bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread Use of High-dose Ceftriaxone Therapy for Uncomplicated Gonorrhea Without Reported Ceftriaxone Treatment Failure: Results From 5 Years of Multicenter Surveillance Data in China
Authors: Han Yan , Yin Yueping , Dai Xiuqin , Chen Shaochun , Yang Ligang , Zhu Bangyong , Zhong Na , Cao Wenling , Zhang Xiaohui , Wu Zhizhou , Yuan Liufeng , Zheng Zhongjie , Feng Lishan , Liu Jun , Chen Xiangsheng 
Published: February 2019

AbstractBackgroundAntimicrobial resistance to Neisseria gonorrhoeae has emerged for each of the antibiotics recommended as first-line therapies following their introduction into clinical practice. To improve rational and effective clinical antibiotic treatment, we analyzed the prescription patterns of antibiotics and their therapeutic effect in the treatment of uncomplicated gonorrhea in China.MethodsWe obtained data from a follow-up multicenter surveillance program. Multinomial logistic regression analyses were conducted to explore the associations between demographic/clinical variables with the levels of sensitivity to ceftriaxone and prescription of high-dose ceftriaxone.ResultsIn this study, 1686 patients infected with N. gonorrhoeae were recruited in a surveillance network during 1 January 2013 through 31 December 2017 in 7 hospitals distributed in 5 provinces. The prevalence of isolates with decreased susceptibility to ceftriaxone was 9.8% (131/1333), fluctuating between 5.6% and 12.1%. Injectable ceftriaxone was chosen as the first-line treatment among 83.1% of patients, and most of them (72.7% [1018/1401]) received &gt;1000 mg dosage. Patients who were previously infected with gonorrhea or other sexually transmitted infections (adjusted odds ratio [AOR], 1.618 [95% confidence interval {CI}, 1.11–2.358]; AOR, 2.08 [95% CI, 1.41–3.069]) or who already used antibiotics for this infection (AOR, 1.599 [95% CI, 1.041–2.454]) were associated with a higher prescribed ceftriaxone dosage. All of the patients recruited in this study were cured regardless of the isolates’ susceptibility to ceftriaxone or the dosage of ceftriaxone they received.ConclusionsNo ceftriaxone treatment failure for uncomplicated gonorrhea was reported in China; however, high-dose ceftriaxone was widely used in China. Its impacts need further study.
A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England
Authors: Ludden Catherine , Moradigaravand Danesh , Jamrozy Dorota , Gouliouris Theodore , Blane Beth , Naydenova Plamena , Hernandez-Garcia Juan , Wood Paul , Hadjirin Nazreen , Radakovic Milorad , Crawley Charles , Brown Nicholas M , Holmes Mark , Parkhill Julian , Peacock Sharon J 
Published: February 2019

Abstract

Background
Klebsiella pneumoniae is a human, animal, and environmental commensal and a leading cause of nosocomial infections, which are often caused by multiresistant strains. We evaluate putative sources of K. pneumoniae that are carried by and infect hospital patients.

Methods
We conducted a 6-month survey on 2 hematology wards at Addenbrooke’s Hospital, Cambridge, United Kingdom, in 2015 to isolate K. pneumoniae from stool, blood, and the environment. We conducted cross-sectional surveys of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer, and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. Isolates were sequenced and their genomes compared.

Results
Klebsiella pneumoniae was isolated from stool of 17/149 (11%) patients and 18/922 swabs of their environment, together with 1 bloodstream infection during the study and 4 others over a 24-month period. Each patient carried 1 or more lineages that was unique to them, but 2 broad environmental contamination events and patient–environment transmission were identified. Klebsiella pneumoniae was isolated from cattle, poultry, hospital sewage, and 12/20 wastewater treatment plants. There was low genetic relatedness between isolates from patients/their hospital environment vs isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from humans/environment and elsewhere but were carried on different plasmids.

