bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using magnetic core‐shell nanoparticles coated with an ionic liquid dispersion assisted by effervescence powder for the micro‐solid‐phase extraction of four beta blockers from human plasma by ultra high performance liquid chromatography with mass spectrometry detection
Authors: Jamshidi Sara , Rofouei Mohammad Kazem , Thorsen Gunnar 
Published: November 2018

AbstractIn this work, a novel, efficient, and green sorbent, SiO2@Fe3O4 has been created and functionalized with 1‐butyl‐3‐methylimidazolium hexafluorophosphate as an ionic liquid. This sorbent was applied for microextraction of four beta blockers, propranolol, metoprolol, atenolol, and alprenolol with bupivacaine as internal standard from human plasma followed by liquid chromatography with mass spectrometric detection. A mixture of sodium bicarbonate and sodium dihydrogen phosphate was used as an extractant dispersive agent (effervescent power) to enhance the interaction between the magnetic sorbent and analytes. Main affecting parameters on microextraction and elution were optimized. Figures of merit for dispersive solid phase extraction with ionic liquid coated magnetic nanoparticles assisted by effervescent powder were calculated under the optimized conditions. The detection limits for propranolol, metoprolol, atenolol, and alprenolol were found at 0.33, 0.62, 0.03, and 0.44 ng/mL, respectively. For all analytes, good linearity was obtained. Intra‐ (n = 5) and interday (n = 10) precision were both under 6.3% while the preconcentration factors were obtained in the range between 15–18. The extraction efficiencies for each analyte ranged from 75 to 91%. The method was successfully applied for determination of trace amounts of the beta blockers in human plasma samples.
Establishment of a highly efficient conjugation protocol for Streptomyces kanamyceticus ATCC12853
Authors: Zhang Shuman , Chen Tiansheng , Jia Jia , Guo Liwen , Zhang Huizheng , Li Chao , Qiao Renzhong 
Published: November 2018

AbstractKanamycin B as the secondary metabolite of wild‐type Streptomyces kanamyceticus (S. kanamyceticus) ATCC12853 is often used for the synthesis of dibekacin and arbekacin. To construct the strain has the ability for kanamycin B production; the pSET152 derivatives from Escherichia coli ET12567 were introduced to S. kanamyceticus by intergeneric conjugal transfer. In this study, we established a reliable genetic manipulation system for S. kanamyceticus. The key factors of conjugal transfer were evaluated, including donor‐to‐recipient ratio, heat‐shock, and the overlaying time of antibiotics. When spores were used as recipient, the optimal conjugation frequency was up to 6.7 × 10−6. And mycelia were used as an alternative recipient for conjugation instead of spores; the most suitable donor‐to‐recipient ratio is 1:1 (107:107). After incubated for only 10–12 hr and overlaid with antibiotics subsequently, the conjugation frequency can reach to 6.2 × 10−5 which is sufficient for gene knockout and other genetic operation. Based on the optimized conjugal transfer condition, kanJ was knocked out successfully. The kanamycin B yield of kanJ‐disruption strain can reach to 543.18 ± 42 mg/L while the kanamycin B yield of wild‐type strain was only 46.57 ± 12 mg/L. The current work helps improve the content of kanamycin B in the fermentation broth of S. kanamyceticus effectively to ensure the supply for the synthesis of several critical semisynthetic antibiotics.
Cycle‐consistent adversarial denoising network for multiphase coronary CT angiography
Authors: Kang Eunhee , Koo Hyun Jung , Yang Dong Hyun , Seo Joon Bum , Ye Jong Chul 
Published: November 2018

