bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
Authors: Hilpert Cécile , Bricheux Geneviève , Debroas Didier
Published: April 2020

Plasmids play important roles in microbial evolution and also in the spread of antibiotic resistance. Plasmid sequences are extensively studied from clinical isolates but rarely from the environment with a metagenomic approach focused on the plasmid fraction referred to as the plasmidome. A clear challenge in this context is to define a workflow for discriminating plasmids from chromosomal contaminants existing in the plasmidome. For this purpose, we benchmarked existing tools from assembly to detection of the plasmids by reference-free methods (cBar and PlasFlow) and database-guided approaches. Our simulations took into account short-reads alone or combined with moderate long-reads like those actually generated in environmental genomics experiments. This benchmark allowed us to select the best tools for limiting false-positives associated to plasmid prediction tools and a combination of reference-guided methods based on plasmid and bacterial databases.
Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization
Authors: Krieger Spencer , Kececioglu John
Published: April 2020

Motivation

Protein secondary structure prediction is a fundamental precursor to many bioinformatics tasks. Nearly all state-of-the-art tools when computing their secondary structure prediction do not explicitly leverage the vast number of proteins whose structure is known. Leveraging this additional information in a so-called template-based method has the potential to significantly boost prediction accuracy.

Method

We present a new hybrid approach to secondary structure prediction that gains the advantages of both template- and non-template-based methods. Our core template-based method is an algorithmic approach that uses metric-space nearest neighbor search over a template database of fixed-length amino acid words to determine estimated class-membership probabilities for each residue in the protein. These probabilities are then input to a dynamic programming algorithm that finds a physically valid maximum-likelihood prediction for the entire protein. Our hybrid approach exploits a novel accuracy estimator for our core method, which estimates the unknown true accuracy of its prediction, to discern when to switch between template- and non-template-based methods.

Results

On challenging CASP benchmarks, the resulting hybrid approach boosts the state-of-the-art Q8 accuracy by more than 2–10%, and Q3 accuracy by more than 1–3%, yielding the most accurate method currently available for both 3- and 8-state secondary structure prediction.

Availability and implementation

A preliminary implementation in a new tool we call Nnessy is available free for non-commercial use at http://nnessy.cs.arizona.edu.
Hopper: a mathematically optimal algorithm for sketching biological data
Authors: DeMeo Benjamin , Berger Bonnie
Published: April 2020

Motivation

Single-cell RNA-sequencing has grown massively in scale since its inception, presenting substantial analytic and computational challenges. Even simple downstream analyses, such as dimensionality reduction and clustering, require days of runtime and hundreds of gigabytes of memory for today’s largest datasets. In addition, current methods often favor common cell types, and miss salient biological features captured by small cell populations.

Results

Here we present Hopper, a single-cell toolkit that both speeds up the analysis of single-cell datasets and highlights their transcriptional diversity by intelligent subsampling, or sketching. Hopper realizes the optimal polynomial-time approximation of the Hausdorff distance between the full and downsampled dataset, ensuring that each cell is well-represented by some cell in the sample. Unlike prior sketching methods, Hopper adds points iteratively and allows for additional sampling from regions of interest, enabling fast and targeted multi-resolution analyses. In a dataset of over 1.3 million mouse brain cells, Hopper detects a cluster of just 64 macrophages expressing inflammatory genes (0.004% of the full dataset) from a Hopper sketch containing just 5000 cells, and several other small but biologically interesting immune cell populations invisible to analysis of the full data. On an even larger dataset consisting of ∼2 million developing mouse organ cells, we show Hopper’s even representation of important cell types in small sketches, in contrast with prior sketching methods. We also introduce Treehopper, which uses spatial partitioning to speed up Hopper by orders of magnitude with minimal loss in performance. By condensing transcriptional information encoded in large datasets, Hopper and Treehopper grant the individual user with a laptop the analytic capabilities of a large consortium.

Availability and implementation

The code for Hopper is available at https://github.com/bendemeo/hopper. In addition, we have provided sketches of many of the largest single-cell datasets, available at http://hopper.csail.mit.edu.
Interactions of circulating estradiol and progesterone on changes in endometrial area and pituitary responsiveness to GnRH†
Authors: Motta Jessica C L , Madureira Guilherme , Silva Lucas O , Alves Rodrigo L O R , Silvestri Mayara , Drum Jéssica N , Consentini Carlos E C , Prata Alexandre B , Pohler Ky G , Wiltbank Milo C , Sartori Roberto
Published: April 2020