Conclusion
We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans. However, our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection.
Prognostic significance of sarcopenia in patients undergoing esophagectomy for superficial esophageal squamous cell carcinoma
Authors: Oguma J , Ozawa S , Kazuno A , Yamamoto M , Ninomiya Y , Yatabe K 
Published: February 2019

SUMMARY
Nononcological prognostic factors in superficial esophageal squamous cell carcinoma (SESCC) patients remain unclear. The aim of this study is to evaluate the relationship between sarcopenia and surgical outcome in patients with SESCC who had undergone definitive surgery. A total of 194 SESCC patients who had undergone thoracic esophagectomy with three-field lymphadenectomy without neoadjuvant therapy at Tokai University Hospital between January 2006 and December 2015 were analyzed retrospectively. Manual tracing using CT imaging was used to measure the cross-sectional areas of the skeletal muscle mass. The cutoff values for the skeletal muscle index used to define sarcopenia were based on the results of a previous study. Twenty-eight patients (14.4%) had sarcopenia, while the remaining 166 patients (85.6%) did not. A multivariate analysis suggested that sarcopenia was an independent risk factor for postoperative pulmonary complications (OR = 3.232, P = 0.026). The overall survival rate and the disease-free survival rate were both significantly worse in the sarcopenia group than in the nonsarcopenia group (P < 0.001). In a multivariate analysis, sarcopenia was an independent prognostic factor affecting overall survival (HR = 7.121, P < 0.001) and disease-free survival (HR = 6.000, P < 0.001). Patients with sarcopenia and lymph node metastasis (n = 18) had a worse outcome than the other patients (P < 0.001). This study suggests that the alleviation of sarcopenia through nutritional support and rehabilitation in SESCC patients scheduled to undergo surgery might help to prevent postoperative pulmonary complications and to improve the long-term outcome.
Survival probability of dental autotransplantation of 366 teeth over 34 years within a hospital setting in the United Kingdom
Authors: Abela Stefan , Murtadha Linda , Bister Dirk , Andiappan Manoharan , Kwok Jerry 
Published: February 2019

Summary

Introduction
The purpose of this retrospective study was to evaluate 34 years’ experience of autotransplantation of teeth during orthodontic treatment.

Methodology
Treatment was completed at Queen Mary’s Hospital, Sidcup, Kent, UK, during the period 1969–2003. A total of 366 teeth were transplanted in 314 patients.

Results
Canines totalled 78 per cent of all autotransplanted teeth; mean age of patient was 19.4 years. Survival probability for the first 5 years post-autotransplantation was 95 per cent, 94 per cent for the subsequent 5 years, and 88 per cent after 15 years. The maximum observation period was 34 years, the median was 2.0 years, and the mean was 3.51 (standard deviation = 3.68) years. Of the observed teeth, 10 failed and these were lost due to unsuccessful periodontal ligament regeneration and persistent mobility grade III (or greater). Apical pathology was observed in 16 per cent of all autotransplanted teeth. In 79 per cent of this subgroup, apical pathology was evident in the first 3 years post-operatively. Seventy per cent of all external resorption also occurred within the first 3 years. Internal resorption was rare but its occurrence was mostly observed between the second and sixth year post-transplantation. A minority of autotransplanted teeth [14 per cent (n = 51)] needed root canal therapy, and this was completed within the first 6 months post-transplantation.

Conclusions
Autotransplantation can be a justified procedure with good survival probability. It can be considered an alternative to other treatments, such as prosthodontic replacement of teeth.
Torsional Alfvén waves in a dipolar magnetic field: experiments and simulations
Authors: Tigrine Z , Nataf H-C , Schaeffer N , Cardin P , Plunian F 
Published: February 2019

