bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network
Authors: Li Wei , Yang Shuai , Xu Peng , Zhang Dapeng , Tong Ying , Chen Lu , Jia Ben , Li Ang , Ru Daoping , Zhang Baolong , Liu Mengxing , Lian Cheng , Chen Cancan , Fu Weihui , Yuan Songhua , Ren Xiaoguang , Liang Ying , Yang Zhicong , Li Wenxuan , Wang Shaoxuan , Zhang Xiaoyan , Lu Hongzhou , Xu Jianqing , Wang Hailing , Yu Wenqiang
Published: November 2020

The COVID-19 pandemic is a widespread and deadly public health crisis. The pathogen SARS-CoV-2 replicates in the lower respiratory tract and causes fatal pneumonia. Although tremendous efforts have been put into investigating the pathogeny of SARS-CoV-2, the underlying mechanism of how SARS-CoV-2 interacts with its host is largely unexplored. Here, by comparing the genomic sequences of SARS-CoV-2 and human, we identified five fully conserved elements in SARS-CoV-2 genome, which were termed as “human identical sequences (HIS)”. HIS are also recognized in both SARS-CoV and MERS-CoV genome. Meanwhile, HIS-SARS-CoV-2 are highly conserved in the primate. Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, andhyaluronan synthase 2(HAS2), which further increases hyaluronan formation. Noteworthily, hyaluronan level in plasma of COVID-19 patients is tightly correlated with severity and high risk for acute respiratory distress syndrome (ARDS) and may act as a predictor for the progression of COVID-19. HIS antagomirs, which downregulate hyaluronan level effectively, and 4-Methylumbelliferone (MU), an inhibitor of hyaluronan synthesis, are potential drugs to relieve the ARDS related ground-glass pattern in lung for COVID-19 treatment. Our results revealed that unprecedented HIS elements of SARS-CoV-2 contribute to the cytokine storm and ARDS in COVID-19 patients. Thus, blocking HIS-involved activating processes or hyaluronan synthesis directly by 4-MU may be effective strategies to alleviate COVID-19 progression.
The fluid dynamics of collective vortex structures of plant-animal worms
Authors: Fortune George T. , Worley Alan , Sendova-Franks Ana B. , Franks Nigel R. , Leptos Kyriacos C. , Lauga Eric , Goldstein Raymond E.
Published: November 2020

Circular milling, a stunning manifestation of collective motion, is found across the natural world, from fish shoals to army ants. It has been observed recently that the plant-animal wormSymsagittifera roscoffensisexhibits circular milling behaviour, both in shallow pools at the beach and in Petri dishes in the laboratory. Here we investigate this phenomenon, through experiment and theory, from a fluid dynamical viewpoint, focusing on the effect that an established circular mill has on the surrounding fluid. Unlike systems such as confined bacterial suspensions and collections of molecular motors and filaments that exhibit spontaneous circulatory behaviour, and which are modelled as force dipoles, the front-back symmetry of individual worms precludes a stresslet contribution. Instead, singularities such as source dipoles and Stokes quadrupoles are expected to dominate. A series of models is analyzed to understand the contributions of these singularities to the azimuthal flow fields generated by a mill, in light of the particular boundary conditions that hold for flow in a Petri dish. A model that treats a circular mill as a rigid rotating disc that generates a Stokes flow is shown to capture basic experimental results well, and gives insights into the emergence and stability of multiple mill systems.
Extending the integrate-and-fire model to account for metabolic dependencies
Authors: Jaras Ismael , Harada Taiki , Orchard Marcos E. , Maldonado Pedro E. , Vergara Rodrigo C.
Published: November 2020

It is widely accepted that the brain, like any other physical system, is subjected to physical constraints restricting its operation. The brain’s metabolic demands are particularly critical for proper neuronal function, but the impact of these constraints is still poorly understood. Detailed single-neuron models are recently integrating metabolic constraints, but the computational resources these models need, make it difficult to explore the dynamics of extended neural networks imposed by such constraints. Thus, there is a need for a simple-enough neuron model that incorporates metabolic activity and allows us to explore neural network dynamics. This work introduces an energy-dependent leaky integrate-and-fire (LIF) neuronal model extension to account for the effects of metabolic constraints on the single-neuron behavior (EDLIF). This simple energy-dependent model shows better performance predicting real spikes trains -inspike coincidencemeasure sense-than the classical leaky integrate-and-fire model. It can describe the relationship between the average firing rate and the ATP cost, and replicate a neuron’s behavior under a clinical setting such as amyotrophic lateral sclerosis. The simplicity of the energy-dependent model presented here, makes it computationally efficient and thus, suitable to study the dynamics of large neural networks.

