bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and isotopic evidence of the distribution of nitrogen-cycling microbial communities in the oxygen minimum zone of the Tropical Mexican Pacific
Authors: Pajares Silvia , Soto-Jiménez Martín F , Merino-Ibarra Martín 
Published: September 2019

Abstract
Microbial communities play a central role in the N cycle of oceanic oxygen minimum zones (OMZs), such as in the Eastern Tropical North Pacific (ETNP). We explored the spatial distribution of the genetic potential for ammonia oxidation (amoA gene for bacteria and archaea), denitrification (nirS and nirK), anammox (hzo) and DNRA (nrfA) and their relationships with the hydrological variables and isotopic composition of nitrate in the ETNP off Mexico. Oxygen concentration, the availability of N chemical forms and the upwelling shaped the distribution of N cycling genes along the water column. The high abundance of N genes and the isotopic composition of nitrate suggest the N cycling is very dynamic in the OMZ core. The accumulation of nitrite, the high abundance of archaeal amoA genes, and the deviation of the N and O isotopes of nitrate from the expected 1:1 ratio for nitrate reduction in the upper portion of this OMZ indicate that nitrification is a relevant process that fuels the denitrifier community. Conversely, the high abundances of nitrate, ammonium, and nrfA genes in the deeper layer indicate that DNRA is a crucial process enhancing anammox there. These results show the need for more detailed studies of the N processes in OMZs.
Detection of Mycobacterium tuberculosis lipoarabinomannan and CFP-10 (Rv3874) from urinary extracellular vesicles of tuberculosis patients by immuno-PCR
Authors: Dahiya Bhawna , Khan Anish , Mor Preeti , Kamra Ekta , Singh Netrapal , Gupta Krishna B , Sheoran Abhishek , Sreenivas Vishnubhatla , Mehta Promod K 
Published: September 2019

ABSTRACT
Extracellular vesicles (EVs), the small circulating vesicles released from urine samples of tuberculosis (TB) patients, contain a pool of biomarkers. We recently detected Mycobacterium tuberculosis lipoarabinomannan (LAM) and CFP-10 (Rv3874) biomarkers from the urinary EVs of pulmonary TB (PTB) and extrapulmonary TB (EPTB) patients by immuno-polymerase chain reaction (I-PCR) assay and the results were compared with the analogous enzyme-linked immunosorbent assay (ELISA). The detection limits of both purified LAM and CFP-10 were determined to be 1 fg/mL with I-PCR, which was 106 times lower than ELISA. Detection of LAM and CFP-10 biomarkers in urinary EVs of TB patients by I-PCR showed superiority over ELISA. Notably, LAM I-PCR revealed sensitivities of 74.3 and 67.9% in PTB (n = 74) and EPTB (n = 53) patients, respectively, with specificities of 91.5–92.8% (n = 116). Moreover, the sensitivities attained with LAM I-PCR were significantly higher (P &lt; 0.01) than with CFP-10 I-PCR. After further improving the sensitivity and specificity of the assay, our I-PCR based on LAM detection in urinary EVs may be used as an adjunct test for rapid diagnosis of TB.
Between Modernity and Nostalgia: The Meanings of Death in Hotels
Authors: Zitzlsperger Ulrike 
Published: September 2019

Abstract
This article takes its cue from the public impact of the deaths of singers, artists and writers in hotels. Particular attention is paid to the murder of Nancy Spungen in New York’s Chelsea Hotel, in 1978. A long tradition of literary and filmic hotel deaths shows similarly strong links with contemporary cultures – illustrating political, social or cultural change and questioning the impact of modernity. However, as well as responding to change, death in the context of hotels is also linked with nostalgia for an irretrievable past. Such are the two poles of cultural criticism in the topos of hotel deaths: they throw modernity into relief, celebrating or criticizing it through the symbolic structure of the hotel; or they inculcate a warm nostalgia, in critical opposition to the world outside on the street. The individual authors and directors under consideration here in exploring these points include Joseph Roth, Vicki Baum, F. W. Murnau, Giuseppi Tomasi di Lampedusa and Friedrich Glauser, highlighting the importance of the theme straddling American and European cultures.
Knots and Solenoids that Cannot Be Attractors of Self-homeomorphisms of ℝ3
Authors: Barge H , Sánchez-Gabites J J 
Published: September 2019