PurposeIn multiphase coronary CT angiography (CTA), a series of CT images are taken at different levels of radiation dose during the examination. Although this reduces the total radiation dose, the image quality during the low‐dose phases is significantly degraded. Recently, deep neural network approaches based on supervised learning technique have demonstrated impressive performance improvement over conventional model‐based iterative methods for low‐dose CT. However, matched low‐ and routine‐dose CT image pairs are difficult to obtain in multiphase CT. To address this problem, we aim at developing a new deep learning framework.MethodWe propose an unsupervised learning technique that can remove the noise of the CT images in the low‐dose phases by learning from the CT images in the routine dose phases. Although a supervised learning approach is not applicable due to the differences in the underlying heart structure in two phases, the images are closely related in two phases, so we propose a cycle‐consistent adversarial denoising network to learn the mapping between the low‐ and high‐dose cardiac phases.ResultsExperimental results showed that the proposed method effectively reduces the noise in the low‐dose CT image while preserving detailed texture and edge information. Moreover, thanks to the cyclic consistency and identity loss, the proposed network does not create any artificial features that are not present in the input images. Visual grading and quality evaluation also confirm that the proposed method provides significant improvement in diagnostic quality.ConclusionsThe proposed network can learn the image distributions from the routine‐dose cardiac phases, which is a big advantage over the existing supervised learning networks that need exactly matched low‐ and routine‐dose CT images. Considering the effectiveness and practicability of the proposed method, we believe that the proposed can be applied for many other CT acquisition protocols.
A Novel Technique to Assess Distal Radioulnar Joint Stability Using Increasing Torque
Authors: Nilsson Klara , Hallberg Peter , Tesselaar Erik , Farnebo Simon 
Published: November 2018

Background Previous studies on computed tomography (CT) in patients with a suspected triangular fibrocartilage complex (TFCC) injury have not been successful in assessing distal radioulnar joint (DRUJ) laxity. The aim of this study was to develop a novel servomotor-driven device for the assessment of DRUJ by applying increasing torque to the DRUJ in pronation and supination.
Methods A custom-built device was designed to function during four-dimensional (4D) CT of the wrist. A torque meter, positioned between the incoming hand holder, and a direct current (DC) servomotor were used for angular positioning and for applying rotational force to the patient's arm. A total of 110 healthy participants were recruited to gather reference values for the range of motion (ROM), maximum torque in neutral and supinated/pronated position, and the ability to withstand an increasing, device-generated torque in these positions. The device was also used during 4D DRUJ CT in five patients with suspected TFCC injuries.
Results A gender- and age-relevant reference chart for ROM and torque was created. Men showed a tendency (ns) toward having a larger ROM and increasing strength with increasing age, whereas women showed the opposite. Also, the dominant hand showed a tendency toward having a larger ROM and being stronger than the nondominant hand (ns). A smaller cohort of patients (n = 5) with suspected TFCC injuries showed a significantly decreased ability to withstand increasing torque in both supination (2.1 ± 0.3 vs. 3.1 ± 0.2 s; p < 0.005) and pronation (2.3 ± 0.5 vs. 3.1 ± 0.4 s; p < 0.0005) and also showed a clear laxity on real-time 4D CT image sequences. Decreased strength at all positions was also found (average 74% decrease compared to noninjured side).
Conclusion Reference values for torque strength and ability to withstand increasing torque can be used clinically in the assessment of patients with symptoms that could represent ligamentous injuries to the TFCC. The ability to use the device during CT enables radiographic evaluation of instability during increasing torque.
Level of Evidence This is a Level II study.
Diagnostic Imaging and Management of Common Intra-articular and Peri-articular Soft Tissue Tumors and Tumorlike Conditions of the Knee
Authors: Evenski Andrea , Stensby James , Rosas Samuel , Emory Cynthia 
Published: November 2018

AbstractIntra-articular (IA) and peri-articular (PA) tumors of the knee are frequently encountered by orthopaedic surgeons. Nonetheless, due to the possibility of great morbidity and potential mortality, it is important to recognize and differentiate between benign and malignant lesions in a timely manner. Therefore, the purpose of this article is to provide a concise, practical, and updated review of commonly encountered IA and PA tumors including intratendinous gout, synovial chondromatosis, schwannoma, pigmented villonodular synovitis, and synovial sarcoma, and a detailed description of differentiating features to include various imaging modalities.
Report of Another Mutation Proven Case of Carbonic Anhydrase II Deficiency
Authors: Satapathy Amit , Pandey Swati , Chaudhary Madhumita , Bagga Arvind , Kabra Madhulika , Uwe Kornak , Gupta Neerja 
Published: November 2018

