bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global data-driven census ofSalmonellasmall proteins and their potential functions in bacterial virulence
Authors: Venturini Elisa , Svensson Sarah L , Maaß Sandra , Gelhausen Rick , Eggenhofer Florian , Li Lei , Cain Amy K , Parkhill Julian , Becher Dörte , Backofen Rolf , Barquist Lars , Sharma Cynthia M , Westermann Alexander J , Vogel Jörg 
Published: October 2020

ABSTRACTSmall proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of comprehensive characterization in microbes other than Escherichia coli. We have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (Transposon-directed insertion sequencing), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrate a virulence and motility defect of a Salmonella ΔmgrB mutant and reveal an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Our study highlights the power of interpreting available ‘omics’ datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.
Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes
Authors: Weiner Agnes K M , Cerón-Romero Mario A , Yan Ying , Katz Laura A 
Published: October 2020

Abstract
Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of &gt;1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.
Hydro-mechanical coupling in porous rocks: hidden dependences to the microstructure?
Authors: Pimienta Lucas , Quintal Beatriz , Caspari Eva 
Published: October 2020

SUMMARY
While hydro-mechanical coupling in rocks is generally well understood, exotic rock poroelastic responses—such as unexpected dependence to fluid diffusion time and low skeleton moduli—have been reported. Hydro-mechanical coupling, or poroelasticity, explains how fluid-saturated rocks respond to either confining or fluid pressure variations. This coupling is usually inferred from the apparent mechanical and hydraulic properties: mechanical properties determine the strain level experienced by the rock when submitted to pressures at a timescale when fluid pressure is equilibrated, which is in turn ruled by hydraulic properties. However, the coupling between properties might not always be straightforward, particularly for rocks in which two distinct families of pore types coexist: spherical pores and cracks. Comparing it with reported laboratory data sets on pressure-dependent hydraulic and elastic properties in sandstones of different porosity confirms that the well-known simple concepts of networks in parallel apply and yield opposite dependencies for the two properties on the two pore families. Because hydro-mechanical coupling implies that the two properties—that depend differently on the pore families—will be interdependent, we further apply the same concept of parallel network. It yields that, although under apparent drained conditions, typical poroelasticity experiments could underestimate the rock compressibility ${C_{\mathrm{ bp}}}$, measured as a response to fluid pressure variation, and underestimate the related skeleton (or unjacketed) bulk modulus ${K_\mathrm{ s}} = \ 1/{C_\mathrm{ s}}$.
GNSS characterization of hydrological loading in South and Southeast Asia
Authors: Materna Kathryn , Feng Lujia , Lindsey Eric O , Hill Emma M , Ahsan Aktarul , Alam A K M Khorshed , Oo Kyaw Moe , Than Oo , Aung Thura , Khaing Saw Ngwe , Bürgmann Roland 
Published: October 2020

SUMMARY
The elastic response of the lithosphere to surface mass redistributions produces geodetically measurable deformation of the Earth. This deformation is especially pronounced in South and Southeast Asia, where the annual monsoon produces large-amplitude hydrological loads. The Myanmar–India–Bangladesh–Bhutan (MIBB) network of about 20 continuously operating Global Navigation Satellite Systems (GNSS) stations, established in 2011, provides an opportunity to study the Earth's response to these loads. In this study, we use GRACE temporal gravity products as an estimate of long-wavelength surface water distribution and use this estimate in an elastic loading calculation. We compare the predicted vertical deformation from GRACE with that observed with GNSS. We find that elastic loading inferred from the GRACE gravity model is able to explain the phase and much of the peak-to-peak amplitude (typically 2–3 cm) of the vertical GNSS oscillations, especially in northeast India and central Myanmar. GRACE-based corrections reduce the RMS scatter of the GNSS data by 30–45% in these regions. However, this approach does not capture all of the seasonal deformation in central Bangladesh and southern Myanmar. We show by a synthetic test that local hydrological effects may explain discrepancies between the GNSS and GRACE signals in these places. Two independent hydrological loading models of water stored in soil, vegetation, snow, lakes and streams display phase lags compared to the GRACE and GNSS observations, perhaps indicating that groundwater contributes to the observed loading in addition to near-surface hydrology. The results of our calculations have implications for survey-mode GNSS measurements, which make up the majority of geodetic measurements in this region. By using the GNSS data together with estimates of hydrological loading from independent observations and models, we may be able to more accurately determine crustal motions caused by tectonic processes in South and Southeast Asia, while also improving our ability to monitor the annual monsoon and resulting water storage changes in the region.
Unravelling the disease mechanism for TSPYL1 deficiency
Authors: Buyse Gunnar , Di Michele Michela , Wijgaerts Anouck , Louwette Sophie , Wittevrongel Christine , Thys Chantal , Downes Kate , Ceulemans Berten , Van Esch Hild , Van Geet Chris , Freson Kathleen 
Published: October 2020