AbstractAs a 1st step to understand how complicated attractors for dynamical systems can be, one may consider the following realizability problem: given a continuum $K \subseteq \mathbb{R}^3$, decide when $K$ can be realized as an attractor for a homeomorphism of $\mathbb{R}^3$. In this paper we introduce toroidal sets as those continua $K \subseteq \mathbb{R}^3$ that have a neighbourhood basis comprised of solid tori and, generalizing the classical notion of genus of a knot, give a natural definition of the genus of toroidal sets and study some of its properties. Using these tools we exhibit knots and solenoids for which the answer to the realizability problem stated above is negative.
Transcriptional Activator OvrA Encoded in O Island 19 Modulates Virulence Gene Expression in Enterohemorrhagic Escherichia coli O157:H7
Authors: Liu Bin , Wang Junyue , Wang Lu , Ding Peng , Yang Pan , Yang Bin 
Published: September 2019

AbstractThe human intestinal pathogen enterohemorrhagic Escherichia coli (EHEC) O157:H7 causes bloody diarrhea, hemorrhagic colitis, and fatal hemolytic uremic syndrome. Its genome contains 177 unique O islands (OIs), which contribute largely to the high virulence and pathogenicity although most OI genes remain uncharacterized. In the current study, we demonstrated that OI-19 is required for EHEC O157:H7 adherence to host cells. Z0442 (OI-encoded virulence regulator A [OvrA]) encoded in OI-19 positively regulated bacterial adherence by activating locus of enterocyte effacement (LEE) gene expression through direct OvrA binding to the gene promoter region of the LEE gene master regulator Ler. Mouse colonization experiments revealed that OvrA promotes EHEC O157:H7 adherence in mouse intestine, preferentially the colon. Finally, OvrA also regulated virulence in other non-O157 pathogenic E. coli, including EHEC strains O145:H28 and O157:H16 and enteropathogenic E. coli strain O55:H7. Our work markedly enriches the understanding of bacterial adherence control and provides another example of laterally acquired regulators that mediate LEE gene expression.
A step closer to nationwide electronic health record–based chronic disease surveillance: characterizing asthma prevalence and emergency department utilization from 100 million patient records through a novel multisite collaboration
Authors: Tarabichi Yasir , Goyden Jake , Liu Rujia , Lewis Steven , Sudano Joseph , Kaelber David C 
Published: September 2019

Abstract

Objective
The study sought to assess the feasibility of nationwide chronic disease surveillance using data aggregated through a multisite collaboration of customers of the same electronic health record (EHR) platform across the United States.

Materials and Methods
An independent confederation of customers of the same EHR platform proposed and guided the development of a program that leverages native EHR features to allow customers to securely contribute de-identified data regarding the prevalence of asthma and rate of asthma-associated emergency department visits to a vendor-managed repository. Data were stratified by state, age, sex, race, and ethnicity. Results were qualitatively compared with national survey-based estimates.

Results
The program accumulated information from 100 million health records from over 130 healthcare systems in the United States over its first 14 months. All states were represented, with a median coverage of 22.88% of an estimated state’s population (interquartile range, 12.05%-42.24%). The mean monthly prevalence of asthma was 5.27 ± 0.11%. The rate of asthma-associated emergency department visits was 1.39 ± 0.08%. Both measures mirrored national survey-based estimates.

Discussion
By organizing the program around native features of a shared EHR platform, we were able to rapidly accumulate population level measures from a sizeable cohort of health records, with representation from every state. The resulting data allowed estimates of asthma prevalence that were comparable to data from traditional epidemiologic surveys at both geographic and demographic levels.

Conclusions
Our initiative demonstrates the potential of intravendor customer collaboration and highlights an organizational approach that complements other data aggregation efforts seeking to achieve nationwide EHR-based chronic disease surveillance.
Preparation of single-chain Fv antibodies in the cytoplasm of Escherichia coli by simplified and systematic chaperone optimization
Authors: Liu Chenjiang , Kobashigawa Yoshihiro , Yamauchi Soichiro , Toyota Yuya , Teramoto Manaka , Ikeguchi Yuka , Fukuda Natsuki , Sato Takashi , Sato Yuko , Kimura Hiroshi , Morioka Hiroshi 
Published: September 2019

