bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scaling tree-based automated machine learning to biomedical big data with a feature set selector
Authors: Le Trang T , Fu Weixuan , Moore Jason H 
Published: June 2019

Abstract

Motivation
Automated machine learning (AutoML) systems are helpful data science assistants designed to scan data for novel features, select appropriate supervised learning models and optimize their parameters. For this purpose, Tree-based Pipeline Optimization Tool (TPOT) was developed using strongly typed genetic programing (GP) to recommend an optimized analysis pipeline for the data scientist’s prediction problem. However, like other AutoML systems, TPOT may reach computational resource limits when working on big data such as whole-genome expression data.

Results
We introduce two new features implemented in TPOT that helps increase the system’s scalability: Feature Set Selector (FSS) and Template. FSS provides the option to specify subsets of the features as separate datasets, assuming the signals come from one or more of these specific data subsets. FSS increases TPOT’s efficiency in application on big data by slicing the entire dataset into smaller sets of features and allowing GP to select the best subset in the final pipeline. Template enforces type constraints with strongly typed GP and enables the incorporation of FSS at the beginning of each pipeline. Consequently, FSS and Template help reduce TPOT computation time and may provide more interpretable results. Our simulations show TPOT-FSS significantly outperforms a tuned XGBoost model and standard TPOT implementation. We apply TPOT-FSS to real RNA-Seq data from a study of major depressive disorder. Independent of the previous study that identified significant association with depression severity of two modules, TPOT-FSS corroborates that one of the modules is largely predictive of the clinical diagnosis of each individual.

Availability and implementation
Detailed simulation and analysis code needed to reproduce the results in this study is available at https://github.com/lelaboratoire/tpot-fss. Implementation of the new TPOT operators is available at https://github.com/EpistasisLab/tpot.

Supplementary information
Supplementary data are available at Bioinformatics online.
Parallel pathways of seizure generalization
Authors: Dabrowska Natalia , Joshi Suchitra , Williamson John , Lewczuk Ewa , Lu Yanhong , Oberoi Samrath , Brodovskaya Anastasia , Kapur Jaideep 
Published: June 2019

Abstract
Generalized convulsive status epilepticus is a life-threatening emergency, because recurrent convulsions can cause death or injury. A common form of generalized convulsive status epilepticus is of focal onset. The neuronal circuits activated during seizure spread from the hippocampus, a frequent site of seizure origin, to the bilateral motor cortex, which mediates convulsive seizures, have not been delineated. Status epilepticus was initiated by electrical stimulation of the hippocampus. Neurons transiently activated during seizures were labelled with tdTomato and then imaged following brain slice clearing. Hippocampus was active throughout the episode of status epilepticus. Neuronal activation was observed in hippocampus parahippocampal structures: subiculum, entorhinal cortex and perirhinal cortex, septum, and olfactory system in the initial phase status epilepticus. The tdTomato-labelled neurons occupied larger volumes of the brain as seizures progressed and at the peak of status epilepticus, motor and somatosensory cortex, retrosplenial cortex, and insular cortex also contained tdTomato-labelled neurons. In addition, motor thalamic nuclei such as anterior and ventromedial, midline, reticular, and posterior thalamic nuclei were also activated. Furthermore, circuits proposed to be crucial for systems consolidation of memory: entorhinal cortex, retrosplenial cortex, cingulate gyrus, midline thalamic nuclei and prefrontal cortex were intensely active during periods of generalized tonic-clonic seizures. As the episode of status epilepticus waned, smaller volume of brain was activated. These studies suggested that seizure spread could have occurred via canonical thalamocortical pathway and many cortical structures involved in memory consolidation. These studies may help explain retrograde amnesia following seizures.
Vector-mediated l-3,4-dihydroxyphenylalanine delivery reverses motor impairments in a primate model of Parkinson’s disease
Authors: Rosenblad Carl , Li Qin , Pioli Elsa Y. , Dovero Sandra , Antunes André SLM , Agúndez Leticia , Bardelli Martino , Linden R. Michael , Henckaerts Els , Björklund Anders , Bezard Erwan , Björklund Tomas 
Published: June 2019

