bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking plant growth promoting arbuscular mycorrhizal colonization with bacterial plant sulfur supply
Authors: Gahan Jacinta , Schmalenberger Achim 
Published: June 2021

AbstractSulfur (S) exists in organically bound complexes (∼95%), predominantly as sulfonates, and are not directly plant available. Specific soil bacteria can mobilise sulfonates but very little is known about these bacteria in the hyphosphere. Since mycorrhizal fungi support growth of the majority of land plants, hyphosphere desulfonating bacteria may be of substantial benefit to the plant host. This study analysed the effect of AM inoculation withRhizophagus irregularis(formerG. intraradices,Glomus) and a mix of six AM species (Mixed) on PGP, microbial communities and sulfonate mobilising bacteria withL. perenne,Agrostis stoloniferaandPlantago lanceolataas plant hosts in bi-compartmental microcosms andA. stoloniferain PGP pot experiments. AM inoculation significantly increased plant growth, percentage root colonisation and the quantity of cultivable desulfonating bacteria in the hyphosphere over pre-inoculated soil for all plants. Community analysis via PCR-DGGE revealed significantly different bacterial and fungal communities post inoculation. Analysis of the sulfonate mobilisingasfAgene revealed a significantly altered community and novel bacterial isolates with this important functional ability post-inoculation. The results demonstrate that AM inoculation increased plant biomass yield, AM root colonisation and altered bacterial and fungal community dynamics in the hyphosphere. AM inoculated microcosms had an increased abundance of desulfonating bacteria that may be beneficial for plant-S supply.Research highlightsInoculation with AM fungi was shown to promote plant growth and harbour larger populations of sulfonate mobilising bacteria.Post-inoculation hyphospheric bacterial and saprotrophic fungal communities were shown to differ significantly in composition and abundance.Analysis of sulfonate mobilising bacteria revealed novel presumptive species in possession of theasfAgene associated with AM hyphae.AM inoculation was shown to significantly impact theasfApositive bacterial community composition.
Extracting Phylogenetic Information of Human Mitochondrial DNA by Linear Autoencoder
Authors: Shimazaki Takuto , Nishimoto Kazuki , Niioka Hirohiko , Miyake Jun 
Published: June 2021

AbstractWe used a linear autoencoder (LAE) and its learning dynamics to analyze the high-order structure of human mitochondrial DNA (mtDNA). A total of 360 complete human mtDNA sequences were collected from the MITOMAP database and transformed into 1024-dimensional vectors of pentanucleotide frequencies. We compressed those into a three-dimensional (3D) coordinates by an LAE at each step of training by gradient descent with respect to the quadratic error function. Along the time axis of training epochs, the compressed 3D coordinates were gradually clustered and separated in accordance with the order of the genetic distance in the phylogenetic tree of human mtDNA haplogroups. This suggests that there is an association between the learning dynamics of LAE and the high-dimensional structure of human mtDNA sequences, similar to that of phylogenetic analysis and evolutionary pathways: the five clusters eventually contained only a single haplogroup of L0, M, N, R, and U, while the L3 cluster contained a small number of M members and The packing was comparable to that realized in learning dynamics similar to genetic classification and evolutionary pathways by LAE in principal component analysis (PCA), but somewhat denser than PCA.
PrISM: Precision for Integrative Structural Models
Authors: Ullanat Varun , Kasukurthi Nikhil , Viswanath Shruthi 
Published: June 2021

AbstractMotivationA single precision value is currently reported for an integrative model. However, precision may vary for different regions of an integrative model owing to varying amounts of input information.ResultsWe develop PrISM (Precision for Integrative Structural Models), to efficiently identify high and low-precision regions for integrative models.AvailabilityPrISM is written in Python and available under the GNU General Public License v3.0 at https://github.com/isblab/prism; benchmark data used in this paper is available at doi:10.5281/zenodo.6241200.Contactshruthiv@ncbs.res.inSupplementary informationSupplementary data are available at Bioinformatics online.
Climatic niche conservatism shapes the ecological assembly of Hawaiian arthropod communities
Authors: Lim Jun Ying , Patiño Jairo , Noriyuki Suzuki , Simmari Luis Cayetano , Gillespie Rosemary G. , Krehenwinkel Henrik 
Published: June 2021

AbstractSpatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai‘i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.
Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model
Authors: Thygesen Christian B. , Al-Sibahi Ahmad Salim , Steenmanns Christian S. , Moreta Lys S. , Sørensen Anders B. , Hamelryck Thomas 
Published: June 2021