SUMMARY
The discovery of torsional Alfvén waves (geostrophic Alfvén waves) in the Earth’s core (Gillet et al. 2010) calls for a better understanding of their properties. We present the first experimental observations of torsional Alfvén waves, performed in the DTS-Ω set-up. In this set-up, 50 L of liquid sodium are confined between an inner sphere (ri = 74 mm) and an outer shell (ro = 210 mm). The inner sphere houses a permanent magnet, imposing a dipolar magnetic field (Bmax = 345 mT). Both the inner sphere and the outer shell can rotate around the vertical axis. Alfvén waves are triggered by a sudden jerk of the inner sphere. We study the propagation of these waves when the fluid is initially at rest, and when it spins at a rotation rate up to 15 Hz. We measure the azimuthal magnetic field of the wave at different radii inside the fluid with magnetometers installed in a sleeve. We also record the electric potential signature on the outer shell at several latitudes. Besides, we probe the associated azimuthal velocity field using ultrasound Doppler velocimetry. With a 15 Hz rotation rate, the dynamical regimes we achieve are characterized by dimensionless numbers in the following ranges: Lundquist number 0.5 < Lu < 12, Lehnert number 0.01 < Le < 0.26, Rossby number Ro ∼ 0.1.
We observe that the magnetic signal propagates away from the inner sphere, strongly damped by magnetic diffusion. Rotation affects the magnetic signature in a subtle way. Its effect is more pronounced on the surface electric potentials, which are sensitive to the actual fluid velocity of the wave. The ultrasound Doppler probes provide the first experimental measurement of the fluid velocity of an Alfvén wave.
To complement these observations, we ran numerical simulations, using the XSHELLS pseudospectral code with parameters as close as possible to the experimental ones. The synthetic magnetic and electric signals match our measurements. The meridional snapshots of the synthetic azimuthal velocity field reveal the formation of geostrophic cylinders expected for torsional Alfvén waves.
We establish scaling laws for the magnetic and kinetic energies of Alfvén waves with and without rotation. In both cases, we find that the magnetic energy EM saturates at a level proportional to $Rm_{\rm jerk}^2$, where Rmjerk = Ujerkro/η is the magnetic Reynolds number built with the maximum azimuthal velocity of the inner sphere during the jerk. The $E_K^{\rm max}/E_M^{\rm max}$ ratio (where $E_K^{\rm max}$ is the maximum kinetic energy), close to 1 for very quick jerks, increases linearly with the jerk duration.
Efficacy of Vedolizumab for Refractory Pouchitis of the Ileo-anal Pouch: Results From a Multicenter US Cohort
Authors: Gregory Martin , Weaver Kimberly N , Hoversten Patrick , Hicks Stephen Bradley , Patel Devin , Ciorba Matthew A , Gutierrez Alexandra M , Beniwal-Patel Poonam , Palam Sowmya , Syal Gaurav , Herfarth Hans H , Christophi George , Raffals Laura , Barnes Edward L , Deepak Parakkal 
Published: February 2019

Abstract

Background and Aims
Inflammation of the pouch after ileal pouch-anal anastomosis (IPAA) can significantly impact quality of life and be difficult to treat. We assessed the effectiveness and safety of vedolizumab in Crohn’s disease (CD) of the pouch and chronic antibiotic-dependent or antibiotic-refractory pouchitis.

Methods
This was a retrospective, multicenter cohort study at 5 academic referral centers in the United States. Adult patients with endoscopic inflammation of the pouch who received vedolizumab were included. The primary outcome was clinical response at any time point. Secondary outcomes included clinical remission, endoscopic response, and remission. Univariate analysis and multivariate analysis were performed for the effect of the following variables on clinical response: fistula, onset of pouchitis less than 1 year after IPAA, younger than 35 years old, gender, previous tumor necrosis factor inhibitor-alpha use, and BMI &gt;30.

Results
Eighty-three patients were treated with vedolizumab for inflammation of the pouch between January 2014 and October 2017. Median follow-up was 1.3 years (interquartile range 0.7–2.1). The proportion of patients that achieved at least a clinical response was 71.1%, with 19.3% achieving clinical remission. Of the 74 patients with a follow-up pouchoscopy, the proportion of patients with endoscopic response and mucosal healing was 54.1% and 17.6%, respectively. Patients who developed pouchitis symptoms less than 1 year after undergoing IPAA were less likely to respond to vedolizumab, even after controlling for other risk factors.

Conclusions
Vedolizumab is safe and effective in the management of CD of the pouch and chronic pouchitis. Further studies are needed to compare vedolizumab with other biologic therapies for pouchitis and CD of the pouch.
Job Flexibility and Occupational Selection in Ghana: An Application of Maximum Simulated Likelihood†
Authors: Lain Jonathan 
Published: February 2019