AbstractCarbonic anhydrase (CA) II deficiency results in an uncommon type of autosomal recessive sclerosing bone dysplasia with renal tubular acidosis and intracerebral calcification. We report a classic case of CA II-associated osteopetrosis with a previously reported homozygous frameshift mutation. Child was evaluated for short stature and failure to thrive. He was diagnosed as osteopetrosis in view of the presence of hepatosplenomegaly and increased bone density though hematological parameters were normal. Further evaluation showed presence of associated distal renal tubular acidosis raising a possibility of CA II deficiency. Mutation analysis revealed a previously reported homozygous frameshift mutation c.143-146delCTGT (p.Ser48Phefs*9) in CA2.Child has normal growth after initiation of alkali therapy.
Demographics and Clinical Outcomes of Patients Undergoing Anterior Cruciate Ligament Reconstruction with a Planned or Unplanned Hybrid Graft
Authors: Kraeutler Matthew J. , Houck Darby A. , Carver Trevor J. , Bravman Jonathan T. , Vidal Armando F. , McCarty Eric C. 
Published: November 2018

AbstractThe purpose of this study was to report the demographics and clinical outcomes of patients at our institution following anterior cruciate ligament reconstruction (ACLR) with a planned or unplanned hybrid autograft–allograft. At a minimum 2-year follow-up, patients at our institution who had undergone primary ACLR with a planned (P) or unplanned (U) hybrid graft using fresh-frozen allografts were contacted to complete a survey containing the Knee Injury and Osteoarthritis Outcome Score, Subjective International Knee Documentation Committee score, Single Assessment Numeric Evaluation, 12-Item Short Form Health Survey, and visual analog scale for activity level. Demographics were compared between groups. Patient-reported outcomes (PROs) and a revision rate were reported for each group. Mean follow-up among all patients was 3.3 years. Revision rate at follow-up was 0.8 and 6.3% in the P and U groups, respectively (p = 0.03). Among patients reached for follow-up (90 P, 30 U), a lower proportion of males was found in the unplanned hybrid graft group (P: 52%, U: 23%, p < 0.01). Unplanned hybrid graft patients were significantly younger at the time of surgery (P: 41.0 years, U: 31.0 years, p < 0.0001). Graft size did not differ between groups (P: 9.1 mm, U: 8.9 mm, p = 0.11). Patients in both groups achieved moderate to high PROs. Demographics differ between patients undergoing ACLR with a planned or unplanned hybrid graft. Patients with a planned hybrid graft are at a significantly reduced risk of postoperative graft failure, likely due to the older age of this group.
Evaluation and Treatment of Alkalosis in Children
Authors: Kopač Matjaž 
Published: November 2018

AbstractAlkalosis is a disorder of acid–base balance defined by elevated pH of the arterial blood. Metabolic alkalosis is characterized by primary elevation of the serum bicarbonate. Due to several mechanisms, it is often associated with hypochloremia and hypokalemia and can only persist in the presence of factors causing and maintaining alkalosis. Respiratory alkalosis is a consequence of dysfunction of respiratory system's control center. There are no pathognomonic symptoms. History is important in the evaluation of alkalosis and usually reveals the cause. It is important to evaluate volemia during physical examination. Treatment must be causal and prognosis depends on a cause.
A NuSTAR study of the 55 ks hard X-ray pulse-phase modulation in the magnetar 4U 0142+61
Authors: Makishima Kazuo , Murakami Hiroaki , Enoto Teruaki , Nakazawa Kazuhiro 
Published: November 2018