Changes in circulating progesterone (P4) and estradiol (E2) during proestrus produce dynamic changes in endometrial function and pituitary release of gonadotropins. Independent and combined effects of P4 and E2 on endometrium and pituitary were evaluated. In a preliminary study, an exogenous hormone model of proestrus was created by removal of corpus luteum and follicles ≥5 mm followed by gradual removal of intravaginal P4 implants during 18 h and treatment with increasing doses of estradiol benzoate during 48 h to mimic proestrus using high E2 (n = 9) or low E2 (n = 9). Decreased P4, increased E2, and increased endometrial area (EA) simulated proestrus in high-E2 cows and this was used subsequently. The main experiment used a 2 × 2 factorial design with: high E2 and low P4 (n = 11); high E2 and high P4 (n = 11); low E2 and high P4 (n = 11); low E2 and low P4 (n = 10). At 48 h, gonadotropin-releasing hormone (GnRH)-induced luteinizing hormone (LH) and follicle stimulating hormone (FSH) release was determined. Variables were analyzed using PROCMIXED of Statistical Analysis System. The EA increased dramatically during 48 h only in high-E2 and low-P4 cows. For FSH, high-E2 cows had greater area under the curve (AUC) and FSH peak after GnRH than low E2, with mild negative effects of high P4. For LH, concentration at peak and AUC were 2-fold greater in high E2 compared to low-E2 groups, with low P4 also 2-fold greater than high-P4 groups. Thus, maximal changes in uterus and pituitary during proestrus depend on both low P4 and high E2, but different physiologic responses are regulated differently by E2 and P4. Changes in endometrium depend on low P4 and high E2, whereas GnRH-induced FSH secretion primarily depends on high E2, and GnRH-induced LH secretion is independently increased by high E2 or reduced by high P4.
Disentangling relationships between the amphi-AdriaticEuphorbia spinosaand Balkan endemicE. glabriflora(Euphorbiaceae)
Authors: Stevanoski Ivana , Kuzmanović Nevena , Dolenc Koce Jasna , Schönswetter Peter , Frajman Božo
Published: April 2020

The Mediterranean region is one of the 25 biodiversity hotspots, with several species distributed on both sides of the Adriatic Sea, i.e. on the Apennine and the Balkan Peninsulas. One of these is Euphorbia spinosa, distributed in the coastal regions of the Ligurian, Tyrrhenian, Ionian and Adriatic Seas, whereas its closest relative, E. glabriflora, occurs in continental regions of the western and southern Balkan Peninsula, mostly on serpentine substrates. They differ morphologically, but transitional forms resembling E. glabriflora can be found within the range of E. spinosa and in the overlapping areas of both species, and phylogenetic relationships between them remain unclear. Using nuclear ribosomal ITS sequences, we here show that these two species form a monophyletic group closely related to the E. acanthothamnos alliance, but the relationships between them remain unresolved. Also, amplified fragment length polymorphism (AFLP) fingerprints are weakly structured, but indicate a north-west to south-east trend in genetic differentiation and two main genetic groups; however, these are not entirely congruent with morphological species boundaries. In addition, morphometric analyses indicate only weak differentiation between the taxa, mostly due to occurrence of morphologically transitional forms in contact areas between the two genetic groups. Based on our results we propose to treat both taxa as subspecies of E. spinosa and provide a taxonomic treatment with descriptions. Finally, based on the high genetic variability on the Balkan Peninsula, we hypothesize a trans-Adriatic dispersal from the Balkans to the Apennine Peninsula, probably during the Pleistocene. This is in line with previous studies of different plants with amphi-Adriatic distributions, with the exception that in E. spinosa the distributions on both peninsulas are of similar size, whereas in most other cases the distribution area on the Balkan Peninsula is larger than on the Apennine Peninsula.
Hindlimb motor responses to unilateral brain injury: spinal cord encoding and left-right asymmetry
Authors: Zhang Mengliang , Watanabe Hiroyuki , Sarkisyan Daniil , Andersen Marlene Storm , Nosova Olga , Galatenko Vladimir , Carvalho Liliana , Lukoyanov Nikolay , Thelin Jonas , Schouenborg Jens , Bakalkin Georgy
Published: April 2020

Mechanisms of motor deficits (e.g. hemiparesis and hemiplegia) secondary to stroke and traumatic brain injury remain poorly understood. In early animal studies, a unilateral lesion to the cerebellum produced postural asymmetry with ipsilateral hindlimb flexion that was retained after complete spinal cord transection. Here we demonstrate that hindlimb postural asymmetry in rats is induced by a unilateral injury of the hindlimb sensorimotor cortex, and characterize this phenomenon as a model of spinal neuroplasticity underlying asymmetric motor deficits. After cortical lesion, the asymmetry was developed due to the contralesional hindlimb flexion and persisted after decerebration and complete spinal cord transection. The asymmetry induced by the left-side brain injury was eliminated by bilateral lumbar dorsal rhizotomy, but surprisingly, the asymmetry after the right-side brain lesion was resistant to deafferentation. Pancuronium, a curare-mimetic muscle relaxant, abolished the asymmetry after the right-side lesion suggesting its dependence on the efferent drive. The contra- and ipsilesional hindlimbs displayed different musculo-articular resistance to stretch after the left but not right-side injury. The nociceptive withdrawal reflexes evoked by electrical stimulation and recorded with EMG technique were different between the left and right hindlimbs in the spinalized decerebrate rats. On this asymmetric background, a brain injury resulted in greater reflex activation on the contra- versus ipsilesional side; the difference between the limbs was higher after the right-side brain lesion. The unilateral brain injury modified expression of neuroplasticity genes analysed as readout of plastic changes, as well as robustly impaired coordination of their expression within and between the ipsi- and contralesional halves of lumbar spinal cord; the effects were more pronounced after the left side compared to the right-side injury. Our data suggest that changes in the hindlimb posture, resistance to stretch and nociceptive withdrawal reflexes are encoded by neuroplastic processes in lumbar spinal circuits induced by a unilateral brain injury. Two mechanisms, one dependent on and one independent of afferent input may mediate asymmetric hindlimb motor responses. The latter, deafferentation resistant mechanism may be based on sustained muscle contractions which often occur in patients with central lesions and which are not evoked by afferent stimulation. The unusual feature of these mechanisms is their lateralization in the spinal cord.
Sclera Recognition Based on Efficient Sclera Segmentation and Significant Vessel Matching
Authors: Xu Dong , Dong Wei , Zhou Han
Published: April 2020