Abstract
A single-chain variable fragment (scFv) antibody is a recombinant protein in which a peptide linker connects the variable regions of the heavy chain and light chain. Due to its smaller molecular size, an scFv can be expressed using Escherichia coli. The presence of two disulphide bonds in the molecule often prevents expression of correctly folded scFv in the E. coli cytoplasm, making a refolding process necessary to regenerate scFv activity. The refolding process is time-consuming and requires large amounts of expensive reagents, such as guanidine hydrochloride, l-arginine and glutathione. Here, to conveniently obtain scFv proteins, we devised a simple and systematic method to optimize the co-expression of chaperone proteins and to combine them with specially engineered E. coli strains that permit the formation of stable disulphide bonds within the cytoplasm. Several scFv proteins were successfully obtained in a soluble form from E. coli cytoplasm. Thermal denaturation experiments and/or surface plasmon resonance measurements revealed that the thus-obtained scFvs possessed a stable tertiary structure and antigen-binding activity. The combined use of engineered E. coli with the simplified and systematic chaperone optimization can be useful for the production of scFv proteins.
The Achmea Judgment and the Applicability of the Energy Charter Treaty in Intra-EU Investment Arbitration
Authors: Basedow J Robert 
Published: September 2019

Abstract
The Energy Charter Treaty is the most frequently used investment treaty worldwide to launch investment arbitration against host states. The vast majority of disputes is of intra-European Union nature in that they involve an EU investor as claimant and an European Union member state as respondent. The recent Achmea judgment of the Court of Justice of the European Union may thus have ramifications for the Energy Charter Treaty. The judgment has triggered a heated legal and political debate within the European Union over the future of intra-European Union investment arbitration. In the context of this debate, the European Commission claimed that the application of the Energy Charter Treaty in intra-European Union investment disputes is based on an incorrect interpretation of this treaty. This article critically assesses the Commission’s statement by evaluating the travaux préparatoires of the Energy Charter Treaty as a supplementary means of interpretation. It finds that the European Union member states and the European Commission in all likelihood opted for a mixed ratification for legal reasons rather than to ensure its intra-European Union applicability. Indeed, the EU initially pushed for a disconnection clause to prevent the application of the Energy Charter Treaty in intra-European Union relations but dropped this request during the negotiations. At least from a historical perspective then, the Commission’s claim that the Energy Charter Treaty is not meant to apply in intra-European Union relations is inaccurate in that the European Union consciously accepted this possibility.
A continent-scale study of the social structure and phylogeography of the bent-wing bat, Miniopterus schreibersii (Mammalia: Chiroptera), using new microsatellite data
Authors: Gürün Kanat , Furman Andrzej , Juste Javier , Ramos Pereira Maria J , Palmeirim Jorge M , Puechmaille Sebastien J , Hulva Pavel , Presetnik Primoz , Hamidovic Daniela , Ibáñez Carlos , Karataş Ahmet , Allegrini Benjamin , Georgiakakis Panagiotis , Scaravelli Dino , Uhrin Marcel , Nicolaou Haris , Abi-Said Mounir R , Nagy Zoltan L , Gazaryan Suren , Bilgin Raşit 
Published: September 2019

AbstractMiniopterus schreibersii is a cave-dwelling bat species with a wide distribution in the western Palearctic spanning southern and central Europe, North Africa, Anatolia, the Middle East, and the Caucasus. We investigated the social structure and its effects on the genetic makeup of this species, using 10 nuclear microsatellite markers and a partial fragment of the mitochondrial cytochrome b gene. Samples were examined from the species' entire circum-Mediterranean range. Local structuring that was previously detected among populations of M. schreibersii using mitochondrial markers was not observed for microsatellite markers, indicating male-biased dispersal for the species. Some support was found for postglacial expansions in Europe, with Anatolia potentially acting as the primary refugium during the Last Glacial Maximum (LGM). However, support for this hypothesis is not as strong as that previously detected using mitochondrial DNA markers. This is likely due to the diminishing effect of male-mediated dispersal, replenishing the nuclear diversity faster than the mitochondrial diversity in regions that are relatively far from the glacial refugia.
Factors Associated With Oncologist Discussions of the Costs of Genomic Testing and Related Treatments
Authors: Yabroff K Robin , Zhao Jingxuan , de Moor Janet S , Sineshaw Helmneh M , Freedman Andrew N , Zheng Zhiyuan , Han Xuesong , Rai Ashish , Klabunde Carrie N 
Published: September 2019