AbstractWe describe a lethal combined nervous and reproductive systems disease in three affected siblings of a consanguineous family. The phenotype was characterized by visceroautonomic dysfunction (neonatal bradycardia/apnea, feeding problems, hyperactive startle reflex), severe postnatal progressive neurological abnormalities (including abnormal neonatal cry, hypotonia, epilepsy, polyneuropathy, cerebral gray matter atrophy), visual impairment, testicular dysgenesis in males and sudden death at infant age by brainstem-mediated cardiorespiratory arrest. Whole-exome sequencing revealed a novel homozygous frameshift variant p.Val242GlufsTer52 in the TSPY-like 1 gene (TSPYL1). The truncated TSPYL1 protein that lacks the nucleosome assembly protein domain was retained in the Golgi of fibroblasts from the three patients, whereas control fibroblasts express full-length TSPYL1 in the nucleus. Proteomic analysis of nuclear extracts from fibroblasts identified 24 upregulated and 20 downregulated proteins in the patients compared with 5 controls with ‘regulation of cell cycle’ as the highest scored biological pathway affected. TSPYL1-deficient cells had prolonged S and G2 phases with reduced cellular proliferation rates. Tspyl1 depletion in zebrafish mimicked the patients’ phenotype with early lethality, defects in neurogenesis and cardiac dilation. In conclusion, this study reports the third pedigree with recessive TSPYL1 variants, confirming that TSPYL1 deficiency leads to a combined nervous and reproductive systems disease, and provides for the first time insights into the disease mechanism.
Theory, hormones and life history stages: an introduction to the symposium epigenetic variation in endocrine systems
Authors: Stevenson Tyler J , Hanson Haley E , Martin Lynn B 
Published: October 2020

SynopsisAll organisms must respond to environmental stimuli, and most metazoans do so through endocrine system regulation. Hormonal fluctuations allow organisms to maintain and return to homeostasis following perturbations, making them vital for survival and fitness. Many components of the endocrine system (e.g., proteins, steroids, receptors, genome response elements, etc.) and the physiological and behavioral processes they regulate are conserved among vertebrates (e.g., the glucocorticoid stress response). However, there are sometimes dramatic differences among and within species, particularly in how hormonal variation affects phenotypes. Some such variation is driven by internal factors such as genetics, developmental stage, sex, individual age, and body condition in addition to external factors such as the type, magnitude, and duration of environmental stimuli. Eco-evolutionary endocrinology has been quite successful in describing this variation among and within species, but we have only just begun to understand how these factors interact to affect phenotypic diversity, ecological function, and evolution. Mounting evidence suggests that various molecular epigenetic modifications of genome structure and activity, such as deoxyribonucleic acid methylation, histone modifications, non-coding RNAs, and small RNAs, mediate the interactions between environmental conditions, individual traits, and the endocrine system. As some epigenetic modifications can be induced or removed by environmental stimuli, they represent promising candidates underlying endocrine regulation and variation, particularly epigenetic marks that can be stably inherited. This symposium discussed the role of epigenetic modifications in endocrine systems, mainly in natural populations.
Microbiome Data Enhances Predictive Models of Lung Function in People With Cystic Fibrosis
Authors: Zhao Conan Y , Hao Yiqi , Wang Yifei , Varga John J , Stecenko Arlene A , Goldberg Joanna B , Brown Sam P 
Published: October 2020

Abstract

Background
Microbiome sequencing has brought increasing attention to the polymicrobial context of chronic infections. However, clinical microbiology continues to focus on canonical human pathogens, which may overlook informative, but nonpathogenic, biomarkers. We address this disconnect in lung infections in people with cystic fibrosis (CF).