The visible blood vein in sclera has unique characteristics for each person, and it can be captured in visible light conditions. Therefore, the sclera vessels have been used as an important feature to improve the performance of identification recognition systems, for example, mobile payment and phone encryption system. But recent studies show that unsatisfactory sclera segmentation and tedious matching process are the two critical issues to degrade the performance of sclera identification system. In this paper, we propose a robust sclera recognition system with high accuracy and efficiency. First, a novel sclera segmentation method that provides adaptive threshold is proposed. Second, we have designed an improved vessels enhancement method based on the local grey distribution and local texture information, and least square linearization and moment invariants are utilized to extract features. Finally, an efficient matching strategy is put forward based on the detected significant vessels. The experimental results on one database with images captured in colour illumination prove that the proposed sclera recognition method has an obvious improvement regarding efficiency and accuracy over other sclera recognition systems.
Public-Key Encryption In The Standard Model Against Strong Leakage Adversary
Authors: Alawatugoda Janaka
Published: April 2020

Over the years, security against adaptively chosen-ciphertext attacks (CCA2) is considered as the strongest security definition for public-key encryption schemes. With the uprise of side-channel attacks, new security definitions are proposed, addressing leakage of secret keys together with the standard CCA2 definition. Among the new security definitions, security against continuous and after-the-fact leakage-resilient CCA2 can be considered as the strongest security definition, which is called as security against (continuous) adaptively chosen-ciphertext leakage attacks (continuous CCLA2). In this paper, we present a construction of a public-key encryption scheme, namely LR-PKE, which satisfies the aforementioned security definition. The security of our public-key encryption scheme is proven in the standard model, under decision BDH assumption. Thus, we emphasize that our public-key encryption scheme LR-PKE is (continuous) CCLA2-secure in the standard model. For our construction of LR-PKE, we have used a strong one-time signature scheme and a leakage-resilient refreshing protocol as underlying building blocks. The leakage bound is $0.15n\log p -1$ bits per leakage query, for a security parameter $k$ and a statistical security parameter $n$, such that $\log p \geq k$ and $n$ is a function of $k$. It is possible to see that LR-PKE is efficient enough to be used for real-world usage.
Automated generation of gene summaries at the Alliance of Genome Resources
Authors: Kishore Ranjana , Arnaboldi Valerio , Van Slyke Ceri E , Chan Juancarlos , Nash Robert S , Urbano Jose M , Dolan Mary E , Engel Stacia R , Shimoyama Mary , Sternberg Paul W , Genome Resources the Alliance of
Published: April 2020

Short paragraphs that describe gene function, referred to as gene summaries, are valued by users of biological knowledgebases for the ease with which they convey key aspects of gene function. Manual curation of gene summaries, while desirable, is difficult for knowledgebases to sustain. We developed an algorithm that uses curated, structured gene data at the Alliance of Genome Resources (Alliance; www.alliancegenome.org) to automatically generate gene summaries that simulate natural language. The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies and Alliance orthology data. The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene. To improve readability of the summaries when numerous gene annotations are present, we developed a new algorithm that traverses ontology graphs in order to group terms by their common ancestors. The algorithm optimizes the coverage of the initial set of terms and limits the length of the final summary, using measures of information content of each ontology term as a criterion for inclusion in the summary. The automated gene summaries are generated with each Alliance release, ensuring that they reflect current data at the Alliance. Our method effectively leverages category-specific curation efforts of the Alliance member databases to create modular, structured and standardized gene summaries for seven member species of the Alliance. These automatically generated gene summaries make cross-species gene function comparisons tenable and increase discoverability of potential models of human disease. In addition to being displayed on Alliance gene pages, these summaries are also included on several MOK gene pages.
Totally minimally invasive esophagectomy versus hybrid minimally invasive esophagectomy: systematic review and meta-analysis
Authors: van Workum Frans , Klarenbeek Bastiaan R , Baranov Nikolaj , Rovers Maroeska M , Rosman Camiel
Published: April 2020