Abstract
In many African labour markets, the vast majority of self-employed workers are female. It is often hypothesised that self-employment enables workers to balance income-generation with caring for children and other domestic tasks and, since responsibility for these activities is divided unequally in the household, this effect is stronger for women than men. However, testing whether ‘job flexibility’ matters is difficult because variables that proxy for domestic obligations—such as the number of dependents in the household—may be endogenous to occupational choice. In this paper, we build a new estimator using maximum simulated likelihood that allows us to use selection on observables as a guide to selection on unobservables within the multinomial choice problem individuals face when deciding their occupation. We apply this approach to detailed cross-sectional data from Ghana. Our results show that having extra dependents in the household pushes women towards own account self-employment substantially more than men, even under more conservative assumptions about the extent of endogeneity.
Crystal structure of bacterial cyclopropane-fatty-acyl-phospholipid synthase with phospholipid
Authors: Ma Yulong , Pan Chunli , Wang Qihai 
Published: February 2019

AbstractThe lipids containing cyclopropane-fatty-acid (CFA) protect bacteria from adverse conditions such as acidity, freeze-drying desiccation and exposure to pollutants. CFA is synthesized when cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase, CFAS) transfers a methylene group from S-adenosylmethionine (SAM) across the cis double bonds of unsaturated fatty acyl chains. Here, we reported a 2.7-Å crystal structure of CFAS from Lactobacillus acidophilus. The enzyme is composed of N- and C-terminal domain, which belong to the sterol carrier protein and methyltransferase superfamily, respectively. A phospholipid in the substrate binding site and a bicarbonate ion (BCI) acting as a general base in the active site were discovered. To elucidate the mechanism, a docking experiment using CFAS from L. acidophilus and SAM was carried out. The analysis of this structure demonstrated that three groups, the carbons from the substrate, the BCI and the methyl of S(CHn)3 group, were close enough to form a cyclopropane ring with the help of amino acids in the active site. Therefore, the structure supports the hypothesis that CFAS from L. acidophilus catalyzes methyl transfer via a carbocation mechanism. These findings provide a structural basis to more deeply understand enzymatic cyclopropanation.
Response to a Synthetic Pheromone Source by OX4319L, a Self-Limiting Diamondback Moth (Lepidoptera: Plutellidae) Strain, and Field Dispersal Characteristics of its Progenitor Strain
Authors: Bolton Michael , Collins Hilda L , Chapman Tracey , Morrison Neil I , Long Stefan J , Linn Charles E , Shelton Anthony M 
Published: February 2019

AbstractThe diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae), is a global pest that infests vegetable and field crops within the Brassica family. A genetically engineered strain of P. xylostella, OX4319L, carrying a ‘self-limiting’ gene, has shown potential for managing P. xylostella populations, using sustained releases of OX4319L male moths. In order for such a strain to provide control, the transgenic individuals must exhibit attraction to female P. xylostella sex pheromone and adequate dispersal in the field. In this study, we tested these key traits. First, we compared the responses of the OX4319L male moths to a synthetic female sex pheromone source in wind tunnel trials to those of males from three other strains. We found that OX4319L males responded comparably to strains of non-engineered males, with all males flying upwind towards the pheromone source. Second, we used mark-release-recapture studies of a wildtype P. xylostella strain, from which the OX4319L strain was originally developed, to assess dispersal under field conditions. Released males were recaptured using both pheromone-baited and passive traps within a 2.83 ha circular cabbage field, with a recapture rate of 7.93%. Males were recaptured up to the boundary of the field at 95 m from the central release point. The median dispersal of males was 14 m. These results showed the progenitor strain of OX4319L retained its ability to disperse within a host field. The results of these experiments are discussed in relation to the potential for the effective use of engineered male-selecting P. xylostella strains under field conditions.
How Efficient Is Fertilization by Traumatic Insemination in Orius insidiosus (Hemiptera: Anthocoridae)?
Authors: Vacacela Ajila Henry E , Michaud J P , Abdelwahab Ahmed H , Kuchta Sara V , Stowe Hannah E 
Published: February 2019