Methods
We collected health information (lung function, age, and body mass index [BMI]) and sputum samples from a cohort of 77 children and adults with CF. Samples were collected during a period of clinical stability and 16S rDNA sequenced for airway microbiome compositions. We use ElasticNet regularization to train linear models predicting lung function and extract the most informative features.

Results
Models trained on whole-microbiome quantitation outperformed models trained on pathogen quantitation alone, with or without the inclusion of patient metadata. Our most accurate models retained key pathogens as negative predictors (Pseudomonas, Achromobacter) along with established correlates of CF disease state (age, BMI, CF-related diabetes). In addition, our models selected nonpathogen taxa (Fusobacterium, Rothia) as positive predictors of lung health.

Conclusions
These results support a reconsideration of clinical microbiology pipelines to ensure the provision of informative data to guide clinical practice.
Frontiers in human factors: integrating human factors and ergonomics to improve safety and quality in Latin American healthcare systems
Authors: Aceves-González Carlos , Rodríguez Yordán , Escobar-Galindo Carlos Manuel , Pérez Elizabeth , Gutiérrez-Moreno Beatriz , Hignett Sue , Lang Alexandra Rosewall 
Published: October 2020

Abstract

Background
The importance of human factors/ergonomics (HFE) is well established in all high-reliability systems but only applied in the healthcare sector relatively recently. Across many sectors, low-/middle-income countries (LMICs) lag behind more economically developed countries in their application of this safety science, due to resource and, in some cases, awareness and expertise. Most previous applications of HFE related to occupational ergonomics rather than healthcare safety.

Methods
The paper details how the reputation of HFE is being developed within healthcare communities of Latin America (LatAm), through increasing awareness and understanding of its role as safety science in the healthcare sector. It starts by articulating the need for HFE and then provides examples from Mexico, Colombia and Peru.

Results
The practical examples for research and education illustrate a developing awareness of the relevance of HFE to the healthcare sectors in LatAm and an appreciation of its worth to improve health service quality and patient safety through healthcare community engagement. A new LatAm Network of HFE in Healthcare Systems (RELAESA) was formed in 2019, which has provided a platform for HFE advice during the COVID-19 pandemic.

Conclusion
There is a real opportunity in LatAm and other LMIC health services to make more rapid and sustainable progress in healthcare-embedded HFE than has been experienced within healthcare services of more developed nations.
Metabolic Rates Predict Baseline Corticosterone and Reproductive Output in a Free-Living Passerine
Authors: Jimeno Blanca , Prichard Mackenzie R , Landry Devin , Wolf Cole , Larkin Beau , Cheviron Zachary , Breuner Creagh 
Published: October 2020

SynopsisOrganisms continuously face environmental fluctuations, and allocation of metabolic investment to meet changing energetic demands is fundamental to survival and reproductive success. Glucocorticoid (GC) hormones (e.g., corticosterone [CORT]) play an important role in energy acquisition and allocation in the face of environmental challenges, partly through mediation of energy metabolism. Although GCs and metabolic rate are expected to covary, surprisingly few empirical studies have demonstrated such relationships, especially in wild animals. Moreover, studies testing for associations between GCs and fitness generally do not account for among-individual differences in energy expenditure or energy allocation. We measured CORT (baseline and stress-induced) and metabolic traits (resting metabolic rate [RMR], cold-induced VO2max [Msum], and aerobic scope [the difference between Msum and RMR]) in female tree swallows (Tachycineta bicolor) during chick-rearing, and tested for their associations with several variables of reproductive performance. We found a positive relationship between RMR and baseline CORT, but no consistent associations between stress-induced CORT (SI-CORT) and Msum. This suggests that while baseline CORT may be a good indicator of an individual’s baseline metabolic investment, SI-CORT responses are not associated with aerobic scope or the upper limits of aerobic performance. Furthermore, we found that metabolic traits were associated with reproductive performance: females with higher reproductive output showed higher Msum, and also tended to show higher RMR. Overall, these results suggest that metabolic traits are better predictors of reproductive output in tree swallows than CORT concentrations. They further point to the maximal aerobic capacity being higher in females investing more heavily in a current reproductive event, but whether this association reflects trade-offs between current and future reproductive efforts remains to be tested.
Natural language processing systems for pathology parsing in limited data environments with uncertainty estimation
Authors: Odisho Anobel Y , Park Briton , Altieri Nicholas , DeNero John , Cooperberg Matthew R , Carroll Peter R , Yu Bin 
Published: October 2020

Abstract

Objective
Cancer is a leading cause of death, but much of the diagnostic information is stored as unstructured data in pathology reports. We aim to improve uncertainty estimates of machine learning-based pathology parsers and evaluate performance in low data settings.