Minimally invasive esophagectomy is increasingly performed for the treatment of esophageal cancer, but it is unclear whether hybrid minimally invasive esophagectomy (HMIE) or totally minimally invasive esophagectomy (TMIE) should be preferred. The objective of this study was to perform a meta-analysis of studies comparing HMIE with TMIE. A systematic literature search was performed in MEDLINE, Embase, and the Cochrane Library. Articles comparing HMIE and TMIE were included. The Newcastle–Ottawa scale was used for critical appraisal of methodological quality. The primary outcome was pneumonia. Sensitivity analysis was performed by analyzing outcome for open chest hybrid MIE versus total TMIE and open abdomen MIE versus TMIE separately. Therefore, subgroup analysis was performed for laparoscopy-assisted HMIE versus TMIE, thoracoscopy-assisted HMIE versus TMIE, Ivor Lewis HMIE versus Ivor Lewis TMIE, and McKeown HMIE versus McKeown TMIE. There were no randomized controlled trials. Twenty-nine studies with a total of 3732 patients were included. Studies had a low to moderate risk of bias. In the main analysis, the pooled incidence of pneumonia was 19.0% after HMIE and 9.8% after TMIE which was not significantly different between the groups (RR: 1.46, 95% CI: 0.97–2.20). TMIE was associated with a lower incidence of wound infections (RR: 1.81, 95% CI: 1.13–2.90) and less blood loss (SMD: 0.78, 95% CI: 0.34–1.22) but with longer operative time (SMD:-0.33, 95% CI: −0.59—-0.08). In subgroup analysis, laparoscopy-assisted HMIE was associated with a higher lymph node count than TMIE, and Ivor Lewis HMIE was associated with a lower anastomotic leakage rate than Ivor Lewis TMIE. In general, TMIE was associated with moderately lower morbidity compared to HMIE, but randomized controlled evidence is lacking. The higher leakage rate and lower lymph node count that was found after TMIE in sensitivity analysis indicate that TMIE can also have disadvantages. The findings of this meta-analysis should be considered carefully by surgeons when moving from HMIE to TMIE.
Disturbance of Fatty Acid Desaturation Mediated by FADS2 in Mesenteric Adipocytes Contributes to Chronic Inflammation of Crohn’s Disease
Authors: Liu Ruiqing , Qiao Shuaihua , Shen Weisong , Liu Yue , Lu Yun , Liangyu Huang , Guo Zhen , Gong Jianfeng , Shui Guanghou , Li Yi , Zhu Weiming
Published: April 2020

Background and Aims

The aim of this study was to investigate the metabolic profile of mesenteric adipocytes and the correlations between key metabolic changes and local inflammation in the context of Crohn’s disease [CD].

Methods

Metabolic dysfunction was shown to be regulated by fatty acid desaturase-2 [FADS2], through metabolomics and functional analyses of mesenteric adipose tissue biopsies and primary mesenteric adipocytes isolated from surgical specimens collected from CD patients and control subjects. FADS2 was overexpressed in vitro and in vivo using a lentiviral vector and an adeno-associated virus [AAV], respectively. The interaction between mesenteric adipocytes and inflammation responses was evaluated by establishing a cell coculture system and a FADS2-AAV treated animal model; 3T3-L1 cells were used to elucidate the mechanism underlying FADS2 deregulation.

Results

We observed significant changes in the levels of metabolites involved in the multi-step synthesis of long-chain polyunsaturated fatty acids [PUFAs]. Gas chromatography analysis revealed impaired desaturation fluxes towards the n-6 and n-3 pathways, which are associated with reduced FADS2 activity in human mesentery tissue. Decreased FADS2 expression at both mRNA and protein levels was confirmed in surgical specimens. The restoration of FADS2 expression, which allows for the endogenous conversion of n-3 fatty acids into proresolving lipid mediators, resulted in a significant reduction in pro-inflammatory macrophage infiltration and attenuated expression of inflammatory cytokines or adipokines.

Conclusions

These findings indicate that impaired fatty acid desaturation and lipid mediator imbalance within mesenteric adipose tissue contributes to chronic inflammation in CD. The therapeutic role of FADS2 may lead to improved CD treatment.
Incidence, Risk Factors and Outcomes of Cancer of the Anal Transitional Zone in Patients with Ulcerative Colitis
Authors: Horio Yuki , Uchino Motoi , Bando Toshihiro , Sasaki Hirofumi , Goto Yoshiko , Kuwahara Ryuichi , Minagawa Tomohiro , Takesue Yoshio , Ikeuchi Hiroki
Published: April 2020

Background and Aims

Performing a mucosectomy with a hand-sewn ileal pouch-anal anastomosis [IPAA] for ulcerative colitis [UC] theoretically reduces the risk of carcinoma arising from the anal transitional zone [ATZ]. Although current guidelines suggest a stapled anastomosis due to the low incidence of cancer after pouch surgery in UC patients, only a few small series have addressed the oncological advantage of mucosectomy. Therefore, we aimed to investigate the incidence of ATZ/pouch cancer.

Methods

A total of 1970 UC patients who underwent surgery between April 1987 and December 2018 were included. We retrospectively analysed the incidences of primary ATZ cancer in the original operative specimen and de novo ATZ/pouch cancer after surgery. Possible risk factors for primary ATZ cancer and the pouch survival rate were assessed.