AbstractTraumatic insemination (TI) can be injurious to females, and females have evolved various paragenital structures to mitigate these impacts. We examined the mating behavior of Orius insidiosus (Say) and the consequences of single and double matings for female fitness. A total of 100 virgin females (4–6-d old) were directly observed while they mated with virgin males. Some of these females were mated a second time with a different, nonvirgin male 3–5 d later, after they oviposited in sunflower stems. Females were held in isolation, fed eggs of Ephestia kuehniella Zeller, and reproductive success was tracked for 30 d. Six females died during their first copulation (6%), and another within 48 h, without laying eggs. Four percent of the females died during their second copulations. Copulations lasting less than 90 s usually did not result in successful fertilization, and duration of copula was positively correlated with egg fertility in singly-mated females. Duration of copula was more than halved in second matings, twice as variable, and negatively correlated with 30 d fecundity. Thirty-seven percent of singly-mated females and 31% of twice-mated females were infertile, with fewer than half of all females producing 88% of all eggs. We conclude that O. insidiosus females are likely monandrous in the wild, and that TI in this species is inefficient, contributing to high variation in female fitness. Thus, mating involves a significant mortality risk for females, despite their possession of complex paragenital structures that ostensibly mitigate copulatory injury.
The prognostic signature of the somatic mutations in Ewing sarcoma: from a network view
Authors: Zhang Yuehui , Song Jia , Shi Qili , Song Xupu , Shen Libing , Zhou Jingqi , Shao Jiang 
Published: February 2019

AbstractBackgroundEwing sarcoma is a malignant bone tumor mainly affecting teenagers and young adults. Its main driver mutation, the EWS-FLI1 fusion gene, has been identified more than 20 years ago, whereas its other somatic mutations have been just recently reported.MethodsIn this study, we organized the somatic mutations from 216 Ewing sarcoma cases into 216 individual protein–protein interaction networks by using interactome information. These mutation networks were then classified into five different clusters based on their structural similarities. The prognostic effect of mutation genes was evaluated according to their network features.ResultsThe cases in cluster two exhibited remarkably high metastasis and mortality rates, and STAG2, TP53 and TTN were the three most significantly mutated genes in this cluster. Microarray data demonstrate that the expression of STAG2, TP53 and TTN are down-regulated in the EWS-FLI1-knockdown Ewing sarcoma cells. However, the mutation effect analysis shows that the somatic mutations in TTN are less damaging than those in STAG2 and TP53. The analyses of functional network modules further revealed that STAG2, TP53 and their interacting gene partners participate in the oncogenic-related biological modules such as cell cycle and regulation of transcription from RNA polymerase II promoter while TTN, TP53 and their interacting gene partners constitute the modules less relevant to oncogenesis. The results of Gene Ontology analyses demonstrated that the uniquely mutated genes associated with poor prognosis in Clusters 1, 4 and 5 were distinctively enriched in epidermal growth factor-related functions and phosphoproteins.ConclusionsOur study identified the highly lethal mutation combination cases and characterized the possible prognostic genes in Ewing sarcoma from a network perceptive.
Practical method of cell segmentation in electron microscope image stack using deep convolutional neural network☆
Authors: Konishi Kohki , Mimura Masafumi , Nonaka Takao , Sase Ichiro , Nishioka Hideo , Suga Mitsuo 
Published: February 2019

Abstract
Segmentation of three-dimensional (3D) electron microscopy (EM) image stacks is an arduous and tedious task. Deep convolutional neural networks (CNNs) work well to automate the segmentation; however, they require a large training dataset, which is a major impediment. In order to solve this issue, especially for sparse segmentation, we used a CNN with a minimal training dataset. We segmented a Cerebellar Purkinje cell from an image stack of a mouse Cerebellum cortex in less than two working days, which is much shorter than that of the conventional method. We concluded that we can reduce the total labor time for the sparse segmentation by reducing the training dataset.
Structural biology of plant sulfur metabolism: from sulfate to glutathione
Authors: Jez Joseph M 
Published: February 2019

AbstractSulfur is an essential element for all organisms. Plants must assimilate this nutrient from the environment and convert it into metabolically useful forms for the biosynthesis of a wide range of compounds, including cysteine and glutathione. This review summarizes structural biology studies on the enzymes involved in plant sulfur assimilation [ATP sulfurylase, adenosine-5'-phosphate (APS) reductase, and sulfite reductase], cysteine biosynthesis (serine acetyltransferase and O-acetylserine sulfhydrylase), and glutathione biosynthesis (glutamate-cysteine ligase and glutathione synthetase) pathways. Overall, X-ray crystal structures of enzymes in these core pathways provide molecular-level information on the chemical events that allow plants to incorporate sulfur into essential metabolites and revealed new biochemical regulatory mechanisms, such as structural rearrangements, protein–protein interactions, and thiol-based redox switches, for controlling different steps in these pathways.