Author summary

Any physical system or biological tissue is restricted by physical constraints bounding their behavior, and the brain is not free from these constraints. Energetic disorders in the brain have been linked to several neurodegenerative diseases, highlighting the relevance of maintaining a critical balance between energy production and consumption in neurons. These observations motivate the development of mathematical tools that can help to understand the dependence of the brain’s behavior in metabolism. One of the essential building blocks to achieve this task is the mathematical representation of neurons through models, allowing computational simulations of single-neurons and neural networks. Here we construct a simple and computational cheap energy-dependent neuron model that allows the study of neuron’s behavior under an energetic perspective. The introduced neuron model is contrasted with one of the widest-used neuron models and shows better prediction capabilities when real neuron recordings are used. Our model is suitable for replicating neuron’s behavior under a specific neurodegenerative disease, which cannot be achieved by the abovementioned popular model. Our simple model is promising because it allows the simulation and study of neuronal networks under a metabolic-dependent perspective.
Varying richness need not imply non-random species co-occurrence: implications for specifying null models
Authors: Fayle Tom M.
Published: November 2020

Background

Non-random species co-occurrence is of fundamental interest to ecologists. One approach to analysing non-random patterns is null modelling. This involves calculation of a metric for the observed dataset, and comparison to a distribution obtained by repeatedly randomising the data. Choice of randomisation algorithm, specifically whether null model species richness is fixed at that of the observed dataset, is likely to affect model results. This is particularly important in cases when there is high variation in species richness between sampling units in the observed data.

Methods

Here I demonstrate the effects of accounting for variation in species richness. I use the C-score, a metric measuring species segregation as “checkerboard units”, applied to 289 datasets. First, I run null models in which sites are equally likely to be occupied (fixed-equiprobable algorithm). I do this both for the original datasets, and for the same datasets where occurrences are randomised with the species richness distribution fixed (pre-randomised datasets). Second, I run null models that fix site species richness to that observed (fixed-fixed algorithm).

Results

For real datasets, using the fixed-equiprobable algorithm (sites are equally likely to be colonised), C-score standardised effect size (SES) was positively related to variability in species richness between sites within a dataset. This effect was also found for pre-randomised datasets, indicating that variability in species richness can be exclusively responsible for detection of non-random species co-occurrence. When using the fixed-fixed algorithm (richness is constrained to that of real sites), there was no relationship between SES and variability in species richness. There was also a reverse in the effect direction, with 94% of significant tests indicating a lower C-score than expected for the fixed-equiprobable algorithm, but 98% of significant tests indicating ahigherC-score than expected for the fixed-fixed algorithm.

Discussion

I speculate that when variation in species richness is high, fewer checkerboard units are possible, regardless of segregation between species. Therefore, use of fixed-equiprobable algorithms in situations where real species richness is highly variable between sites within a dataset will yield significant results, even if species co-occur randomly within the constraints of the species richness distribution. Consequently, use of such tests makes the a priori assumption that high within-dataset variation in species richness indicates non-random species co-occurrence. I recommend using algorithms that explicitly take into account species richness distributions when one wants to eliminate the effect of richness variation in terms of producing significant but spurious positive co-occurrence results. Alternatively, non-null mechanistic models can be created, in which hypothesised species assembly processes must be explicitly stated and tested.
The oncogenic E3 ligase TRIP12 suppresses epithelial-mesenchymal transition (EMT) and metastasis-related processes through ZEB1/2
Authors: Lee Kwok Kin , Rajagopalan Deepa , Bhatia Shreshtha Sailesh , Chng Wee Joo , Jha Sudhakar
Published: November 2020

Thyroid hormone receptor interactor 12 (TRIP12) is an E3 ligase most notably involved in the proteolytic degradation of the tumor suppressor p14ARF. Through this process, it is proposed that TRIP12 plays an oncogenic role in tumor initiation and growth. However, its role in other cancer processes such as metastasis is unknown. In this study, using publicly available cancer patient datasets, we found TRIP12 to be associated with distant metastasis-free survival in breast cancer, suggesting a contrary cancer process inhibitory role in metastasis. Following TRIP12 depletion in the MCF10A breast epithelial cell model, an epithelial-mesenchymal transition (EMT) shift occurred with concomitant changes in EMT cell adhesion markers identified through RNA-seq. In line with EMT changes, TRIP12-depleted cells lose polarity and dislodge from bulk cells at a higher frequency. Furthermore, ectopic TRIP12 expression sensitized cells to anoikis, a major barrier against metastasis. Mechanistically, TRIP12 suppresses EMT through inhibiting ZEB1/2 gene expression and ZEB1/2 depletion rescues EMT markers and cellular behavior. Overall, our study delineates TRIP12’s role in inhibition of EMT and metastasis-related processes, and implies a suppression role in breast cancer metastasis.
Deep brain stimulation modulates the dynamics of resting-state networks in patients with Parkinson’s Disease
Authors: Gomes Maria T. , Fernandes Henrique M. , Cabral Joana
Published: November 2020

