bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insuring crops from space: the potential of satellite-retrieved soil moisture to reduce farmers’ drought risk exposure
Authors: Vroege Willemijn , Bucheli Janic , Dalhaus Tobias , Hirschi Martin , Finger Robert 
Published: January 2021

Abstract
Crop producers face significant and increasing drought risks. We evaluate whether insurances based on globally and freely available satellite-retrieved soil moisture data can reduce farms’ financial drought risk exposure. We design farm individual soil moisture index insurances for wheat, maize and rapeseed production using a case study for Eastern Germany. We find that the satellite-retrieved soil moisture index insurances significantly decrease risk exposure for these crops compared to the situation where production is not insured. The satellite-retrieved index also outperforms one based on soil moisture estimates derived from meteorological measurements at ground stations. Important implications for insurers and policy makers are that they could and should develop better suited insurances. Available satellite-retrieved data can be used to increase farmers’ resilience in a changing climate.
Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei
Authors: Davey John W , Catta-Preta Carolina M C , James Sally , Forrester Sarah , Motta Maria Cristina M , Ashton Peter D , Mottram Jeremy C 
Published: January 2021

Abstract
Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.
A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data
Authors: Tian Hai-Feng , Hu Qiao-Mu , Li Zhong 
Published: January 2021

Abstract
The swamp eel (Monopterus albus) is one economically important fish in China and South-Eastern Asia and a good model species to study sex inversion. There are different genetic lineages and multiple local strains of swamp eel in China, and one local strain of M. albus with deep yellow and big spots has been selected for consecutive selective breeding due to superiority in growth rate and fecundity. A high-quality reference genome of the swamp eel would be a very useful resource for future selective breeding program. In the present study, we applied PacBio single-molecule sequencing technique (SMRT) and the high-throughput chromosome conformation capture (Hi-C) technologies to assemble the M. albus genome. A 799 Mb genome was obtained with the contig N50 length of 2.4 Mb and scaffold N50 length of 67.24 Mb, indicating 110-fold and ∼31.87-fold improvement compared to the earlier released assembly (∼22.24 Kb and 2.11 Mb, respectively). Aided with Hi-C data, a total of 750 contigs were reliably assembled into 12 chromosomes. Using 22,373 protein-coding genes annotated here, the phylogenetic relationships of the swamp eel with other teleosts showed that swamp eel separated from the common ancestor of Zig-zag eel ∼49.9 million years ago, and 769 gene families were found expanded, which are mainly enriched in the immune system, sensory system, and transport and catabolism. This highly accurate, chromosome-level reference genome of M. albus obtained in this work will be used for the development of genome-scale selective breeding.
Visualizing population structure with variational autoencoders
Authors: Battey C J , Coffing Gabrielle C , Kern Andrew D 
Published: January 2021

Abstract
Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs)—generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data—for visualizing population genetic variation. VAEs incorporate nonlinear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.
Triplex Direct Quantitative Polymerase Chain Reaction for the Identification of Streptococcus pneumoniae Serotypes
Authors: Ouattara Mahamoudou , Tamboura Mamadou , Kambiré Dinanibè , Lê Kim Anh , Van Phan Thanh , Velusamy Srinivasan , Nguyen Hien Anh , Trang Dai Vo Thi , Lessa Fernanda C , Iijima Makiko , Nguyen Dac Trung , Schwartz Stephanie B , McGee Lesley , Traoré Rasmata Ouédraogo , Beall Bernard 
Published: January 2021

Abstract
The quantitative polymerase chain reaction (qPCR) method presented in this study allows the identification of pneumococcal capsular serotypes in cerebrospinal fluid without first performing DNA extraction. This testing approach, which saves time and resources, demonstrated similar sensitivity and a high level of agreement between cycle threshold values when it was compared side-by-side with the standard qPCR method with extracted DNA.
Evaluation of methods for detection of β-lactamase production in MSSA
Authors: Skov Robert , Lonsway David R , Larsen Jesper , Larsen Anders Rhod , Samulioniené Jurgita , Limbago Brandi M 
Published: January 2021

Abstract

Objectives
Correct determination of penicillin susceptibility is pivotal for using penicillin in the treatment of Staphylococcus aureus infections. This study examines the performance of MIC determination, disc diffusion and a range of confirmatory tests for detection of penicillin susceptibility in S. aureus.

Methods
A total of 286 consecutive penicillin-susceptible S. aureus blood culture isolates as well as a challenge set of 62 MSSA isolates were investigated for the presence of the blaZ gene by PCR and subjected to penicillin-susceptibility testing using broth microdilution MIC determination, disc diffusion including reading of the zone edge, two nitrocefin tests and the cloverleaf test.

