bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Summary
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

AbstractBackground and AimsThe 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].MethodsMetabolic 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.ResultsWe 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.ConclusionsThese 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

Abstract

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 &lt; 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

AbstractImmature 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

Abstract

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

SUMMARYUniaxial 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

AbstractThe 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

Abstract
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

Abstract
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

AbstractInsects 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

Abstract

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

AbstractIntroductionPrehospital 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 MethodsThis 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.ResultsBased 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.ConclusionWB 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.