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is increasingly used for the treatment of Parkinson’s Disease (PD), but despite its success, the neural mechanisms behind this surgical procedure remain partly unclear. As one working hypothesis, it was proposed that DBS works by restoring the balance of the brain’s resting-state networks (RSNs), which is reported to be disrupted in people with PD. Hence, to elucidate the effects that STN-DBS induces on disseminated networks, we analyzed an fMRI dataset of 20 PD patients at rest under DBS ON and OFF conditions. Moving beyond ‘static’ functional connectivity studies, we employ a recently developed fMRI analysis tool, the Leading Eigenvector Dynamic Analysis (LEiDA), to characterize the recurrence of brain-wide phase-locking patterns overlapping with known RSNs. Here, STN-DBS seems to increase the Default Mode Network (DMN) occurrence in individuals with PD. Since the DMN is usually disturbed in PD patients presenting deficits in cognition, our observation might be suggestive that STN-DBS contributes to a normalization of the PD-induced cognitive impairment.

Moreover, we addressed the effects of DBS lead placement on RSNs balance, considering the overlap between the DBS-induced electric field and 3 STN subsections. We found that the Visual Network (VN) probability of occurrence increased proportionally to the electric field-limbic STN overlap. Our finding might be indicative that stimulation of the limbic STN is related to the stabilization of visual symptoms sometimes presented by PD patients, which are usually accompanied by VN disruption.

Overall, this study offers new insights into the fine-grained temporal dynamics of brain states portraying the effects of STN-DBS in patients with PD, while at the same time trying to pave the way to improved planning strategies for this surgical procedure.
Integrated Analysis of Cell Shape and Movement in Moving Frame
Authors: Heryanto Yusri Dwi , Cheng Chin-Yi , Uchida Yutaka , Mimura Kazushi , Ishii Masaru , Yamada Ryo
Published: November 2020

The cell movement and morphological change are two interrelated cellular processes. The integrated analysis is needed to explore the relationship between them. However, it has been challenging to investigate them as a whole. The cell trajectory can be described by its speed, curvature, and torsion. On the other hand, the 3-Dimensional (3D) cell shape can be studied by using a shape descriptor such as Spherical harmonic (SH) descriptor which is an extension of Fourier transform in 3D space.

To integrate these shape-movement data, we propose a method to use a parallel-transport (PT) moving frame as the 3D-shape coordinate system. This moving frame is purely determined by the velocity vector. On this moving frame, the movement change will influence the coordinate system for shape analysis. By analyzing the change of the SH coefficients over time in the moving frame, we can observe the relationship between shape and movement.

We illustrate the application of our approach using simulational and real datasets in this paper.
Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
Authors: Lee Brian R. , Budzillo Agata , Hadley Kristen , Miller Jeremy A. , Jarsky Tim , Baker Katherine , Hill DiJon , Kim Lisa , Mann Rusty , Ng Lindsay , Oldre Aaron , Rajanbabu Ram , Trinh Jessica , Braun Thomas , Dalley Rachel , Gouwens Nathan W. , Kalmbach Brian E. , Kim Tae Kyung , Smith Kimberly , Soler-Llavina Gilberto J. , Sorensen Staci A. , Tasic Bosiljka , Ting Jonathan T. , Lein Ed S. , Zeng Hongkui , Murphy Gabe J. , Berg Jim
Published: November 2020

The Patch-seq approach is a powerful variation of the standard patch clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at a scale and quality that can be integrated with high-throughput dissociated cell transcriptomic data, we have optimized the technique by identifying and refining key factors that contribute to the efficient collection of high-quality data. To rapidly generate high-quality electrophysiology data, we developed patch clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized a substantial improvement in transcriptomic data quality when the nucleus was extracted following the recording. For morphology success, the importance of maximizing the neuron’s membrane integrity during the extraction of the nucleus was much more critical to success than varying the duration of the electrophysiology recording. We compiled the lab protocol with the analysis and acquisition software athttps://github.com/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate Patch-seq data across diverse mammalian species and that is compatible with recent large-scale publicly available Allen Institute Patch-seq datasets.
Community health worker knowledge, attitudes and practices towards COVID-19: learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique
Authors: Feldman Mitra , Krylova Vera Lacey , Farrow Poppy , Donovan Laura , Zandamela Edson , Rebelo Joaquim , Rodrigues Maria , Bulo Antonio , Ferraz Carlos , Gonzalez Juan Romero , Rodrigues Humberto , Roca-Feltrer Arantxa , Baker Kevin
Published: November 2020

Healthcare workers (HCWs) are at the frontline of the Coronavirus Disease 2019 (COVID-19) pandemic response, yet there is a paucity of literature on their knowledge, attitudes and practices (KAP) in relation to the pandemic. Community Health Workers (CHWs) in Mozambique are known locally as agentes polivalentes elementares (APEs). While technical guidance surrounding COVID-19 is available to support APEs, communicating this information has been challenging due to restrictions on travel, face-to-face group meetings and training, imposed from May to August 2020. A digital health platform, upSCALE, that already supports 1,213 APEs and 299 supervisors across three provinces, is being used to support APEs on effective COVID-19 management by delivering COVID-19 sensitive SMS messages, training modules and a COVID-19 KAP survey.