Abstract
Ever since its introduction 40 years ago l-3,4-dihydroxyphenylalanine (l-DOPA) therapy has retained its role as the leading standard medication for patients with Parkinson’s disease. With time, however, the shortcomings of oral l-DOPA treatment have become apparent, particularly the motor fluctuations and troublesome dyskinetic side effects. These side effects, which are caused by the excessive swings in striatal dopamine caused by intermittent oral delivery, can be avoided by delivering l-DOPA in a more continuous manner. Local gene delivery of the l-DOPA synthesizing enzymes, tyrosine hydroxylase and guanosine-tri-phosphate-cyclohydrolase-1, offers a new approach to a more refined dopaminergic therapy where l-DOPA is delivered continuously at the site where it is needed i.e. the striatum. In this study we have explored the therapeutic efficacy of adeno-associated viral vector-mediated l-DOPA delivery to the putamen in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated rhesus monkeys, the standard non-human primate model of Parkinson’s disease. Viral vector delivery of the two enzymes, tyrosine hydroxylase and guanosine-5’-tri-phosphate-cyclohydrolase-1, bilaterally into the dopamine-depleted putamen, induced a significant, dose-dependent improvement of motor behaviour up to a level identical to that obtained with the optimal dose of peripheral l-DOPA. Importantly, this improvement in motor function was obtained without any adverse dyskinetic effects. These results provide proof-of-principle for continuous vector-mediated l-DOPA synthesis as a novel therapeutic strategy for Parkinson’s disease. The constant, local supply of l-DOPA obtained with this approach holds promise as an efficient one-time treatment that can provide long-lasting clinical improvement and at the same time prevent the appearance of motor fluctuations and dyskinetic side effects associated with standard oral dopaminergic medication.
Breeding origins and migratory connectivity at a northern roost of Vaux’s Swift, a declining aerial insectivore
Authors: Smith Ellis L , Reudink Matthew W , Marra Peter P , Mckellar Ann E , Van Wilgenburg Steven L 
Published: June 2019

ABSTRACTPopulations of Vaux’s Swift (Chaetura vauxi), like those of many aerial insectivores, are rapidly declining. Determining when and where populations are limited across the annual cycle is important for their conservation. Establishing the linkages between wintering and breeding sites and the strength of the connections between them is a necessary first step. In this study, we analyzed 3 stable isotopes (δ13C, δ15N, δ2H) from feathers collected during spring migration from Vaux’s Swifts that perished during a stopover on Vancouver Island, British Columbia, Canada. We previously analyzed claw tissue (grown during winter) from the same individuals, revealing that the swifts likely wintered in 2 or 3 locations/habitats. Here, we used stable isotope analysis of flight feathers presumed to have been grown on, or near, the breeding grounds to determine the likely previous breeding locations and presumed destinations for the swifts. Stable isotope values (δ13C, δ15N, δ2H) showed no meaningful variation between age classes, sexes, or with body size. Surprisingly, ~26% of the birds sampled had feather isotope values that were not consistent with growth on their breeding grounds. For the remaining birds, assigned breeding origins appeared most consistent with molt origins on Vancouver Island. Overall, migratory connectivity of this population was relatively weak (rM = 0.07). However, the degree of connectivity depended on how many winter clusters were analyzed; the 2-cluster solution suggested no significant connectivity, but the 3-cluster solution suggested weak connectivity. It is still unclear whether low migratory connectivity observed for Vaux’s Swift and other aerial insectivores may make their populations more or less vulnerable to habitat loss; therefore, further efforts should be directed to assessing whether aerial insectivores may be habitat limited throughout the annual cycle.
Higher Sedation Requirements Among Inflammatory Bowel Disease Patients Undergoing Colonoscopy for Disease Activity Assessment or Dysplasia Surveillance
Authors: Weber Andrew T , Ather Nimah , Tran Vivy , Sauk Jenny , Ha Christina 
Published: June 2019

Abstract

Background and Aims
Patients with inflammatory bowel disease (IBD) require colonoscopy for diagnosis, disease activity assessment, and dysplasia surveillance. Few studies have evaluated anesthesia needs of IBD patients during procedures. This study aimed to examine sedation requirements of IBD patients undergoing colonoscopy.

Methods
A retrospective cohort study of IBD and non-IBD patients presenting for colonoscopy between August 2015 and December 2016 was undertaken. Data collected included patient and procedure focused variables. Sedation was categorized as intravenous conscious sedation (IVCS) or monitored anesthesia care (MAC).