AbstractFragment libraries are often used in protein structure prediction, simulation and design as a means to significantly reduce the vast conformational search space. Current state-of-the-art methods for fragment library generation do not properly account for aleatory and epistemic uncertainty, respectively due to the dynamic nature of proteins and experimental errors in protein structures. Additionally, they typically rely on information that is not generally or readily available, such as homologous sequences, related protein structures and other complementary information. To address these issues, we developed BIFROST, a novel take on the fragment library problem based on a Deep Markov Model architecture combined with directional statistics for angular degrees of freedom, implemented in the deep probabilistic programming language Pyro. BIFROST is a probabilistic, generative model of the protein backbone dihedral angles conditioned solely on the amino acid sequence. BIFROST generates fragment libraries with a quality on par with current state-of-the-art methods at a fraction of the run-time, while requiring considerably less information and allowing efficient evaluation of probabilities.
Similar neuronal imprint and absence of cross-seeded partner fibrils in α-synuclein aggregates from MSA and Parkinson’s disease brains
Authors: Laferrière Florent , Claverol Stéphane , Bezard Erwan , De Giorgi Francesca , Ichas François 
Published: June 2021

ABSTRACTAggregated alpha-synuclein (α-syn) is a principal constituent of Lewy bodies (LBs) and glial cytoplasmic inclusions (GCIs) observed respectively inside neurons in Parkinson’s disease (PD) and oligodendrocytes in multiple system atrophy (MSA). Yet, the cellular origin, the pathophysiological role, and the mechanism of formation of these inclusions bodies (IBs) remain to be elucidated. It has recently been proposed that α-syn IBs eventually cause the demise of the host cell by virtue of the cumulative sequestration of partner proteins and organelles. In particular, the hypothesis of a local cross-seeding of other fibrillization-prone proteins like tau or TDP-43 has also been put forward. We submitted sarkosyl-insoluble extracts of post-mortem brain tissue from PD, MSA and control subjects to a comparative proteomic analysis to address these points. Our studies indicate that: i) α-syn is by far the most enriched protein in PD and MSA extracts compared to controls; ii) PD and MSA extracts share a striking overlap of their sarkosyl-insoluble proteomes, consisting of a vast majority of mitochondrial and neuronal synaptic proteins, and (iii) other fibrillization-prone protein candidates possibly cross-seeded by α-syn are neither found in PD nor MSA extracts. Thus, our results (i) support the idea that pre-assembled building blocks originating in neurons serve to the formation of GCIs in MSA, (ii) show no sign of amyloid cross-seeding in either synucleinopathy, and (iii) point to the sequestration of mitochondria and of neuronal synaptic components in both LBs and GCIs.
Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade
Authors: Yagi-Utsumi Maho , Aoki Kazuhiro , Watanabe Hiroki , Song Chihong , Nishimura Seiji , Satoh Tadashi , Yanaka Saeko , Ganser Christian , Tanaka Sae , Schnapka Vincent , Goh Ean Wai , Furutani Yuji , Murata Kazuyoshi , Uchihashi Takayuki , Arakawa Kazuharu , Kato Koichi 
Published: June 2021

AbstractAnhydrobiosis is one of the most extensively studied forms of cryptobiosis that is induced in certain organisms as a response to desiccation. Anhydrobiotic species has been hypothesized to produce substances that can protect their biological components and/or cell membranes without water. In extremotolerant tardigrades, highly hydrophilic and heat-soluble protein families, cytosolic abundant heat-soluble (CAHS) proteins, have been identified, which are postulated to be integral parts of the tardigrades’ response to desiccation. However, the molecular mechanisms underlying these protein functions remain to be fully elucidated. In this study, we perfomed in vitro and in vivo characterizations of the self-assembling property of CAHS1 protein, a major isoform of CAHS proteins from Ramazzottius varieornatus, using a series of spectroscopic and microscopic techniques. Our in vitro observations showed that CAHS1 proteins homo-oligomerized via the C-terminal α-helical region and formed a hydrogel as their concentration increased, and that these molecular assembling processes were reversible. Furthermore, our in vivo observations demonstrated that the overexpressed CAHS1 proteins formed condensates under desiccation-mimicking conditions. These data strongly suggested that, upon drying, the CAHS1 proteins form oligomers and eventually underwent sol-gel transition in tardigrade cytosols. Thus, it is proposed that the CAHS1 proteins form the cytosolic fibrous condensates, which presumably have variable mechanisms for the desiccation tolerance of tardigrades. These findings provide insights into the protective mechanisms involved in the anhydrobiosis of tardigrades.
Human DC3 Antigen Presenting Dendritic Cells from Induced Pluripotent Stem Cells
Authors: Satoh Taiki , Toledo Marcelo A. S. , Boehnke Janik , Olschok Kathrin , Flosdorf Niclas , Götz Katrin , Küstermann Caroline , Sontag Stephanie , Seré Kristin , Koschmieder Steffen , Brümmendorf Tim H. , Chatain Nicolas , Tagawa Yoh-ichi , Zenke Martin 
Published: June 2021