AbstractBackgroundUse of genomic testing is increasing in the United States. Testing can be expensive, and not all tests and related treatments are covered by health insurance. Little is known about how often oncologists discuss costs of testing and treatment or about the factors associated with those discussions.MethodsWe identified 1220 oncologists who reported discussing genomic testing with their cancer patients from the 2017 National Survey of Precision Medicine in Cancer Treatment. Multivariable polytomous logistic regression analyses were used to assess associations between oncologist and practice characteristics and the frequency of cost discussions. All statistical tests were two-sided.ResultsAmong oncologists who discussed genomic testing with patients, 50.0% reported often discussing the likely costs of testing and related treatments, 26.3% reported sometimes discussing costs, and 23.7% reported never or rarely discussing costs. In adjusted analyses, oncologists with training in genomic testing or working in practices with electronic medical record alerts for genomic tests were more likely to have cost discussions sometimes (odds ratio [OR] = 2.09, 95% confidence interval [CI] = 1.19 to 3.69) or often (OR = 2.22, 95% CI = 1.30 to 3.79), respectively, compared to rarely or never. Other factors statistically significantly associated with more frequent cost discussions included treating solid tumors (rather than only hematological cancers), using next-generation sequencing gene panel tests, having higher patient volume, and working in practices with higher percentages of patients insured by Medicaid, or self-paid or uninsured.ConclusionsInterventions targeting modifiable oncologist and practice factors, such as training in genomic testing and use of electronic medical record alerts, may help improve cost discussions about genomic testing and related treatments.
Combined Therapy With Hyperbaric Oxygen and Melatonin Effectively Reduce Brain Infarct Volume and Preserve Neurological Function After Acute Ischemic Infarct in Rat
Authors: Lin Kun-Chen , Chen Kuan-Hung , Wallace Christopher Glenn , Chen Yi-Ling , Ko Sheung-Fat , Lee Mel S , Yip Hon-Kan 
Published: September 2019

AbstractThis study tested the hypothesis that combined hyperbaric oxygen (HBO) and melatonin (Mel) was superior to either one for protecting the brain functional and parenchymal integrity from acute ischemic stroke (IS) injury. Adult-male Sprague-Dawley rats were divided into groups 1 (sham-operated control), 2 (IS), 3 (IS + HBO), 4 (IS + Mel), and 5 (IS + HBO-Mel). By day 28 after IS, the brain infarct area (BIA) was lowest in group 1, highest in group 2, significantly higher in groups 3 and 4 than in group 5, but not different between groups 3 and 4. The neurological function at day 7, 14, and 28 exhibited an opposite pattern to BIA among the 5 groups. The protein expressions of inflammatory (IL-1β/IL-6/iNOS/TNF-α/p-NF-κB), apoptotic (cleaved-caspase3/cleaved-PARP/mitochondrial Bax), mitochondrial/DNA-damaged (cytochrome-C/γ-H2AX), oxidative stress (NOX-1/NOX-2), and autophagy (i.e. ratio of CL3B-II/CL3B-I) biomarkers displayed an identical pattern of BIA among 5 groups. Cellular expressions of inflammation (F4/80+/GFAP+) and DNA-damaged biomarker (γ-H2AX+) exhibited an identical pattern, whereas the integrities of myelin sheath/neuron (MPB+/NeuN+), endothelial cell (CD31+/vWF+), and number of small vessels exhibited an opposite pattern of BIA among the 5 groups. Combined HBO-Mel therapy offered an additional benefit in protecting the brain against IS injury.
Cumulative cellulolytic enzyme activities and initial litter quality in prediction of cellulose degradation in an alpine meadow of the eastern Tibetan Plateau
Authors: Chen Yamei , Liu Yang , Zhang Jian , Yang Wanqin , Deng Changchun , He Runlian 
Published: September 2019

