South African libraries are faced with challenges including the addition of 15 per cent value added tax to print and online resources. In this environment, libraries are expected by university authorities to demonstrate return on investment. This study, therefore, is located within the realm of determining return on investment for the funds spent by universities to build dedicated postgraduate library spaces. This study will further benefit librarians and the university administrators by helping them to better understand the postgraduate students space needs, as well as the challenges being encountered.
Structural change and technical efficiency: a study of Indian pulp and paper industry
Authors: Kathuria Vinish
Published: November 2019

Purpose

The pulp and paper industry has been the focus of government policies ever since independence. This is the only industry where government plays a multi-dimensional role – not only as the regulator but also as the supplier of raw material and as the buyer. Despite the government's omnipotent role, there is evidence that industry is not very competitive, as it has very high energy and water intensity and poor productivity. A potent factor identified in the literature for the underperformance of the industry or for that matter any economy is the kind of technology used by the firms in the sector. This paper aims to look into the role of government policy in affecting the growth of the industry and what role embodied technology has played in influencing the efficiency of firms in Indian pulp and paper industry.

Design/methodology/approach

For the first question, the study uses 66 years of production data of the industry from 1951 to 2016 and tests for the structural break. For the second question, the study uses cross-section plant-level data for the year 2011-2012 of 160 paper manufacturing units to first estimate the stochastic production frontier (stochastic frontier analysis [SFA]) and then uses the output of SFA to find an association between embodied technology gap (TG) and technical efficiency. A methodological problem in earlier literature is the use of the productivity gap as a proxy for embodied TG. The present study uses technical parameters of papermaking – machine deckle and operating speed – to construct an index of TG.

Findings

The results show a structural break in the production trend occurring in 1999 with the delicensing in July 1997 as the possible cause. The SFA results show that the average technical inefficiency (TE) of the firms in the sector is 74 per cent with half of the firms having TE higher than 76 per cent. The study, however, does not find any impact of embodied TG on technical efficiency; rather it is the age, size, ownership and location that have an impact on it.

Originality/value

This is an original research, as the author has not come across any study in Indian context or elsewhere using technical parameters to construct TG variable.
One Belt One Road: will it increase the gravity between China and Eurasia
Authors: Rahman Nida , Rahman Mohd Nayyer
Published: November 2019

Purpose

Globalisation has remained a subjective term as the magnitude unfolded. Every new decade witnesses new opportunities for global integration of the economies. One among such initiatives, it is argued, is the One Belt One Road initiative of the People’s Republic of China. It is assumed to be beneficial for the world and at least for the region, if not to say more. The world has witnessed efforts and trends of protectionism as well, but China comes up with new vigour. One Belt One Road has entered into consistent talks and deliberations at the world level. It is therefore imperative to identify the emerging linkages between the participant countries in One Belt One Road. This study aims to take up the task of enquiring about the effect of One Belt One Road on the gravity between China and the nations of Eurasia. This study looks for the realisation of the expected economic ties and internationalisation emerging from One Belt One Road and the evidence for the same. This will be identified in the present study. The paper also attempts to theorise a model for One Belt One Road.

Design/methodology/approach

This study takes up the task of enquiring about the effect of One Belt One Road on the gravity between China and the nations of Eurasia. The hypothesised economic ties and internationalisation will be a reality or not. And what are the evidences for the same. This will be identified in the proposed study. An attempt to theorise the model for One Belt One Road is also taken.

Findings

It is perceived that the mega project would fill the wedge between China and Eurasia and convergence will follow with the start of the One Belt One Road.