Results
Using PCR-based detection of blaZ as the gold standard, both broth microdilution MIC testing and disc diffusion testing resulted in a relatively low accuracy (82%–93%) with a sensitivity ranging from 49%–93%. Among the confirmatory tests, the cloverleaf test performed with 100% accuracy, while zone edge interpretation and nitrocefin-based tests increased the sensitivity of β-lactamase detection to 96%–98% and 82%–96% when using MIC determination or disc diffusion as primary test, respectively.

Conclusions
This investigation showed that reliable and accurate detection of β-lactamase production in S. aureus can be obtained by MIC determination or penicillin disc diffusion followed by interpretation of the zone edge as a confirmatory test for apparently penicillin-susceptible isolates. The more cumbersome cloverleaf test can also be used. Nitrocefin-based tests should not be used as the only test for confirmation of a presumptive β-lactamase-negative isolate.
Vertical restraints under Indian Competition Law: whither law and economics
Authors: Kathuria Vikas 
Published: January 2021

ABSTRACT
The correct welfare assessment of vertical agreements in competition law is a difficult craft. The more mature jurisdictions such as the EU and the US have struggled to develop the optimal framework. This article scrutinizes vertical agreements cases of the Competition Commission of India (CCI) that is now 11 years old. The objective is to assist the CCI in strengthening its legal and economic framework vis-à-vis vertical agreements in its formative stage. The scrutiny of some leading cases revealed three types of infirmities in CCI’s cases. First, there are some legal ambiguities in the interpretation of the legislation. Secondly, the economic analysis is largely incoherent and truncated. Thirdly, there is a visible overreliance on the EU jurisprudence that does not conform to the legislative scheme of the Indian Competition Act, 2002. The article draws out some lessons towards the end.
Comparison of models for missing pedigree in single-step genomic prediction
Authors: Masuda Yutaka , Tsuruta Shogo , Bermann Matias , Bradford Heather L , Misztal Ignacy 
Published: January 2021

Abstract
Pedigree information is often missing for some animals in a breeding program. Unknown-parent groups (UPGs) are assigned to the missing parents to avoid biased genetic evaluations. Although the use of UPGs is well established for the pedigree model, it is unclear how UPGs are integrated into the inverse of the unified relationship matrix (H-inverse) required for single-step genomic best linear unbiased prediction. A generalization of the UPG model is the metafounder (MF) model. The objectives of this study were to derive 3 H-inverses and to compare genetic trends among models with UPG and MF H-inverses using a simulated purebred population. All inverses were derived using the joint density function of the random breeding values and genetic groups. The breeding values of genotyped animals (u2) were assumed to be adjusted for UPG effects (g) using matrix Q2 as u2∗=u2+Q2g before incorporating genomic information. The Quaas–Pollak-transformed (QP) H-inverse was derived using a joint density function of u2∗ and g updated with genomic information and assuming nonzero cov(u2∗,g′). The modified QP (altered) H-inverse also assumes that the genomic information updates u2∗ and g, but cov(u2∗,g′)=0. The UPG-encapsulated (EUPG) H-inverse assumed genomic information updates the distribution of u2∗. The EUPG H-inverse had the same structure as the MF H-inverse. Fifty percent of the genotyped females in the simulation had a missing dam, and missing parents were replaced with UPGs by generation. The simulation study indicated that u2∗ and g in models using the QP and altered H-inverses may be inseparable leading to potential biases in genetic trends. Models using the EUPG and MF H-inverses showed no genetic trend biases. These 2 H-inverses yielded the same genomic EBV (GEBV). The predictive ability and inflation of GEBVs from young genotyped animals were nearly identical among models using the QP, altered, EUPG, and MF H-inverses. Although the choice of H-inverse in real applications with enough data may not result in biased genetic trends, the EUPG and MF H-inverses are to be preferred because of theoretical justification and possibility to reduce biases.
Di-ANFIS: an integrated blockchain–IoT–big data-enabled framework for evaluating service supply chain performance
Authors: Bamakan Seyed Mojtaba Hosseini , Faregh Najmeh , ZareRavasan Ahad 
Published: January 2021

AbstractService supply chain management is a complex process because of its intangibility, high diversity of services, trustless settings, and uncertain conditions. However, the traditional evaluating models mostly consider the historical performance data and fail to predict and diagnose the problems’ root. This paper proposes a distributed, trustworthy, tamper-proof, and learning framework for evaluating service supply chain performance based on blockchain and adaptive network-based fuzzy inference systems (ANFIS) techniques, named Di-ANFIS. The main objectives of this research are as follows: (1) presenting hierarchical criteria of service supply chain performance to cope with the diagnosis of the problems’ root; (2) proposing a smart learning model to deal with the uncertainty conditions by a combination of neural network and fuzzy logic; and (3) introducing a distributed blockchain-based framework due to the dependence of ANFIS on big data and the lack of trust and security in the supply chain. Furthermore, the proposed six-layer conceptual framework consists of the data layer, connection layer, blockchain layer, smart layer, ANFIS layer, and application layer. This architecture creates a performance management system using the Internet of Things, smart contracts, and ANFIS based on the blockchain platform. The Di-ANFIS model provides a performance evaluation system without needing a third party and a reliable intermediary that provides an agile and diagnostic model in a smart and learning process. It also saves computing time and speeds up information flow.
Hoping for the Worst? A Paradoxical Preference for Bad News
Authors: Barasz Kate , Hagerty Serena F 
Published: January 2021