The KAP survey, conducted from June 2020 to August 2020, consisted of 10 questions. Of 1,065 active upSCALE APEs, 28 percent completed the survey. Results indicate that only a small proportion of APEs listed the correct COVID-19 symptoms, transmission routes and appropriate prevention measures (25 percent, 16 percent and 39 percent, respectively) specifically included in national health education materials. Misconceptions were mainly related to transmission routes, high risk individuals and asymptomatic patients. 84 percent said they followed all government prevention guidelines. The results from the KAP survey were used to support the rapid development and deployment of targeted COVID-19 awareness and education materials for the APEs. SMS messages were continually adjusted based on the KAP survey results and a series of seven COVID-19 training modules were developed and disseminated. A follow-up KAP survey is planned for November 2020.

Adapting the existing upSCALE platform enabled a better understanding, in real time, of the KAP of APEs around COVID-19 management. Subsequently, supported improved delivery of tailored messages and education, vital for ensuring a successful COVID-19 response.
Evaluation of a home-based 7-day infection control strategy for healthcare workers following high-risk exposure to SARS-CoV-2: a cohort study
Authors: Benea Carla , Rendon Laura , Papenburg Jesse , Frenette Charles , Imcaoudene Ahmed , McDonald Emily G , Nguyen Quoc Dinh , Rajda Ewa , Tran Estelle , Vameghestahbanati Motahareh , Benedetti Andrea , Behr Marcel A , Smith Benjamin M
Published: November 2020

Background

Evidence-based infection control strategies are needed for healthcare workers (HCWs) following high-risk exposure to SARS-CoV-2. This study evaluated the negative predictive value (NPV) of a home-based 7-day infection control strategy.

Methods

HCWs advised by their Infection Control or Occupational Health officer to self-isolate due to a high-risk SARS-CoV-2 exposure were enrolled between May-September 2020. The strategy consisted of symptom-triggered nasopharyngeal SARS-CoV-2 RNA testing from day 0-6 post exposure, followed by standardized home-based nasopharyngeal swab and saliva testing on day 7. The NPV of this strategy was calculated for i) clinical COVID-19 diagnosis from day 8-14 post exposure, and for ii) asymptomatic SARS-CoV-2 detected by standardized nasopharyngeal swab and saliva specimens collected at days 9-10 and 14 post exposure. Interim results are reported in the context of a second wave threatening this essential workforce.

Results

Among 30 HCWs enrolled to date (age 31±9 years, 24 [80.0%] female), 3 were diagnosed with COVID-19 by day 14 post exposure (secondary attack rate 10.0%), with all cases detected by the 7-day infection control strategy: NPV for subsequent clinical COVID-19 or asymptomatic SARS-CoV-2 detection by day 14 was 100.0% (95%CI: 93.1-100.0%).

Interpretation

Among HCWs with high-risk exposure to SARS-CoV-2, a home-based 7-day infection control strategy may have a high NPV for subsequent COVID-19 and asymptomatic SARS-CoV-2 detection. While ongoing data collection and data sharing are needed to improve the precision of the estimated NPV, we report interim results to inform infection control strategies in light of a second wave threatening this essential workforce.
Psychological resilience, coping behaviours, and social support among healthcare workers during the COVID-19 pandemic: A systematic review of quantitative studies
Authors: Labrague Leodoro J.
Published: November 2020

Aim

To appraise and synthesize studies examining resilience, coping behaviours, and social support among healthcare workers during the coronavirus pandemic.

Background

A wide range of evidence has shown that healthcare workers, currently on the frontlines in the fight against COVID-19, are not spared from the psychological and mental health-related consequences of the pandemic. Studies synthesizing the role of coping behaviours, resilience, and social support in safeguarding the mental health of healthcare workers during the pandemic is largely unknown.

Evaluation

This is a systematic review with a narrative synthesis. A total of 31 articles were included in the review.

Key Issues

Healthcare workers utilized both problem-centred and emotion-centred coping to manage the stress-associated with the coronavirus pandemic. Coping behaviours, resilience, and social support were associated with positive mental and psychological health outcomes.

Conclusion

Substantial evidence supports the effectiveness of coping behaviours, resilience, and social support to preserve psychological and mental health among healthcare workers during the COVID-19 pandemic.

Implications for Nursing Management

In order to safeguard the mental health of healthcare workers during the pandemic, hospital and nursing administrators should implement proactive measures to sustain resilience in HCWs, build coping skills, and implement creative ways to foster social support in healthcare workers through theory-based interventions, supportive leadership, and fostering a resilient work environment.
Parental perceptions of COVID-19-like illness in their children
Authors: Hodson Ava , Woodland Lisa , Smith Louise E , Rubin G James
Published: November 2020

Objectives

To explore parents’ perceptions of COVID-19-like symptoms in their child and attitudes towards isolating from others in the household when unwell.