Originality/value

The emergence of China in the global world order as the initiator of mega deals and projects and its dominion in every realm of economic activity is a topic of scrutiny for the entire world. In this context, the One Belt One Road initiative offers huge potential for exploration. As the project is in its early stages of planning and execution, its prospects of tying entire Europe and Russia with China through two of the revived ancient routes are essential to the entire world.
Can employees perform well if they fear for their lives? Yes – if they have a passion for work
Authors: Haq Inam Ul , De Clercq Dirk , Azeem Muhammad Umer
Published: November 2019

Purpose

With a basis in conservation of resources theory, the purpose of this paper is to investigate the mediating role of championing behaviour in the relationship between employees’ fear of terror and their job performance, as well as the buffering role of their passion for work, as a personal resource, in this process.

Design/methodology/approach

The tests of the hypotheses rely on three-wave, time-lagged data collected from employees and their supervisors in Pakistan.

Findings

An important reason that concerns about terrorist attacks diminish performance is that employees refrain from championing their own entrepreneurial ideas. This mediating role of idea championing is less salient, however, to the extent that employees feel a strong passion for their work.

Practical implications

For human resource managers, this study pinpoints a key mechanism – a reluctance to mobilize active support for entrepreneurial ideas – by which fears about terrorism attacks can spill over into the workplace and undermine employees’ ability to meet their performance requirements. It also reveals how this mechanism can be better contained by the presence of adequate personal resources.

Originality/value

This study adds to burgeoning research on the interplay between terrorism and organizational life by specifying how and when employees’ ruminations about terrorism threats might escalate into diminished performance outcomes at work.
Investment funds and underpricing of shares
Authors: Castilho Hitalo Alberto de Souza Faria , Resende Matheus Souza De , Montoro Eduardo Ramos de Oliveira Franco , Shotoko Vinicius Akio De Almeida , Jucá Michele Nascimento , Junior Eli Hadad
Published: November 2019

Purpose

The purpose of this paper is to assess whether greater participation of venture capital/private equity (VC/PE) funds in the companies’ capital structure at the moment of initial public offering (IPO) contributes to the reduction in the underpricing of their shares.

Design/methodology/approach

Descriptive statistics, correlation analysis, mean difference test and cross-sectional regression were used. The final sample consisted of 89 companies making IPO in Brasil Bolsa Balcão between 2007 and 2017.

Findings

The participation of VC/PE funds was shown to mitigate the effect of information asymmetry on managers and shareholders, thus reducing the underpricing of companies at the moment of IPO (H1). However, the expectation that a greater participation of these funds promotes further reduction in a potential underpricing (H2) was not confirmed.

Research limitations/implications

One can highlight the small amount of IPOs during the sampling period due to the occurrence of international and national economic crises, as well as the difficulty in obtaining information on the participation of VC/PE funds in the companies’ capital structure.

Practical implications

It was observed that information asymmetry had a mitigating effect from the presence of these funds in the companies, which can improve the pricing of their shares, decrease the costs and make volume captions viable for investments, in addition to giving credibility to the market information effectiveness.

Originality/value

This study differs from others in that it assesses not only the influence of VC/PE funds on the reduction of the underpricing of IPO shares, but also the participation of these funds in the capital of these companies.
The relationship between TQM practices and organisational innovation outcomes
Authors: Abu Salim Taghreed , Sundarakani Balan , Lasrado Flevy
Published: November 2019

Purpose

The purpose of this paper is to study the role of slack (both moderating and mediating) to stimulate the relationship between total quality management (TQM) factors and innovation outcomes relative to gaining competitive industry advantages.

Design/methodology/approach

The research methodology includes a multi-item scale questionnaire completed in three waves between 2016 and 2017, and later analysed in 2018. A final response rate of 29.5 per cent was obtained, representing 190 organisations from both manufacturing and service industries in the United Arab Emirates (UAE). Partial least squares structural equation modelling was used to test the multi-collinearity, moderation and mediation analysis.

Findings

Analysis confirmed that factors such as continuous improvement (CI), human resource management (HRM) and information measurement (IM) were positively linked to innovation. However, when slack was introduced as a moderator, innovation outcomes were stimulated through HRM and IM. The results indicate that slack acts as a full mediator for management leadership but only partially mediates supplier quality, IM, CI, HRM and process management.