Results: A total of
522 consecutive colonoscopies (212 IBD, 310 non-IBD) between August 2015 and December 2016 met criteria for inclusion. In total, 323 cases utilized IVCS (56 IBD, 267 non-IBD) and 196 used MAC (155 IBD, 41 non-IBD). Compared with non-IBD patients (13.2%), more IBD patients (73.1%) required MAC (P &lt; 0.01). For IVCS cases, IBD patients required more midazolam (5.73 mg versus non-IBD 4.31 mg; P &lt;0.01) and opioid (IBD 157.59 µg fentanyl equivalents versus non-IBD 119.41 µg; P &lt; 0.01). Diphenhydramine was more frequently added to IVCS for IBD cases (IBD 25.0% versus non-IBD 1.9%; P &lt; 0.01). For MAC cases, propofol dosage was not significantly different between groups (IBD 355.64 mg versus non-IBD 317.104 mg; P = 0.29). IBD colonoscopies took longer (IBD 22.7 versus non-IBD 17.2 min; P &lt; 0.01) and more patients had recent narcotic use (IBD 21.2% versus non-IBD 9.0%; P &lt; 0.01).

Conclusions
IBD patients required more IVCS, including greater diphenhydramine use with longer procedure times compared with non-IBD patients. These findings suggest MAC should be considered for IBD procedural sedation.
Evidence of Disturbed Gut Microbial Metabolic Activity in Pediatric Crohn’s Disease
Authors: Sundqvist Tommy , Stenhammar Lars , Tjellström Bo , Magnusson Karl-Eric , Midtvedt Tore , Norin Elisabeth , Högberg Lotta 
Published: June 2019

AbstractBackgroundDysbiosis, that is, disturbed gut microbial balance, is well documented in Crohn’s disease (CD). We aimed at studying CD-linked dysbiosis in children by analyzing fecal microbe-associated characteristics, previously not reported in children.MethodsThis observational study included 28 children with active CD and healthy controls. We assessed the following three indicators of gut microbiota metabolism in the feces: the presence of tryptic activity, the conversion of cholesterol to coprostanol, and the conversion of bilirubin to urobilinogen.ResultsThe fecal tryptic activity was significantly higher in children with active CD compared to the control group (P &lt; 0.01). The fecal coprostanol of the CD children was close to zero and differed significantly from the controls (P &lt; 0.001). Furthermore, the children with CD had very low fecal urobilinogen, differing significantly from the control group (P &lt; 0.001).ConclusionsThe significant differences in levels of fecal bacterial metabolites in patients with active CD compared to healthy controls reflect major perturbation of gut microbial functions and have not previously been reported in children. This fits well with the prevailing concept of a dysbiotic gut microbiota in CD and may have important clinical implications by bringing the dysbiosis back into balance.
Distribution of the Specialist Aphid Uroleucon nigrotuberculatum (Homoptera: Aphididae) in Response to Host Plant Semiochemical Induction by the Gall Fly Eurosta solidaginis (Diptera: Tephritidae)
Authors: Thomas Austin M , Williams Ray S , Swarthout Robert F 
Published: June 2019

AbstractMany plants use terpenoids and other volatile compounds as semiochemicals. Reception of plant volatiles by conspecifics may trigger a defensive phytochemical response. These same compounds can also function as host recognition signals for phytophagous insects. In this experiment, we find that when the specialist gall-forming fly Eurosta solidaginis (Fitch; Diptera: Tephritidae) attacks its tall goldenrod (Solidago altissima (L.; Asterales: Asteraceae)) host plant, the fly indirectly induces a phytochemical response in nearby tall goldenrod plants. This phytochemical response may, in turn, act as a positive signal attracting the goldenrod specialist aphid Uroleucon nigrotuberculatum (Olive; Hemiptera: Aphididae). Laboratory-based experiments exposing ungalled tall goldenrod plants to the volatiles released by E. solidaginis galls demonstrated a consistent increase in foliar terpenoid concentrations in ungalled plants. Analysis of tall goldenrod stem and gall tissue chemistry revealed induction of terpenoids in gall tissue, with a simultaneous decrease in green leaf volatile concentrations. Field experiments demonstrated a consistent spatial relationship in tall goldenrod foliar terpenoid concentrations with distance from an E. solidaginis gall. Both laboratory and field experiments establish consistent induction of the terpene β-farnesene, and that this compound is a strong positive predictor of U. nigrotuberculatum aphid presence on goldenrod plants along with plant biomass and several other foliar terpenoids. These findings suggest E. solidaginis induced phytochemistry, especially β-farnesene, may be acting as a kairomone, driving aphid distribution in the field.
Early growth, mortality, and partial migration of striped bass (Morone saxatilis) larvae and juveniles in the St. Lawrence estuary, Canada
Authors: Vanalderweireldt Lucie , Winkler Gesche , Mingelbier Marc , Sirois Pascal 
Published: June 2019