AbstractNine studies investigate when and why people may paradoxically prefer bad news—for example, hoping for an objectively worse injury or a higher-risk diagnosis over explicitly better alternatives. Using a combination of field surveys and randomized experiments, the research demonstrates that people may hope for relatively worse (vs. better) news in an effort to preemptively avoid subjectively difficult decisions (studies 1 and 2). This is because when worse news avoids a choice (study 3A)—for example, by “forcing one’s hand” or creating one dominant option that circumvents a fraught decision (study 3B)—it can relieve the decision-maker’s experience of personal responsibility (study 3C). However, because not all decisions warrant avoidance, not all decisions will elicit a preference for worse news; fewer people hope for worse news when facing subjectively easier (vs. harder) choices (studies 4A and B). Finally, this preference for worse news is not without consequence and may create perverse incentives for decision-makers, such as the tendency to forgo opportunities for improvement (studies 5A and B). The work contributes to the literature on decision avoidance and elucidates another strategy people use to circumvent difficult decisions: a propensity to hope for the worst.
Why put a museum in a book? Ferrante Imperato and the image of natural history in sixteenth-century Naples
Authors: Findlen Paula 
Published: January 2021

Abstract
The first image of a natural history museum appeared in Ferrante Imperato’s ‘Natural History’ (1599), a book that is, nonetheless, not a catalogue of the contents of his museum. This article explores contemporary accounts of the Neapolitan apothecary’s collection, and offers a close reading of its portrayal in this woodcut, in relation to the contents of the ‘Natural History’. How did Imperato’s museum reflect his relations with other naturalists, in Naples and beyond, and the politics of knowledge in Spanish Naples? What kind of civic monument was Imperato’s museum?
Phytohormones and their crosstalk in regulating stomatal development and patterning
Authors: Wei Hongbin , Jing Yifeng , Zhang Lei , Kong Dexin 
Published: January 2021

Abstract
Phytohormones play important roles in regulating various aspects of plant growth and development as well as in biotic and abiotic stress responses. Stomata are openings on the surface of land plants that control gas exchange with the environment. Accumulating evidence shows that various phytohormones, including abscisic acid, jasmonic acid, brassinosteroids, auxin, cytokinin, ethylene, and gibberellic acid, play many roles in the regulation of stomatal development and patterning, and that the cotyledons/leaves and hypocotyls/stems of Arabidopsis exhibit differential responsiveness to phytohormones. In this review, we first discuss the shared regulatory mechanisms controlling stomatal development and patterning in Arabidopsis cotyledons and hypocotyls and those that are distinct. We then summarize current knowledge of how distinct hormonal signaling circuits are integrated into the core stomatal development pathways and how different phytohormones crosstalk to tailor stomatal density and spacing patterns. Knowledge obtained from Arabidopsis may pave the way for future research to elucidate the effects of phytohormones in regulating stomatal development and patterning in cereal grasses for the purpose of increasing crop adaptive responses.
The Feasibility of a Novel Index From a Wireless Doppler Ultrasound Patch to Detect Decreasing Cardiac Output in Healthy Volunteers
Authors: Kenny Jon-Émile S , Eibl Andrew M , Parrotta Matthew , Long Bradley F , Eibl Joseph K 
Published: January 2021

ABSTRACTIntroductionEarly hemorrhage is often missed by traditional vital signs because of physiological reserve, especially in the young and healthy. We have developed a novel, wearable, wireless Doppler ultrasound patch that tracks real-time blood velocity in the common carotid artery.Materials and MethodsWe studied eight healthy volunteers who decreased their cardiac output using a standardized Valsalva maneuver. In all eight, we simultaneously monitored the velocity time integral (VTI) of the common carotid artery (using the ultrasound patch) as well as the descending aorta (using a traditional pulsed wave duplex imaging system); the descending aortic VTI was used as a surrogate for left ventricular stroke volume (SV). Additionally, in a subset of four, we simultaneously measured SV using a noninvasive pulse contour analysis device.ResultsFrom baseline to peak effect of Valsalva, there was a statistically significant fall in descending aortic and common carotid VTI of 37% (P = 0.0005) and 23% (P &lt; 0.0001), respectively. Both values returned to baseline on recovery. Additionally, a novel index from the carotid ultrasound patch (i.e., the heart rate divided by the carotid artery VTI) detected a 10% fall in aortic VTI with high sensitivity and specificity (100% and 100%, respectively); this novel index also accurately detected a 10% decrease in SV as measured by the noninvasive SV monitor. The mean arterial pressure, measured by the noninvasive pulse contour device, did not correctly detect the fall in SV.ConclusionIn summary, a novel index from a wireless Doppler ultrasound patch may be more sensitive and specific for detecting decreased cardiac output than standard vital signs in healthy volunteers.
From the Dexterous Surgical Skill to the Battlefield—A Robotics Exploratory Study
Authors: Gonzalez Glebys T , Kaur Upinder , Rahman Masudur , Venkatesh Vishnunandan , Sanchez Natalia , Hager Gregory , Xue Yexiang , Voyles Richard , Wachs Juan 
Published: January 2021