Research limitations/implications

In terms of geographical coverage, research was limited to the UAE. Organisations striving for excellence through innovation may benefit from the outcomes, as they help in understanding the relationship between TQM and innovation moderated and/or mediated by slack. This could also lead businesses to develop new strategies that harmonise TQM policies with “rationale” slack policies, thus, promoting innovation.

Originality/value

This study is the first to examine the use of slack to stimulate the relationship between TQM factors and innovation outcomes. Using slack as a mediator can help in understanding when TQM might influence innovation, while slack as a moderator could invert the relationship between the two.
Effects of stress reduction on geomechanical and acoustic relationship of overconsolidated sands
Authors: Narongsirikul Sirikarn , Mondol Nazmul Haque , Jahren Jens
Published: November 2019

Relationship between different geomechanical and acoustic properties measured from seven laboratory‐tested unconsolidated natural sands with different mineralogical compositions and textures were presented. The samples were compacted in the uniaxial strain configuration from 0.5 to 30 MPa effective stress. Each sand sample was subjected to three loading–unloading cycles to study the influence of stress reduction. Geomechanical, elastic and acoustic parameters are different between normal compaction and overconsolidation (unloaded and reloaded). Stress path (K0) data differ between normal consolidated and overconsolidated sediments. TheK0value of approximately 0.5 is founded for most of the normal consolidated sands, but varies during unloading depending on mineral compositions and textural differences. TheK0and overconsolidation ratio relation can be further simplified and can be influenced by the material compositions.K0can be used to estimate horizontal stress for drilling applications. The relationship between acoustic velocity and geomechanical is also found to be different between loading and unloading conditions. The static moduli of the overconsolidated sands are much higher than normal consolidated sands as the deformation is small (small strain). The correlation between dynamic and static elastic moduli is stronger for an overconsolidation stage than for a normal consolidation stage. The results of this study can contribute to geomechanical and acoustic dataset which can be applied for many seismic‐geomechanics applications in shallow sands where mechanical compaction is the dominant mechanism.
Autophagy inhibits the mesenchymal stem cell aging induced by D‐galactose through ROS/JNK/p38 signalling
Authors: Zhang Dayong , Chen Yifan , Xu Xianbin , Xiang Haoyi , Shi Yizhan , Gao Ying , Wang Xiaowen , Jiang Xuefan , Li Na , Pan Jianping
Published: November 2019

Autophagy and cellular senescence are two critical responses of mammalian cells to stress and may have a direct relationship given that they respond to the same set of stimuli, including oxidative stress, DNA damage, and telomere shortening. Mesenchymal stem cells (MSCs) have emerged as reliable cell sources for stem cell transplantation and are currently being tested in numerous clinical trials. However, the effects of autophagy on MSC senescence and corresponding mechanisms have not been fully evaluated. Several studies demonstrated that autophagy level increases in aging MSCs and the downregulation of autophagy can delay MSC senescence, which is inconsistent with most studies that showed autophagy could play a protective role in stem cell senescence. To further study the relationship between autophagy and MSC senescence and explore the effects and mechanisms of premodulated autophagy on MSC senescence, we induced the up‐ or down‐regulation of autophagy by using rapamycin (Rapa) or 3‐methyladenine, respectively, before MSC senescence induced by D‐galactose (D‐gal). Results showed that pretreatment with Rapa for 24 hours remarkably alleviated MSC aging induced by D‐gal and inhibited ROS generation. p‐Jun N‐terminal kinases (JNK) and p‐38 expression were also clearly decreased in the Rapa group. Moreover, the protective effect of Rapa on MSC senescence can be abolished by enhancing the level of ROS, and p38 inhibitor can reverse the promoting effect of H2O2on MSC senescence. In summary, the present study indicates that autophagy plays a protective role in MSC senescence induced by D‐gal, and ROS/JNK/p38 signalling plays an important mediating role in autophagy‐delaying MSC senescence.