AbstractDendritic cells (DC) are professional antigen-presenting cells that develop from hematopoietic stem cells. Different DC subsets exist based on ontogeny, location and function, including the recently identified proinflammatory DC3 subset. DC3 have the prominent activity to polarize CD8+ T cells into CD8+ CD103+ tissue resident T cells. Here we describe human DC3 differentiated from induced pluripotent stem cells (iPS cells). iPS cell-derived DC3 have the gene expression and surface marker make-up of blood DC3 and polarize CD8+ T cells into CD8+ CD103+ tissue-resident memory T cells in vitro. To test the impact of malignant JAK2 V617F mutation on DC3, we differentiated patient-specific iPS cells with JAK2 V617Fhet and JAK2 V617Fhom mutations into JAK2 V617Fhet and JAK2 V617Fhom DC3. The JAK2 V617F mutation enhanced DC3 production and caused a bias towards erythrocytes and megakaryocytes. The patient-specific iPS cell-derived DC3 are expected to allow studying DC3 in human diseases and developing novel therapeutics.Graphical Abstract
Dystonia-specific mutations in THAP1 alter transcription of genes associated with neurodevelopment and myelin
Authors: Domingo Aloysius , Yadav Rachita , Shah Shivangi , Hendriks William T. , Erdin Serkan , Gao Dadi , O’Keefe Kathryn , Currall Benjamin , Gusella James F. , Sharma Nutan , Ozelius Laurie J. , Ehrlich Michelle E. , Talkowski Michael E. , Cristopher Bragg D. 
Published: June 2021

ABSTRACTDystonia is a neurologic disorder associated with an increasingly large number of variants in many genes, resulting in characteristic disturbances in volitional movement. Dissecting the relationships between these mutations and their functional outcomes is a critical step in understanding the key pathways that drive dystonia pathogenesis. Here we established a pipeline for characterizing an allelic series of dystonia-specific mutations in isogenic induced pluripotent stem cells (iPSCs). We used this strategy to investigate the molecular consequences of variation in THAP1, which encodes a transcription factor that has been linked to neural differentiation. Multiple pathogenic mutations that have been associated with dystonia cluster within distinct THAP1 functional domains and are predicted to alter its DNA binding properties and/or protein interactions differently, yet the relative impact of these varied changes on molecular signatures and neural deficits is unclear. To determine the effects of these mutations on THAP1 transcriptional activity, we engineered an allelic series of eight mutations in a common iPSC background and differentiated these lines into a panel of near-isogenic neural stem cells (n = 94 lines). Transcriptome profiling of these neural derivatives followed by joint analysis of the most robust individual signatures across mutations identified a convergent pattern of dysregulated genes functionally related to neurodevelopment, lysosomal lipid metabolism, and myelin. Based on these observations, we examined mice bearing Thap1-disruptive alleles and detected significant changes in myelin gene expression and reduction of myelin structural integrity relative to tissue from control mice. These results suggest that deficits in neurodevelopment and myelination are common consequences of dystonia-associated THAP1 mutations and highlight the potential role of neuron-glial interactions in the pathogenesis of dystonia.
Hyperactive WNT/CTNNB1 signaling induces a competing cell proliferation and epidermal differentiation response in the mouse mammary epithelium
Authors: Mourao Larissa , Zeeman Amber L. , Wiese Katrin E. , Bongaarts Anika , Oudejans Lieve L. , Martinez Isabel Mora , van de Grift Yorick B.C. , Jonkers Jos , van Amerongen Renée 
Published: June 2021

ABSTRACTIn the past forty years, the WNT/CTNNB1 signaling pathway has emerged as a key player in mammary gland development and homeostasis. While also evidently involved in breast cancer, much unclarity continues to surround its precise role in mammary tumor formation and progression. This is largely due to the fact that the specific and direct effects of hyperactive WNT/CTNNB1 signaling on the mammary epithelium remain unknown. Here we use a primary mouse mammary organoid culture system to close this fundamental knowledge gap. We show that hyperactive WNT/CTNNB1 signaling induces competing cell proliferation and differentiation responses. While proliferation is dominant at lower levels of WNT/CTNNB1 signaling activity, higher levels cause reprogramming towards an epidermal cell fate. We show that this involves de novo activation of the epidermal differentiation cluster (EDC) locus and we identify master regulatory transcription factors that likely control the process. This is the first time that the molecular and cellular dose-response effects of WNT/CTNNB1 signaling in the mammary epithelium have been dissected in such detail. Our analyses reveal that the mammary epithelium is exquisitely sensitive to small changes in WNT/CTNNB1 signaling and offer a mechanistic explanation for the squamous differentiation that is observed in some WNT/CTNNB1 driven tumors.
On the α-connections and the α-conformal equivalence on statistical manifolds
Authors: Addad Khadidja , Ouakkas Seddik 
Published: June 2021