Results

Fourteen [6.4%] primary ATZ cancers developed in 220 UC-colorectal cancer [CRC] cases. Multiple (odds ratio [OR] = 8.79, 95% confidence interval [CI] 2.77–27.83, p < 0.01) and rectal [OR = 6.48, 95% CI 1.41–29.7, p = 0.01] cancers were identified as independent risk factors for primary ATZ cancer. Four of 1970 [0.2%] patients developed de novo ATZ/pouch cancer and dysplasia. The 10-year estimated cumulative pouch survival rate was not significantly different between stapled IPAA and hand-sewn IPAA cases [95.9% and 97.3%, p = 0.25].

Conclusion

The risk of de novo ATZ/pouch cancer and dysplasia was rare. The decision to perform a hand-sewn or a stapled IAA should be made on a case-by-case basis. However, the relatively high incidence of primary ATZ cancer in UC patients with CRC suggests that mucosectomy should be recommended for this patient group.
Behavioral and Electroantennographic Responses of Adults of Guava Weevil, Conotrachelus dimidiatus (Coleoptera: Curculionidae), to Synthetic Host-Associated and Conspecific Volatiles
Authors: García-Díaz Esmeralda , Tafoya Felipe , Elizalde-González María P
Published: April 2020

Immature guava fruits (Psidium guajava L.) of commercial orchards in Mexico are affected by adults of Conotrachelus dimidiatus (Champion) causing economic losses to producers. The aim of this study was to assess the behavioral and electrophysiological responses of the weevil to selected semiochemicals emitted by the host plant fruit and to conspecifics. Volatile organic compounds isolated from host plant as β-caryophyllene, (S)-(−)-limonene, hexanal, and nonanal significantly attracted adults of both sexes in behavioral bioassays. Electroantennogram recordings showed largest responses to papayanal and grandlure III + IV released by C. dimidiatus and C. nenuphar, respectively. Our results indicate that behavioral and electroantennographic assays using synthetic compounds from host plant volatiles and insect volatile pheromones produce olfactometry and electroantennographic responses in C. dimidiatus. This is the first report of intraspecific chemical communication in this weevil. We discuss the significance of these responses for the natural behavior in guava orchards and their potential use in a pest management strategy.
Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry
Authors: Feldmann Mitchell J , Hardigan Michael A , Famula Randi A , López Cindy M , Tabb Amy , Cole Glenn S , Knapp Steven J
Published: April 2020

Background

Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuously variable trait and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the Principal Progression of k Clusters (PPKC). We use these human-recognizable shape categories to select quantitative features extracted from multiple morphometric analyses that are best fit for genetic dissection and analysis.

Results

We transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered 4 principal shape categories, and inferred progression using PPKC. We extracted 68 quantitative features from digital images of strawberries using a suite of morphometric analyses and multivariate statistical approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68% to 99% for the newly created phenotypic variables for describing a shape.

Conclusions

Our results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches that we applied in strawberry should apply to other fruits, vegetables, and specialty crops.
AE event rate characteristics of flawed granite: from damage stress to ultimate failure
Authors: Zhang Jian-Zhi , Zhou Xiao-Ping
Published: April 2020

Uniaxial compression tests with combined acousto-optical monitoring techniques are conducted on flawed granite specimens, with the aim of investigating the fracture-related acoustic emission (AE) event rate characteristics at the unstable cracking phase in flawed rocks. The interevent time (IET) function F(τ) is adopted to interpret the AE time-series from damage stress (σcd) to ultimate failure, and photographic data are used to evaluate unstable cracking behaviours in flawed granite. The results show that a high AE event rate is always registered but intermittently interrupted by macrofracturing at the unstable cracking phase. The reversed U-shaped curve relation between the AE event rate and the loading time is documented in unstable flawed granite for the first time. The acoustic quiescence has a mechanismic linkage and quantitative correlation with stress drop, and this synchronous acousto-mechanical behaviour is a typical result of the initiation, growth and coalescence of macrocracks initiated from the flaw tips. Moreover, the reactivation and intensification of fracture process zones (FPZs) by increasing loads are the dominant mechanism triggering unstable crack growth in flawed granite.
Multi-path Allocation Scheduling Optimization Algorithm for Network Data Traffic Based on SDN Architecture
Authors: Lu Lihua
Published: April 2020

The explosive growth of network data traffic puts new demands on traffic scheduling. In this paper, the scheduling algorithm based on the software-defined network (SDN) architecture is studied. Firstly, the SDN architecture was introduced, then an SDN-based adaptive multi-path load balancing algorithm was proposed and finally the algorithm was simulated on the Mininet simulation platform to compare the performance of the proposed algorithm and traditional equal-cost multi-path routing algorithm by using Ryu as the controller. It was found that the proposed algorithm had greater throughput, higher bandwidth utilization and shorter transmission time in allocation scheduling of network data traffic, which could effectively reduce network congestion and ensure the reliability of the network. This study verifies the effectiveness of the proposed method in allocation scheduling of network data traffic and provides some theoretical bases for the further application of the SDN architecture-based allocation scheduling algorithm.
Enhancing Quality Using the Inspection Program (EQUIP): A Primer for Radiologists
Authors: Gerlach Karen E , Phalak Kanchan , Parikh Jay R
Published: April 2020