Study Design

Qualitative, semi-structured interviews.

Methods

30 semi-structured telephone interviews with parents of children between 4 and 18 years.

Results

We found four themes relating to symptom attribution (‘normalising symptoms’, ‘err on the side of caution’, ‘experience of temperature’, ‘symptoms not normal for us’). In general, parents were more likely to attribute symptoms to COVID-19 if a temperature was present or the symptoms were perceived as ‘unusual’ for their family. Four themes relating to self-isolation (‘difficult to prevent contact with children’, ‘isolation would be no different to lockdown life’, ‘ability to get food and supplies’, ‘limited space’). Parents believed they would find isolation within the household difficult or impossible if they had dependent children, had limited space or could not shop for groceries.

Conclusions

The findings highlight complexities in symptom perception, attribution, and household isolation. We suggest that they can be overcome by a) providing better guidance on what symptoms require action, b) providing guidance as to how to prevent infection within the household, and c) by supporting families with grocery shopping through a potential second or third wave.
What support do frontline workers want? A qualitative study of health and social care workers’ experiences and views of psychosocial support during the COVID-19 pandemic
Authors: Billings Jo , Seif Nada Abou , Hegarty Siobhan , Ondruskova Tamara , Soulios Emilia , Bloomfield Michael , Greene Talya
Published: November 2020

Background

The COVID-19 pandemic has placed a significant burden on the mental health and wellbeing of frontline health and social care workers. The need to support frontline staff has been recognised. However, there is to date little research specifically on how best to support the mental health needs of frontline workers, and none on their own experiences and views about what might be most helpful.

Aims

We set out to redress this research gap by qualitatively exploring UK frontline health and social care workers’ own experiences and views of psychosocial support during the pandemic.

Method

Frontline health and social care workers were recruited purposively through social media and by snowball sampling via healthcare colleagues. Workers who volunteered to take part in the study were interviewed remotely following a semi-structured interview guide. Transcripts of the interviews were analysed by the research team following the principles of Reflexive Thematic Analysis.

Results

We conducted 25 interviews with frontline workers from a variety of professional groups working in health and social care settings across the UK. Themes derived from our analysis showed that workers’ experiences and views about psychosocial support were complex. Peer support was many workers’ first line of support but could also be experienced as a burden. Workers were ambivalent about support shown by organisations, media and the public. Whilst workers valued psychological support services, there were many disparities in provision and barriers to access.

Conclusions

The results of this study show that frontline health and social care workers are likely to need a flexible system of support including peer, organisational and professional support. More research is needed to fully unpack the structural, systemic and individual barriers to accessing psychosocial support. Greater collaboration, consultation and co-production of support services and their evaluation is warranted.
SLAMF7 engagement super-activates macrophages in acute and chronic inflammation
Authors: Simmons Daimon P. , Nguyen Hung N. , Gomez-Rivas Emma , Jeong Yunju , Chen Antonia F. , Lange Jeffrey K. , Dyer George S. , Blazar Philip , Earp Brandon E. ,   Accelerating Medicines Partnership (AMP) RA/SLE Network, Rao Deepak A. , Kim Edy Y. , Brenner Michael B.
Published: November 2020

Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a super-activated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression. Engaging this receptor drove an exuberant wave of inflammatory cytokine expression, and induction of TNF-α following SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients, but in gut macrophages from active Crohn’s disease patients and lung macrophages from severe COVID-19 patients. This suggests a central role for SLAMF7 in macrophage super-activation with broad implications in pathology.
CRISPRidentify: identification of CRISPR arrays using machine learning approach
Authors: Mitrofanov Alexander , Alkhnbashi Omer S. , Shmakov Sergey A. , Makarova Kira S. , Koonin Eugene V. , Backofen Rolf
Published: November 2020

CRISPR–Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR– Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are produced by processing of pre-crRNA, the transcript of CRISPR arrays, and guide Cas protein(s) to the cognate invading nucleic acids, enabling their destruction. Several bioinformatics tools have been developed to detect CRISPR arrays based solely on DNA sequences, but all these tools employ the same strategy of looking for repetitive patterns, which might correspond to CRISPR array repeats. The identified patterns are evaluated using a fixed, built-in scoring function, and arrays exceeding a cut-off value are reported. Here, we instead introduce a data-driven approach that uses machine learning to detect and differentiate true CRISPR arrays from false ones based on several features. Our CRISPR detection tool, CRISPRidentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false positive rate. In contrast to the existing tools, our approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as a practical measure of the likelihood that a given genomic region is a CRISPR array.
Ultra-precise quantification of mRNA targets across a broad dynamic range with nanoreactor beads
Authors: Loncarevic Ivan F. , Toepfer Susanne , Hubold Stephan , Klinger Susanne , Kanitz Lea , Ellinger Thomas , Steinmetzer Katrin , Ernst Thomas , Hochhaus Andreas , Ermantraut Eugen
Published: November 2020