Materials and methods
Our data comes from the Urologic Outcomes Database at UCSF which includes 3232 annotated prostate cancer pathology reports from 2001 to 2018. We approach 17 separate information extraction tasks, involving a wide range of pathologic features. To handle the diverse range of fields, we required 2 statistical models, a document classification method for pathologic features with a small set of possible values and a token extraction method for pathologic features with a large set of values. For each model, we used isotonic calibration to improve the model’s estimates of its likelihood of being correct.

Results
Our best document classifier method, a convolutional neural network, achieves a weighted F1 score of 0.97 averaged over 12 fields and our best extraction method achieves an accuracy of 0.93 averaged over 5 fields. The performance saturates as a function of dataset size with as few as 128 data points. Furthermore, while our document classifier methods have reliable uncertainty estimates, our extraction-based methods do not, but after isotonic calibration, expected calibration error drops to below 0.03 for all extraction fields.

Conclusions
We find that when applying machine learning to pathology parsing, large datasets may not always be needed, and that calibration methods can improve the reliability of uncertainty estimates.
Toward productivity in future construction: mapping knowledge and finding insights for achieving successful offsite construction projects
Authors: Jang Junyoung , Ahn Seungjun , Cha Seung Hyun , Cho Kyeongwoon , Koo Choongwan , Kim Tae Wan 
Published: October 2020

Abstract
Although offsite construction (OSC) has emerged as a promising solution to low productivity issues in the construction industry, knowledge for effective management of OSC projects is yet to be explored and developed further. To enhance our understanding of the landscape of the current OSC management knowledge, this study identified and reviewed 83 operation-level OSC management papers. By mapping the papers on three dimensions (i.e. OSC project type, project phase, and management area), this review sheds light on the knowledge areas addressed more frequently than the other areas over time in a detailed manner. The review also shows that papers on planning, manufacturing, maintenance phases and schedule, resources, and stakeholder management areas have a relatively large number of citations, implying a great interest in these research areas. Finally, the review discusses that substantial research work is still required in the areas of OSC execution strategy, emerging technologies in offsite manufacturing and schedule management, internet of things (IoT)-based material logistics planning and tracking, building information model-based visualization and decision support, and social and environmental effects of stakeholder engagement in OSC projects.
Profile of Fork-Tailed Bush Katydid (Orthoptera: Tettigoniidae) Feeding on Fruit of Clementine Mandarins
Authors: Cass Bodil N , Kahl Hanna M , Mueller Tobias G , Xi Xinqiang , Grafton-Cardwell Elizabeth E , Rosenheim Jay A 
Published: October 2020

Abstract
Sweet oranges (Citrus sinensis (L.) Osbeck Sapindales: Rutaceae) dominated commercial citrus production in California until recently when there has been a shift to mandarins, mostly Citrus reticulata (Blanco) mandarins and Citrus clementina (hort. ex Tanaka) clementines. Past analyses of commercial field scouting and harvest data indicated that fork-tailed bush katydids (Scudderia furcata Brunner von Wattenwyl), a major pest in oranges, are present in clementine groves, but that fruit scarring attributed to katydids is rare. Conversely, jagged or web-like scarring attributed to caterpillars was more prevalent than expected. We used two field experiments in four representative cultivars of clementines to test four explanatory hypotheses for this observation: 1) katydids do not feed on clementine fruit, 2) damaged clementine fruit recover, 3) damaged clementine fruit preferentially abscise, and 4) katydid scars on clementine fruit have a different, undocumented morphology, not recognized as katydid damage. We find support for the latter two hypotheses. Katydids fed readily on the clementine fruit of all cultivars tested, chewing irregular holes that developed into jagged or web-like scars of a range of shapes and often led to splitting and abscission of maturing fruit. The katydid scars often more closely resembled chewing caterpillar damage than the round katydid scars in oranges, suggesting that katydid damage is being misclassified in clementines. The resistance documented in some other mandarins was not observed. Katydids are clearly a frugivorous pest causing previously unrecognized scarring in clementines.