AbstractAfter being extirpated from the St. Lawrence Estuary (SLE), striped bass (Morone saxatilis) were reintroduced in 2002, and by 2008 they were naturally reproducing. The increase of this reintroduced population prompted the need to document its nursery habitats utilization, which contribute to species recruitment. We analysed mortality-dispersion rates and the growth of larvae and juveniles in relation to their occurrence and migration patterns. From June to September 2014, we collected striped bass distributed in four estuarine habitats: the upstream freshwater section (UP), the oligohaline (O-ETM) and the mesohaline (M-ETM) estuarine turbidity maximum zone, and the downstream polyhaline section (DOWN). Based on otolith microstructure and microchemistry, 305 back-calculated growth and 36 migration trajectories have been reconstructed. The UP and the O-ETM provided optimal conditions wherein which larvae and juveniles exhibited fastest growth. In the SLE, we emphasized the co-existence of a freshwater resident contingent and two migrant contingents to the M-ETM and DOWN. We propose that migrants adopt an adaptive migration behaviour to avoid suboptimal conditions and strong intraspecific competition from resident in the upstream habitats. The potential advantage of a downstream migration later in the season might be an adaptative strategy to promote their survival during the early life stages.
Dialogic remedies
Authors: Roach Kent 
Published: June 2019

Abstract
Remedies have in the past and should in the future occupy a central place in constitutional theory. It is a sign of its maturity that dialogic theories of judicial review have produced new remedies such as suspended declarations of invalidity and declarations of incompatibility. Dialogic remedies, like dialogic theories in general, are vulnerable to critiques from judicial constitutionalists that they weaken the role of courts. This article responds by outlining a two-track approach to remedies inspired in part by Alexander Bickel. In the first track, successful litigants should generally receive some tangible remedy from a court, but in the second track, courts should generally defer to the superior ability of legislatures and the executive to select among a range of systemic remedies to produce better compliance with rights in the future. Such an approach follows the aspirations of dialogic theories in drawing on the distinctive and complementary strengths of judicial and political constitutionalism. The two-track approach is applied to remedial decisions involving both laws and executive actions. Examples include a Canadian decision that employed a suspended declaration of invalidity but also allowed judicial exemptions from an assisted suicide offense and South African cases that prevent evictions and provide remedies for individual students while ordering engagement to achieve systemic housing and educational remedies.
High colonization rate of a novel carbapenem-resistant Klebsiella lineage among migratory birds at Qinghai Lake, China
Authors: Liao Xiaoping , Yang Run-Shi , Xia Jing , Chen Liang , Zhang Rongmin , Fang Liang-Xing , Lei Fumin , Song Gang , Jia Ling , Han Lu , Bai Shuancheng , Bai Rina , Sun Jian , Liu Ya-Hong 
Published: June 2019

Abstract

Objectives
The emergence of carbapenemase-positive Enterobacteriaceae poses a serious threat to public health worldwide. Here we conducted a molecular surveillance study on carbapenem-resistant Enterobacteriaceae (CRE) colonization among migratory birds at Qinghai Lake in China.

Methods
A total of 420 samples from migratory birds and their surrounding environment were collected at three sites along the Qinghai Lake bird island. Carbapenem-non-susceptible isolates were identified by 16S rDNA sequencing and MALDI-TOF MS. Carbapenemase producers were determined by Carba NP testing. Antimicrobial susceptibility testing, transfer ability and PFGE were also performed, and 46 isolates from different pulsotypes were analysed by WGS.