The new Enhancing Quality Using the Inspection Program (EQUIP) law places more responsibility for quality assurance on the interpreting radiologists and the lead interpreting physician (LIP). Compliance with the law will require addressing three specific questions related to quality assurance and clinical image corrective action, continued compliance, and ensuring LIP oversight. This process enables the radiologist to exemplify added value through physician leadership, team integration, and improved patient care.
Infection of the Pacific saury Cololabis saira (Brevoort, 1856) (Teleostei: Beloniformes: Scomberesocidae) by Pennella sp. (Copepoda: Siphonostomatoida: Pennellidae) south of the Subarctic Front
Authors: Suyama Satoshi , Kakehi Shigeho , Yanagimoto Takashi , Chow Seinen
Published: April 2020

The Pacific saury (Cololabis saira) is a fish of commercial importance subject to unpredictable epidemics of infection by Pennella sp., a parasitic copepod. We analyzed the distribution of fish presenting with newly attached Pennella to determine the region and season in which Pennella first infect the fish. Pacific sauries migrate northward in the spring to spend the summer in the subarctic region, successively crossing the Subarctic Boundary (SAB) and the Subarctic Front (SAF). The fish then return to subtropical waters in the fall and overwinter there. Pacific sauries infected with Pennella were observed on both the north and south sides of the SAF from May to December. Newly attached Pennella, however, were observed mainly to the south of the SAF during the northward migration of the fish in May and June, and only to the south of the SAB during the southward migration in November and December. These results indicate that the intermediate host or hosts of Pennella inhabit the region south of the SAF, with infection of Pacific saury occurring during late fall and spring. Such information may assist in identifying the intermediate host(s).
Induction of Heat Shock Protein Genes is the Hallmark of Egg Heat Tolerance in Agasicles hygrophila (Coleoptera: Chrysomelidae)
Authors: Jia Dong , Liu Yan-Hong , Zhang Bin , Ji Zhou-Yu , Wang Yuan-Xin , Gao Ling-ling , Ma Rui-Yan
Published: April 2020

Insects are ecotothermic organisms. Their development, survival, reproduction as well as distribution and abundance are affected by temperature. Heat shock protein (HSP) gene expression is closely associated with temperature variation and influences the adaptation of organisms to adverse environments. The beetle Agasicles hygrophila has successfully been used for biological control of the invasive plant alligator weed (Alternanthera philoxeroides). As A. hygrophila populations are substantially inhibited by high temperatures in the summer, increasing global temperatures may limit the efficacy of this control agent. We previously established that A. hygrophila eggs have low tolerance to heat and this factored into the decreased numbers of A. hygrophila beetles at temperatures of 37.5°C and above. Here, we identified 26 HSP genes in A. hygrophila and examined the relationship between the transcript levels of these genes and heat tolerance. The temperature at which the expression of these 21 HSP genes peaked (Tpeak) was 37.5°C, which is in line with the limit of the high temperatures that A. hygrophila eggs tolerate. Therefore, we speculate that the Tpeak of HSP gene expression in eggs indicates the upper limit of temperatures that A. hygrophila eggs tolerate. This study identifies HSP genes as potential robust biomarkers and emphasizes that determining species’ heat tolerance in their natural habitats remains an important consideration for biocontrol. HSP gene expression data provide information about a species’ heat tolerance and may be used to predict its geographical distribution.
Longitudinal Associations Between Pain and Psychosocial Adjustment in Youth With Spina Bifida
Authors: Ohanian Diana M , Murray Caitlin B , Shirkey Kezia C , Wartman Elicia C , Winning Adrien M , Stiles-Shields Colleen , Ramirez Sonia B , Holmbeck Grayson N
Published: April 2020

Objective

This study examined: (a) the nature and prevalence of pain in youth with spina bifida (SB) (b) common coping responses to pain, and (c) longitudinal, bi-directional associations between internalizing symptoms and pain characteristics.

Methods

Data were collected from youth (N = 140, 53.6% female, ages 8–15 at Time 1) and their parents and teachers at two time points spaced 2 years apart. Youth reported on several pain characteristics and coping responses. Multiple informants reported on child internalizing symptoms. Evaluation of Aims 1–3 was based on descriptive analyses, bivariate correlations, and linear and logistic regressions.

Results

About 25% of the sample reported chronic pain (e.g., experiencing pain one or more times per week over the past 3 months) at Time 1 or 2, with roughly one-third of this chronic pain subsample reporting chronic pain both time points. Pain was usually rated as mild in intensity for the full sample and most commonly experienced in the head, abdomen, and back, and described as “aching.” Youth with chronic pain reported significantly higher pain intensity and tended to use condition-specific methods to cope with pain (e.g., taking off braces). In 2 of 10 analyses, internalizing symptoms at Time 1 were associated with chronic pain and pain intensity at Time 2.

Conclusions

Roughly one-fourth of youth with SB are at risk for experiencing chronic pain, highlighting the need for increased assessment and treatment of pain in this population. Youth psychological functioning appears to more often precede, rather than being a consequence of pain symptoms.
Practical Considerations for a Military Whole Blood Program
Authors: Bahr Marshall , Cap Andrew P , Dishong Devin , Yazer Mark H
Published: April 2020

Introduction

Prehospital care in the combat environment has always been of great importance to the U.S. military, and trauma resuscitation has remained a cornerstone. More evidence continues to demonstrate the advantages of intervention with early transfusion of blood products at the point of injury. The military has recognized these benefits; as such, the Department of Defense Joint Trauma System and the Committee on Tactical Combat Casualty Care have developed new advanced resuscitation guidelines, which now encourage the use of whole blood (WB) in the prehospital setting.