ABSTRACT

Introduction
Short response time is critical for future military medical operations in austere settings or remote areas. Such effective patient care at the point of injury can greatly benefit from the integration of semi-autonomous robotic systems. To achieve autonomy, robots would require massive libraries of maneuvers collected with the goal of training machine learning algorithms. Although this is attainable in controlled settings, obtaining surgical data in austere settings can be difficult. Hence, in this article, we present the Dexterous Surgical Skill (DESK) database for knowledge transfer between robots. The peg transfer task was selected as it is one of the six main tasks of laparoscopic training. In addition, we provide a machine learning framework to evaluate novel transfer learning methodologies on this database.

Methods
A set of surgical gestures was collected for a peg transfer task, composed of seven atomic maneuvers referred to as surgemes. The collected Dexterous Surgical Skill dataset comprises a set of surgical robotic skills using the four robotic platforms: Taurus II, simulated Taurus II, YuMi, and the da Vinci Research Kit. Then, we explored two different learning scenarios: no-transfer and domain-transfer. In the no-transfer scenario, the training and testing data were obtained from the same domain; whereas in the domain-transfer scenario, the training data are a blend of simulated and real robot data, which are tested on a real robot.

Results
Using simulation data to train the learning algorithms enhances the performance on the real robot where limited or no real data are available. The transfer model showed an accuracy of 81% for the YuMi robot when the ratio of real-tosimulated data were 22% to 78%. For the Taurus II and the da Vinci, the model showed an accuracy of 97.5% and 93%, respectively, training only with simulation data.

Conclusions
The results indicate that simulation can be used to augment training data to enhance the performance of learned models in real scenarios. This shows potential for the future use of surgical data from the operating room in deployable surgical robots in remote areas.
Hypocalcemia in Military Casualties From Point of Injury to Surgical Teams in Afghanistan
Authors: Conner Jeffrey R , Benavides Linda C , Shackelford Stacy A , Gurney Jennifer M , Burke Edward F , Remley Michael A , Ditzel Ricky M , Cap Andrew P 
Published: January 2021

ABSTRACT

Introduction
Hypocalcemia is a known sequela of citrated blood product transfusion. Civilian data suggest hypocalcemia on hospital admission is associated with worse outcomes. Initial calcium levels in military casualties have not previously been analyzed. The objective of this retrospective review aimed to assess the initial calcium levels in military trauma casualties at different Forward Surgical Teams (FST) locations in Afghanistan and describe the effects of prehospital blood product administration on arrival calcium levels.

Materials and Methods
This is a retrospective cohort analysis of military casualties arriving from point of injury to one of two FSTs in Afghanistan from August 2018 to February 2019 split into four locations. The primary outcome was incidence of hypocalcemia (ionized calcium &lt; 1.20 mmol/L).

Results
There were 101 patients included; 55 (54.5%) experienced hypocalcemia on arrival to the FST with a mean calcium of 1.16 mmol/L (95% confidence interval [CI], 1.14 to 1.18). The predominant mechanism of injury consisted of blast patterns, 46 (45.5%), which conferred an increased risk of hypocalcemia compared to all other patterns of injury (odds ratio = 2.42, P = .042). Thirty-eight (37.6%) patients required blood product transfusion. Thirty-three (86.8%) of the patients requiring blood product transfusion were hypocalcemic on arrival. Mean initial calcium of patients receiving blood product was 1.13 mmol/L (95% CI, 1.08 to 1.18), which was significantly lower than those who did not require transfusion (P = .01). Eight (7.9%) of the patients received blood products before arrival, with 6/8 (75%) presenting with hypocalcemia.

Conclusions
Hypocalcemia develops rapidly in military casualties and is prevalent on admission even before transfusion of citrated blood products. Blast injuries may confer an increased risk of developing hypocalcemia. This data support earlier use of calcium supplementation during resuscitation.