Results
Three hundred and fifty isolates were carbapenemase producers based on Carba NP testing, while 233 Klebsiella spp. and 2 Escherichia coli isolates were NDM-5-carriers. PFGE was performed and showed that the isolates were grouped into five pulsotypes; among these, type A was predominant (86.7%, n = 202) and belonged to a novel Klebsiella lineage, ST1697. WGS analysis indicated that ST1697 strains may be a hybrid of the recombination of Klebsiella quasipneumoniae subsp. similipneumoniae and Klebsiella pneumoniae genomes.

Conclusions
This high frequency of carbapenemase producers in migratory birds is unexpected. These results provide new insight into the spread of antibiotic resistance, and highlight that continued vigilance for MDR carbapenemase-producing Enterobacteriaceae in migratory birds is urgently needed.
Advancing health equity and access using telemedicine: a geospatial assessment
Authors: Khairat Saif , Haithcoat Timothy , Liu Songzi , Zaman Tanzila , Edson Barbara , Gianforcaro Robert , Shyu Chi-Ren 
Published: June 2019

Abstract

Introduction
Health disparity affects both urban and rural residents, with evidence showing that rural residents have significantly lower health status than urban residents. Health equity is the commitment to reducing disparities in health and in its determinants, including social determinants.

Objective
This article evaluates the reach and context of a virtual urgent care (VUC) program on health equity and accessibility with a focus on the rural underserved population.

Materials and Methods
We studied a total of 5343 patient activation records and 2195 unique encounters collected from a VUC during the first 4 quarters of operation. Zip codes served as the analysis unit and geospatial analysis and informatics quantified the results.

Results
The reach and context were assessed using a mean accumulated score based on 11 health equity and accessibility determinants calculated for each zip code. Results were compared among VUC users, North Carolina (NC), rural NC, and urban NC averages.

Conclusions
The study concluded that patients facing inequities from rural areas were enabled better healthcare access by utilizing the VUC. Through geospatial analysis, recommendations are outlined to help improve healthcare access to rural underserved populations.
Economic Valuation of Bee Pollination Services for Passion Fruit (Malpighiales: Passifloraceae) Cultivation on Smallholding Farms in São Paulo, Brazil, Using the Avoided Cost Method
Authors: Popak Allan E , Markwith Scott H 
Published: June 2019

Abstract
This paper estimates the economic value of ecosystem services provided by Brazilian native bee, Xylocopa spp. Latreille (Hymenoptera: Apidae), pollination on a scale relevant to individual smallholder farmers that produce yellow passion fruit (Passiflora edulis Sims). The study areas are located in the vicinity of Pedro de Toledo and Itariri (Sao Paulo State—Brazil), in the Atlantic Forest region. The local economy is based on family farms, small stores, and ecotourism. The value was obtained using the ecological economics Avoided Cost Method, also known as replacement cost. Farms from this region informally hire temporary day laborers to supplement natural pollination with manual pollination of passion fruit flowers, so the cost of contracting temporary laborers was used to estimate the economic value of bee pollination. The value of pollination services was estimated at US$ 2,583.00 per hectare over 2 yr of P. edulis farming. Our estimates based on passion fruit farmer surveys and ecological valuation over 2 yr suggest that manual pollination accounts for 44–48% of production costs and results in a loss of ~58% of profits when wild bee pollination services are not available and manual pollination is required. We suggest that smallholder farmers follow the suggestions of previous studies and conserve adequate forest habitat for bee nesting and foraging, plan pesticide use around flowering and pollination, and supplement bee populations to maximize the benefit of the pollination ecosystem service and profits.
Revisiting the Role of the Security Council Concerning the International Criminal Court’s Crime of Aggression
Authors: Trahan Jennifer 
Published: June 2019

Abstract
This article revisits the role of the United Nations (UN) Security Council in making referrals of the crime of aggression to the International Criminal Court (ICC). It examines the increase in significance of the role of the Security Council caused by the apparent jurisdictional limitations in the resolution activating the ICC’s jurisdiction over the crime when cases are initiated through State Party referral or proprio motu. Since these jurisdictional limitations seemingly decrease the possibility for ICC crime of aggression cases to be initiated without Security Council referral, they also render the Prosecutor less able to play a role in prevention or providing early warning regarding the crime. This increases the need for the Security Council to fulfil this prevention or early warning function, which is entirely appropriate given the Security Council’s primary responsibility under the UN Charter for the maintenance of international peace and security. The General Assembly may, although to a lesser extent, be able to play a similar role.