Materials and Methods

This general review of peer-reviewed journal articles was performed through an extensive electronic search from the databases of PubMed Central (MEDLINE) and the Cochrane Library.

Results

Based on this literature search, the current evidence suggests that transfusion with WB is safe and efficacious. Additionally, soldier function is preserved after donating fresh WB in the field. Currently, the collection and implementation of WB is accomplished through several different protocol-driven techniques.

Conclusion

WB has become the favored transfusion product as it provides all of the components of blood in a convenient package that is easy to store and transport. Specifically, group O WB containing low titers of anti-A and -B antibodies has become the transfusion product of choice, offering the ability to universally fluid resuscitate patients despite not knowing their blood group. This new ability to obtain low titer group O WB has transformed the approach to the management of hemorrhagic shock in the prehospital combat environment.
Assessment of supervised machine learning for atmospheric retrieval of exoplanets
Authors: Nixon Matthew C , Madhusudhan Nikku
Published: April 2020

Atmospheric retrieval of exoplanets from spectroscopic observations requires an extensive exploration of a highly degenerate and high-dimensional parameter space to accurately constrain atmospheric parameters. Retrieval methods commonly conduct Bayesian parameter estimation and statistical inference using sampling algorithms such as Markov chain Monte Carlo or Nested Sampling. Recently several attempts have been made to use machine learning algorithms either to complement or to replace fully Bayesian methods. While much progress has been made, these approaches are still at times unable to accurately reproduce results from contemporary Bayesian retrievals. The goal of this work is to investigate the efficacy of machine learning for atmospheric retrieval. As a case study, we use the Random Forest supervised machine learning algorithm which has been applied previously with some success for atmospheric retrieval of the hot Jupiter WASP-12b using its near-infrared transmission spectrum. We reproduce previous results using the same approach and the same semi-analytic models, and subsequently extend this method to develop a new algorithm that results in a closer match to a fully Bayesian retrieval. We combine this new method with a fully numerical atmospheric model and demonstrate excellent agreement with a Bayesian retrieval of the transmission spectrum of another hot Jupiter, HD 209458b. Despite this success, and achieving high computational efficiency, we still find that the machine learning approach is computationally prohibitive for high-dimensional parameter spaces that are routinely explored with Bayesian retrievals with modest computational resources. We discuss the trade-offs and potential avenues for the future.
Asymmetric distributions of H2O and SiO masers towards V627 Cas
Authors: Yang Haneul , Cho Se-Hyung , Yun Youngjoo , Yoon Dong-Hwan , Kim Dong-Jin , Kim Hyosun , Yoon Sung-Chul , Dodson Richard , Rioja María J , Imai Hiroshi
Published: April 2020

We performed simultaneous observations of the $\rm H_2O$ 61,6 − 52,3 (22.235080 GHz) and SiO v = 1, 2, J = 1 → 0, SiO v = 1, J = 2 → 1, 3 → 2 (43.122080, 42.820587, 86.243442, and 129.363359 GHz) masers towards the suspected D-type symbiotic star, V627 Cas, using the Korean VLBI Network. Here, we present astrometrically registered maps of the $\rm H_2O$ and SiO v = 1, 2, J = 1 → 0, SiO v = 1, J = 2 → 1 masers for five epochs from January 2016 to June 2018. Distributions of the SiO maser spots do not show clear ring-like structures, and those of the $\rm H_2O$ maser are biased towards the north–north-west to west with respect to the SiO maser features according to observational epochs. These asymmetric distributions of $\rm H_2O$ and SiO masers are discussed based on two scenarios of a bipolar outflow and the presence of the hot companion, a white dwarf, in V627 Cas. We carried out ring fitting of SiO v = 1, and v = 2 masers and estimated the expected position of the cool red giant. The ring radii of the SiO v = 1 maser are slightly larger than those of the SiO v = 2 maser, as previously known. Our assumption for the physical size of the SiO maser ring of V627 Cas to be the typical size of a SiO maser ring radius (∼4 au) of red giants yields the distance of V627 Cas to be ∼1 kpc.
Non-thermal models for infrared flares from Sgr A*
Authors: Petersen Eric , Gammie Charles
Published: April 2020

Recent observations with mm very long baseline interferometry (mm-VLBI) and near-infrared (NIR) interferometry provide mm images and NIR centroid proper motion for Sgr A*. Of particular interest are the NIR flares that have more than an order of magnitude higher flux density than the quiescent state. Here, we model the flares using time-dependent, axisymmetric, general relativistic magnetohydrodynamic (GRMHD) simulations with an electron distribution function that includes a small, variable, non-thermal component motivated by magnetic reconnection models. The models simultaneously match the observed mm mean flux density, mm image size, NIR quiescent flux density, NIR flare flux density, and NIR spectral slope. They also provide a better fit to the observed NIR flux density probability density function than previously reported models by reproducing the power-law tail at high flux density, though with some discrepancy at low flux density. Further, our modelled NIR image centroid shows very little movement: centroid excursions of more than 10 μas (the resolution of GRAVITY) are rare and uncorrelated with flux.
Relationship Between Preoperative Opioid Use and Postoperative Pain in Patients Undergoing Minimally Invasive Stand-Alone Lateral Lumbar Interbody Fusion
Authors: Kim Song , Ozpinar Alp , Agarwal Nitin , Hacker Emily , Alan Nima , Okonkwo David O , Kanter Adam S , Hamilton D Kojo
Published: April 2020