PurposeIn this paper, we give some properties of the α-connections on statistical manifolds and we study the α-conformal equivalence where we develop an expression of curvature R¯ for ∇¯ in relation to those for ∇ and ∇^.Design/methodology/approachIn the first section of this paper, we prove some results about the α-connections of a statistical manifold where we give some properties of the difference tensor K and we determine a relation between the curvature tensors; this relation is a generalization of the results obtained in [1]. In the second section, we introduce the notion of α-conformal equivalence of statistical manifolds treated in [1, 3], and we construct some examples.FindingsWe give some properties of the difference tensor K and we determine a relation between the curvature tensors; this relation is a generalization of the results obtained in [1]. In the second section, we introduce the notion of α-conformal equivalence of statistical manifolds, we give the relations between curvature tensors and we construct some examples.Originality/valueWe give some properties of the difference tensor K and we determine a relation between the curvature tensors; this relation is a generalization of the results obtained in [1]. In the second section, we introduce the notion of α-conformal equivalence of statistical manifolds, we give the relations between curvature tensors and we construct some examples.
Forecasting uncertainty: Cindy March at Veracity
Authors: Erath Alexandra 
Published: June 2021

Study level/applicability
This case is appropriate for use in undergraduate and MBA courses.

Subject area
This case can be used in courses in business ethics, leading teams and organizations or business strategy. The focus of the case aligns well with discussions of managing up, navigating changes in top leadership and conflicts between executive vision and future company growth. Instructors that choose to emphasize the ethical approach could assign this case to explore tradeoffs between loyalty to current and future bosses.

Case overview
Associate Director of Forecasting Cindy March faces a multi-faceted dilemma as biotech firm Veracity’s acquisition date by pharmaceutical giant Makhola approaches. After a new competitor enters the market, March expects Veracity drug Sangren’s future revenue to drop to $600m in 2019, but the outgoing Veracity CEO refuses to accept a forecast of less than $700m. March suspects that the CEO is intent on handing over a financially successful company and is overly optimistic about Sangren’s ability to maintain market share. In two weeks, March is due to present a 2019 Sangren forecast to incoming Makhola leadership, who she anticipates becoming her direct boss after the acquisition. Should March present the inflated forecasts and accept the poor reflection on her professional abilities or should she refuse to present numbers she does not believe in?

Expected learning outcomes
By analyzing and discussing the case, students should be able to:Evaluate the potential business and ethical conflicts arising from decision-making based on both data and intuition. Synthesize an appropriate strategy for navigating tradeoffs between current and future leadership.Analyze the gender dynamics of male-dominated executive leadership structures and strategies for female employees to combat gender biases.

Supplementary materials
The Behavioral Science Guys, 2015. One Simple Skill to Curb Unconscious Gender Bias. YouTube. https://www.youtube.com/watch?v=SEHi4yauhu8&ab_channel=VitalSmartsVideoTeaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 6: Human resources.
The smart, sustainable neighborhood
Authors: Myers Robert 
Published: June 2021

Study level/applicability
Applicable to both undergraduate and graduate courses in managing technology or sustainability.

Subject area
Technology strategy.
Business Model evaluation.
Sustainable technologies.

Case overview
In this case study, gas and electric utility holding company Southern Company has embarked on an ambitious experiment to learn more about energy usage at a household level, as well as community scale microgrids. Every minute, 62 homes in Reynolds Landing upload appliance and electrical outlet level data to Southern Company. How can Southern Company use this vast amount of data to promote energy efficiency? Are microgrids a key to creating a more sustainable and resilient energy future? At a higher level, how can microgrids impact or change traditional power generation business models like those used by Southern Company?

Expected learning outcomes
1. To explore why companies develop technologies that are counter to current business models.
2. To understand how new technology can lead to new business models for existing businesses.
3. To understand the drivers of company led R&D.
4. To discuss “technology push” applications. Where technology is developed and then a market or markets are sought.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Social implications
Two parts here. The first is looking at sustainable energy solutions such as solar farms and micro-grids. The second is this case challenges students to ask how this research helps the 45% of consumers making less than $40,000/yr.

Subject code
CSS 11: Strategy.