Precise quantification of molecular targets in a biological sample across a wide dynamic range is a key requirement in many diagnostic procedures, such as monitoring response to therapy or detection of measurable residual disease. State of the art digital PCR assays provide for a dynamic range of four orders of magnitude. However digital assays are complex and require sophisticated microfluidic tools. Here we present an assay format that enables ultra-precise quantification of RNA targets in a single measurement across a dynamic range of more than seven orders of magnitude. The approach is based on hydrogel beads that provide for microfluidic free compartmentalization of the sample as they are used as digital nanoreactors for reverse transcription, PCR amplification and combined real time and digital detection of gene transcripts. We have applied these nanoreactors for establishing an assay for the detection and quantification of BCR-ABL1 fusion transcripts. The assay has been characterized for its accuracy and linear dynamic range. A comparison of the new method against the current clinical standard procedure with clinical samples from patients with chronic myeloid leukemia (CML) revealed good agreement between the results obtained with the respective method.
iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome
Authors: Kosanke Maike , Davenport Colin , Szepes Monika , Wiehlmann Lutz , Kohrn Tim , Dorda Marie , Gruber Jonas , Menge Kaja , Sievert Maike , Melchert Anna , Gruh Ina , Martin Ulrich
Published: November 2020

While human induced pluripotent stem cells (iPSCs) offer fascinating prospects for research and clinics, evaluating their genomic stability before applications is of utmost importance. During reprogramming, clonal hiPSC lines derived from the same parental cell population were observed to harbor different mitochondrial DNA (mtDNA) variants and variant heteroplasmy levels. It is unknown to date to which extent this unequal segregation of heteroplasmies between cells arises from mosaicism in the parental cell population, selection on mutated mtDNA molecules on the cellular or organelle level, genetic drift during reduction of mtDNA during reprogramming (genetic bottleneck), or de novo mutations. We analyzed mtDNA variants in 26 clonal iPSC lines by mtDNA sequencing. We did not observe a strong bottleneck or any selection for cells with specific mtDNA variants (clonal eliteness) during reprogramming. iPSC culture expansion, however, selects against putatively actionable mutations in the mitochondrial genome that may affect mitochondrial function and cell metabolism. In contrast, heteroplasmy levels of neutral variants remained stable or increased within clonal iPSC lines during culture expansion. Interestingly, the mtDNA copy number per cell got transiently reduced during targeted differentiation of iPSCs into cardiomyocytes, but mtDNA heteroplasmy levels were not affected. Altogether, our results point towards a scenario in which intra-cellular selection on mtDNA during culture expansion, but not during reprogramming or differentiation, pivotally shapes the mutational landscape of the mitochondrial genome in iPSCs. Other mechanisms such as inter-cellular selection, genetic bottleneck, and genetic drift exert minor impact.
Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling
Authors: Eiyama Akinori , Aaltonen Mari J , Nolte Hendrik , Tatsuta Takashi , Langer Thomas
Published: November 2020

Lipid transfer proteins of the Ups1/PRELID1 family facilitate the transport of phospholipids across the intermembrane space of mitochondria in a lipid-specific manner. Heterodimeric complexes of yeast Ups1/Mdm35 or human PRELID1/TRIAP1 shuttle phosphatidic acid (PA) synthesized in the endoplasmic reticulum (ER) to the inner membrane, where it is converted to cardiolipin (CL), the signature phospholipid of mitochondria. Loss of Ups1/PRELID1 proteins impairs the accumulation of CL and broadly affects mitochondrial structure and function. Unexpectedly and unlike yeast cells lacking the cardiolipin synthase Crd1, Ups1 deficient yeast cells exhibit glycolytic growth defects, pointing to functions of Ups1-mediated PA transfer beyond CL synthesis. Here, we show that the disturbed intramitochondrial transport of PA inups1Δ cells leads to altered phospholipid composition of the ER membrane, independent of disturbances in CL synthesis. The impaired flux of PA into mitochondria is associated with the increased synthesis of phosphatidylcholine (PC) and a reduced phosphatidylethanolamine (PE)/PC ratio in the ER ofups1Δ cells which suppresses the unfolded protein response (UPR). Moreover, we observed inhibition of TORC1 signaling in these cells. Activation of either UPR by ER protein stress or of TORC1 signaling by disruption of its negative regulator, the SEACIT complex, increased cytosolic protein synthesis and restored glycolytic growth ofups1Δ cells. These results demonstrate that PA influx into mitochondria is required to preserve ER membrane homeostasis and that its disturbance is associated with impaired glycolytic growth and cellular stress signaling.
Memory shapes microbial populations
Authors: Gokhale Chaitanya S. , Giaimo Stefano , Remigi Philippe
Published: November 2020