BACKGROUND

Opioid use in the management of pain secondary to spinal disorders has grown significantly in the United States. However, preoperative opioid use may complicate recovery in patients undergoing surgical procedures.

OBJECTIVE

To test our hypothesis that prolonged preoperative opioid use may lead to poorer patient outcomes following minimally invasive stand-alone lateral lumbar interbody fusion (LLIF) for lumbar degenerative disc disease.

METHODS

A consecutive series of patients from a single institution undergoing LLIF between December 2009 and January 2017 was retrospectively analyzed. Patients were categorized according to the presence or absence of prescribed preoperative opioid use for at least 3 mo. Outcomes included the Oswestry Disability Index (ODI), visual analog scale (VAS), and Short Form 36 Physical and Mental Summary Scores (SF-36 PCS, SF-36 MCS).

RESULTS

Of 107 patients, 57 (53.1%) were prescribed preoperative opioids. There was no significant difference in preoperative ODI, VAS score, SF-36 PCS, or SF-36 MCS between opioid use groups. Mean postoperative ODI was greater in patients with preoperative opioid use at 41.7 ± 16.9 vs 22.2 ± 16.0 (P = .002). Mean postoperative VAS score was greater in patients prescribed preoperative opioids, while magnitude of decrease in VAS score was greater in opioid-naïve patients (P = .001). Postoperative SF-36 PCS was 33.1 ± 10.6 in the opioid use group compared to 43.7 ± 13.1 in the nonuse group (P = .001).

CONCLUSION

Following LLIF, patients prescribed preoperative opioids had increased postoperative lumbar pain, disability, and subjective pain.
The social brain in female autism: a structural imaging study of twins
Authors: Cauvet Élodie , van’t Westeinde Annelies , Toro Roberto , Kuja-Halkola Ralf , Neufeld Janina , Mevel Katell , Bölte Sven
Published: April 2020

A female advantage in social cognition (SoC) might contribute to women’s underrepresentation in autism spectrum disorder (ASD). The latter could be underpinned by sex differences in social brain structure. This study investigated the relationship between structural social brain networks and SoC in females and males in relation to ASD and autistic traits in twins. We used a co-twin design in 77 twin pairs (39 female) aged 12.5 to 31.0 years. Twin pairs were discordant or concordant for ASD or autistic traits, discordant or concordant for other neurodevelopmental disorders or concordant for neurotypical development. They underwent structural magnetic resonance imaging and were assessed for SoC using the naturalistic Movie for the Assessment of Social Cognition. Autistic traits predicted reduced SoC capacities predominantly in male twins, despite a comparable extent of autistic traits in each sex, although the association between SoC and autistic traits did not differ significantly between the sexes. Consistently, within-pair associations between SoC and social brain structure revealed that lower SoC ability was associated with increased cortical thickness of several brain regions, particularly in males. Our findings confirm the notion that sex differences in SoC in association with ASD are underpinned by sex differences in brain structure.
A Rat Liver Transcriptomic Point of Departure Predicts a Prospective Liver or Non-liver Apical Point of Departure
Authors: Johnson Kamin J , Auerbach Scott S , Costa Eduardo
Published: April 2020

Identifying a toxicity point of departure (POD) is a required step in human health risk characterization of crop protection molecules, and this POD has historically been derived from apical endpoints across a battery of animal-based toxicology studies. Using rat transcriptome and apical data for 79 molecules obtained from Open TG-GATES (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System) (632 datasets), the hypothesis was tested that a short-term exposure, transcriptome-based liver biological effect POD (BEPOD) could estimate a longer-term exposure “systemic” apical endpoint POD. Apical endpoints considered were body weight, clinical observation, kidney weight and histopathology and liver weight and histopathology. A BMDExpress algorithm using Gene Ontology Biological Process gene sets was optimized to derive a liver BEPOD most predictive of a systemic apical POD. Liver BEPODs were stable from 3 h to 29 days of exposure; the median fold difference of the 29-day BEPOD to BEPODs from earlier time points was approximately 1 (range: 0.7–1.1). Strong positive correlation (Pearson R = 0.86) and predictive accuracy (root mean square difference = 0.41) were observed between a concurrent (29 days) liver BEPOD and the systemic apical POD. Similar Pearson R and root mean square difference values were observed for comparisons between a 29-day systemic apical POD and liver BEPODs derived from 3 h to 15 days of exposure. These data across 79 molecules suggest that a longer-term exposure study apical POD from liver and non-liver compartments can be estimated using a liver BEPOD derived from an acute or subacute exposure study.