AbstractAimsPlant litter decomposition is a key ecosystem process that determines carbon and nutrient cycling in terrestrial ecosystems. As a main component of litter, cellulose is a vital energy source for the microbes associated with litter decomposition. The important role of cellulolytic enzymes in litter cellulose degradation is well understood, but seasonal patterns of cellulose degradation and whether cumulative enzyme activities and litter quality forecast cellulose degradation in an alpine meadow remain elusive, which limits our understanding of cellulose degradation in herbaceous plant litter.MethodsA two-year field litterbag experiment involving three dominant species (Ajuga ovalifolia, Festuca wallichanica, and Pedicularis roylei) was conducted in an alpine meadow of the eastern Tibetan Plateau to explore the seasonal patterns of cellulose degradation and how cumulative cellulolytic enzyme activities and initial litter quality impact cellulose degradation.Important findingsOur study demonstrates that cellulose degraded rapidly and exceeded 50% during the first year, which mainly occurred in the first growing season (31.9%–43.3%). At two years of decomposition, cellulose degradation was driven by cumulative endoglucanase (R2 = 0.70), cumulative cellobiohydrolase (R2 = 0.59) and cumulative 1,4-β-glucosidase (R2 = 0.57). In addition, the concentrations of cellulose, dissolved organic carbon, total phenol, lignin and lignin/N accounted for 52%–78% of the variation in cellulose degradation during the two years of decomposition. The best model for predicting cellulose degradation was the initial cellulose concentration (R2 = 0.78). The enzymatic efficiencies and the allocation of cellulolytic enzyme activities were different among species. The cellulolytic enzyme efficiencies were higher in the litter of F. wallichanica with relatively lower quality. For the complete cellulose degradation of the leaf litter, A. ovalifolia and F. wallichanica required 4-fold and 6.7-fold more endoglucanase activity, 3-fold and 4.5-fold more cellobiohydrolase activity and 1.2-fold and 1.4-fold more 1,4-β-glucosidase activity, respectively, than those required by P. roylei. Our results demonstrated that although microbial activity and litter quality both have significant impacts on cellulose degradation in an alpine meadow, using cellulose concentration to predict cellulose degradation is a good way to simplify the model of cellulose degradation and C cycling during litter decomposition.
Iatrogenic injury to a vesicourachal diverticulum during laparoscopic appendectomy successfully managed conservatively
Authors: Alobaysi Saad , Alsairi Saud , Aljasser Abdullah , Alkhaddam Ahmad , Alshamrani Abdullah 
Published: September 2019

Abstract
A vesicourachal diverticulum is a rare congenital anomaly that arises from the incomplete closure of the urachus at the bladder end. We describe a 12-year-old boy who presented with severe persistent right iliac fossa pain associated with subjective fever, nausea, vomiting, and anorexia. A computed tomography (CT) scan of the abdomen and pelvis revealed findings consistent with appendicitis. The patient underwent a laparoscopic appendectomy; however, his postoperative course was remarkable for a low urine output and urine leakage from the suprapubic port site. A CT cystography showed a vesicourachal diverticulum and conservative management was offered. This management consisted of Foley catheter placement, hourly monitoring of the patient’s urine output, antibiotic prophylaxis, daily laboratory investigations and a cystography performed after 7 days. Overall, injury to the vesicourachal diverticulum is rare, and surgeons should be aware of this rare clinical entity and exercise caution during port placement. Surgeons should also have a high index of suspicion to identify these injuries and appropriately manage the condition early.
The presence of interstellar scintillation in the 15 GHz interday variability of 1158 OVRO-monitored blazars
Authors: Koay J Y , Jauncey D L , Hovatta T , Kiehlmann S , Bignall H E , Max-Moerbeck W , Pearson T J , Readhead A C S , Reeves R , Reynolds C , Vedantham H 
Published: September 2019

ABSTRACTWe have conducted the first systematic search for interday variability in a large sample of extragalactic radio sources at 15 GHz. From the sample of 1158 radio-selected blazars monitored over an ∼10 yr span by the Owens Valley Radio Observatory 40-m telescope, we identified 20 sources exhibiting significant flux density variations on 4-d time-scales. The sky distribution of the variable sources is strongly dependent on the line-of-sight Galactic H α intensities from the Wisconsin H α Mapper Survey, demonstrating the contribution of interstellar scintillation (ISS) to their interday variability. 21 per cent of sources observed through sightlines with H α intensities larger than 10  rayleighs exhibit significant ISS persistent over the ∼10 yr period. The fraction of scintillators is potentially larger when considering less significant variables missed by our selection criteria, due to ISS intermittency. This study demonstrates that ISS is still important at 15 GHz, particularly through strongly scattered sightlines of the Galaxy. Of the 20 most significant variables, 11 are observed through the Orion–Eridanus superbubble, photoionized by hot stars of the Orion OB1 association. The high-energy neutrino source TXS 0506+056 is observed through this region, so ISS must be considered in any interpretation of its short-term radio variability. J0616−1041 appears to exhibit large ∼20 per cent interday flux density variations, comparable in magnitude to that of the very rare class of extreme, intrahour scintillators that includes PKS0405−385, J1819+3845, and PKS1257−326; this needs to be confirmed by higher cadence follow-up observations.