Correct decision making is fundamental for all living organisms to thrive under environmental changes. The patterns of environmental variation and the quality of available information define the most favourable strategy among multiple options, from randomly adopting a phenotypic state to sensing and reacting to environmental cues. Memory – a phenomenon often associated with, but not restricted to, higher multicellular organisms – can help when temporal correlations exist. How does memory manifest itself in unicellular organisms? Through a combination of deterministic modelling and stochastic simulations, we describe the population-wide fitness consequences of phenotypic memory in microbial populations. Moving beyond binary switching models, our work highlights the need to consider a broader range of switching behaviours when describing microbial adaptive strategies. We show that multiple cellular states capture the empirical observations of lag time distributions, overshoots, and ultimately the phenomenon of phenotypic heterogeneity. We emphasise the implications of our work in understanding antibiotic tolerance, and, in general, survival under fluctuating environments.
The outcome of neutrophil-T cell contact differs depending on activation status of both cell types
Authors: Minns Danielle , Smith Katie J , Hardisty Gareth , Rossi Adriano , Findlay Emily Gwyer
Published: November 2020

Neutrophils and T cells exist in close proximity in lymph nodes and inflamed tissues during health and disease. They are able to form stable interactions, with profound effects on the phenotype and function of the T cells. However, the outcome of these effects are frequently contradictory; in some systems neutrophils suppress T cell proliferation, in others they are activatory or present antigen directly. Published protocols modelling these interactionsin vitrodo not reflect the full range of interactions foundin vivo; they do not examine how activated and naïve T cells differentially respond to neutrophils, or whether de-granulating or resting neutrophils induce different outcomes. Here, we established a culture protocol to ask these questions with human T cells and autologous neutrophils. We find that resting neutrophils suppress T cell proliferation, activation and cytokine production but that de-granulating neutrophils do not, and neutrophil released intracellular contents are pro-activatory. Strikingly, we also demonstrate that T cells early in the activation process are susceptible to suppression by neutrophils, while later-stage T cells are not, and naïve T cells do not respond at all. Our protocol therefore allows nuanced analysis of the outcome of interaction of these cells and may explain contradictory results observed previously.
Aurora Kinase A proximity interactome reveals centriolar satellites as regulators of its function during primary cilium biogenesis
Authors: Arslanhan Melis D. , Rauniyar Navin , Yates John R. , Firat-Karalar Elif N.
Published: November 2020

Aurora kinase A (AURKA) is a conserved kinase that plays crucial roles in numerous cellular processes. Although AURKA overexpression is frequent in human cancers, its pleiotropic functions and complex spatiotemporal regulation have presented challenges in its therapeutic targeting. An essential step to overcome these challenges is the identification of the full range of AURKA regulators and substrates, which are often weak and transient. Previous proteomic studies were limited in monitoring dynamic and non-mitotic AURKA interactions. Here, we generated the firstin vivoproximity interactome of AURKA, which consisted of over 100 proteins involving multiple biological processes and cellular compartments. Importantly, AURKA had extensive proximity interactions to centriolar satellites, key regulators of the primary cilium. Affinity pulldown and phosphoproteomics experiments confirmed this proximity relationship at the physical level. Loss-of-function experiments defined satellites as negative regulators of AURKA activity, abundance and localization in quiescent cells. Notably, loss of satellites increased AURKA activation at the basal body and resulted in defective cilium assembly and enhanced cilium disassembly. Collectively, our results provide a powerful resource for dissecting AURKA function and regulation and uncover proteostatic regulation of AURKA by centriolar satellites as a new regulatory mechanism for its non-mitotic functions.
Deep generative selection models of T and B cell receptor repertoires with soNNia
Authors: Isacchini Giulio , Walczak Aleksandra M. , Mora Thierry , Nourmohammad Armita
Published: November 2020

Subclasses of lymphocytes carry different functional roles to work together and produce an immune response and lasting immunity. Additionally to these functional roles, T and B-cell lymphocytes rely on the diversity of their receptor chains to recognize different pathogens. The lymphocyte subclasses emerge from common ancestors generated with the same diversity of receptors during selection processes. Here we leverage biophysical models of receptor generation with machine learning models of selection to identify specific sequence features characteristic of functional lymphocyte repertoires and subrepertoires. Specifically, using only repertoire level sequence information, we classify CD4+and CD8+T-cells, find correlations between receptor chains arising during selection, and identify T-cell subsets that are targets of pathogenic epitopes. We also show examples of when simple linear classifiers do as well as more complex machine learning methods.
Fine-scale coexistence between Mediterranean mesocarnivores is mediated by spatial, temporal and trophic resource partitioning
Authors: Ferreiro-Arias Iago , Isla Jorge , Jordano Pedro , Benítez-López Ana
Published: November 2020

The partition of the ecological niche can enhance the coexistence of predators due to differences in how they exploit three main resources: food, space, and time, the latter being an axis that often remains unexplored.

We studied niche segregation in a Mediterranean mesocarnivore community composed byVulpes vulpes, Genetta genetta, Meles melesandHerpestes ichneumon, addressing simultaneously different niche axes: the temporal, trophic and spatial axes.

We assessed temporal segregation between mesopredators and prey and between potential competitors, using camera trap data between 2018-2020 in a Mediterranean landscape in Southern Spain. We deployed camera traps in 35 stations in three sites with varying vegetation cover within Doñana National Park. We further examined the spatial overlap in activity centers and trophic preferences between potential competitors using diet information from studies performed in the study area.

We found an overall temporal segregation between trophic generalist species, with species showing higher temporal overlap differing in their trophic preferences and/or showing limited spatial overlap. Furthermore, we observed an overall high overlap between the activity patterns of predators and their major prey in the area (the common genet vs small mammals and the red fox vs European rabbit).

Our study suggests that coexistence of the different species that compose the mesocarnivore assemblage in Mediterranean landscapes can be facilitated by subtle differences along the three main niche axes, with temporal segregation being a most pronounced mechanism. Our findings reinforce the idea that the coexistence mechanisms underlying community structure are multidimensional.
MaXrd updated with emphasis on model construction and reciprocal-space simulations
Authors: Ramsnes Stian Penev , Larsen Helge Bøvik , Thorkildsen Gunnar
Published: November 2020

A major revision of the Mathematica
X-ray Diffraction Package (MaXrd) has been undertaken, where developments have focused upon construction of crystal structure models, in particular host–guest systems, and subsequent simulations of reciprocal space through the external programs DISCUS and DIFFUSE (ZMC).
(3,5-Dimethyl-1H-pyrazol-1-yl)trimethylsilane
Authors: Böhme Uwe , Bitto Florian
Published: November 2020

The title compound, C8H16N2Si, crystallizes in the the orthorhombic space groupP212121with one molecule in the asymmetric unit. The Si—N bond is 1.782 (2) Å, which is substantially longer than is found in comparable (3,5-dimethylpyrazolyl)silanes. The trimethylsilyl group adopts a staggered conformation with respect to the planar 3,5-dimethylpyrazolyl unit. C—H...N hydrogen bonds between neighboring molecules form a strand of molecules along theb-axis direction.
The interplay between entrepreneurial orientation and control mechanisms on decision-making and new product performance
Authors: Leckie Civilai , McDonald Heath
Published: November 2020

Purpose

This study aims to investigate whether an organization that is entrepreneurial oriented can benefit from having a formal control structure and process in new product development (NPD). This study investigates two well-known control mechanisms in NPD, namely, stage-gate system (SGS) and project management (PM), as well as decision-making comprehensiveness (DMC), reflecting the amount of information processing and investigative activities undertaken.

Design/methodology/approach

Survey data were collected from 238 Australian small and medium enterprises. Structural equation modeling was used to test the hypotheses.

Findings

The findings of this study suggest that entrepreneurial orientation (EO) directly impacts new product performance and indirectly does so through DMC. While both control mechanisms positively impact DMC, they affect the EO–DMC relationship differently. While SGS positively moderates the EO–DMC relationship, PM negatively does so. However, the use of SGS and PM enhances the effect of EO on DMC.

Practical implications

This research provides managers with insights into the design of structure and process in NPD to support interfunctional coordination and firm strategy. The findings of this study suggest that managers should be amenable to the application of control mechanisms and DMC. The calibration of the right mix of control systems is required to ensure that EO can contribute to decision-making in the NPD process.

Originality/value

On the surface, the implementation of EO requires flexibility while the control mechanisms and extensive information processing are seen as restricted structures for NPD activities. However, rather than viewing EO and control structure as counterintuitive elements in NPD, the results suggest that appropriate use of control structure can support organizational strategy and decision-making activities, which subsequently enhance NPD outcomes.
A review of the strategic planning process in the Hong Kong Police Force
Authors: Cheung Hoi-yan , Yu Eddie
Published: November 2020

Purpose

The purpose of this paper is to review the strategic planning process of the Hong Kong Police Force (the Force) and its outcomes for the planning cycle of 2019-2021.

Design/methodology/approach

Based on an insider's perspective drawn from documentation, internal reports and field observation, this study is an analysis of the five-step strategic planning process of the Force as a case study over the two-year period by using the 3-H (Heart-Head-Hand) framework and futures studies.

Findings

This study demonstrates the Force's strategic management in practice. The 3-H framework and the Six Pillars Foresight Process are found to be useful tools in strategic planning. When the Heart, Head and Hand elements are developed and integrated as a mindset during the process, they help theorise the practice and experience of police officers towards a holistic and effective strategic management. Coupled with the foresight process, the Force will be more agile and outward focused in the Volatile, Uncertain, Complex and Ambiguous (VUCA) world.

Originality/value

This is the first study to apply the 3-H framework and futures thinking in analysing the process in a police organisation in Hong Kong. While strategic planning is an important process to set directions for an organisation to move forward, this study describes the process in terms of relevant practice and theoretical concepts. It is hoped that such experience can serve as reference for practitioners in other government departments and police organisations.