Abstract
Archival NuSTAR data of the magnetar 4U 0142+61, acquired in 2014 March for a total time span of 258 ks, were analyzed. This is to reconfirm the 55 ks modulation in the hard X-ray pulse phases of this source, found with a Suzaku observation in 2009 (Makishima et al., 2014, Phys. Rev. Lett., 112, 171102). Indeed, the 10–70 keV X-ray pulsation, detected with NuSTAR at 8.68917 s, was found to be also phase-modulated (at &gt;98% confidence) at the same ∼55 ks period, or half that value. Furthermore, a brief analysis of another Suzaku data set of 4U 0142+61, acquired in 2013, reconfirmed the same 55 ks phase modulation in the 15–40 keV pulses. Thus, the hard X-ray pulse-phase modulation was detected with Suzaku (in 2009 and 2013) and NuSTAR (in 2014) at a consistent period. However, the modulation amplitude varied significantly; A ∼ 0.7 s with Suzaku (in 2009), A ∼ 1.2 s with Suzaku (in 2013), and A ∼ 0.17 s with NuSTAR. In addition, the phase modulation properties detected with NuSTAR differed considerably between the first 1/3 and the latter 2/3 of the observation. In energies below 10 keV, the pulse-phase modulation was not detected with either Suzaku or NuSTAR. These results reinforce the view of Makishima et al. (2014, Phys. Rev. Lett., 112, 171102); the neutron star in 4U 0142+61 keeps free precession, under a slight axial deformation due probably to ultra-high toroidal magnetic fields of ∼1016 G. The wobbling angle of precession should remain constant, but the pulse-phase modulation amplitude varies on time scales of months to years, presumably as asymmetry of the hard X-ray emission pattern around the star’s axis changes.
Convolutional models of RNA energetics
Authors: Wu Michelle J. 
Published: November 2018

AbstractNucleic acid molecular biology and synthetic biology are undergoing rapid advances with the emergence of designer riboswitches controlling living cells, CRISPR/Cas9-based genome editing, high-throughput RNA-based silencing, and reengineering of mRNA translation. Many of these efforts require the design of nucleic acid interactions, which relies on accurate models for DNA and RNA energetics. Existing models utilize nearest neighbor rules, which were parameterized through careful optical melting measurements. However, these relatively simple rules often fail to quantitatively account for the biophysical behavior of molecules even in vitro, let alone in vivo. This is due to the limited experimental throughput of optical melting experiments and the infinitely large space of possible motifs that can be formed. Here, we present a convolutional neural network architecture to model the energies of nucleic acid motifs, allowing for learning of representations of physical interactions that generalize to arbitrary unmeasured motifs. First, we used existing parameterizations of motif energies to train the model and demonstrate that our model is expressive enough to recapitulate the current model. Then, through training on optical melting datasets from the literature, we have shown that the model can accurately predict the thermodynamics of hairpins containing unmeasured motifs. This work demonstrates the utility of convolutional models for capturing the thermodynamic parameters that underlie nucleic acid interactions.
MCS2: Minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks
Authors: Miraskarshahi Reza , Zabeti Hooman , Stephen Tamon , Chindelevitch Leonid 
Published: November 2018

AbstractMotivationConstraint-based modeling of metabolic networks helps researchers gain insight into the metabolic processes of many organisms, both prokaryotic and eukaryotic. Minimal Cut Sets (MCSs) are minimal sets of reactions whose inhibition blocks a target reaction in a metabolic network. Most approaches for finding the MCSs in constrained-based models require, either as an intermediate step or as a byproduct of the calculation, the computation of the set of elementary flux modes (EFMs), a convex basis for the valid flux vectors in the network. Recently, Ballerstein et al. [BvKKH11] proposed a method for computing the MCSs of a network without first computing its EFMs, by creating a dual network whose EFMs are a superset of the MCSs of the original network. However, their dual network is always larger than the original network and depends on the target reaction.Here we propose the construction of a different dual network, which is typically smaller than the original network and is independent of the target reaction, for the same purpose. We prove the correctness of our approach, MCS2, and describe how it can be modified to compute the few smallest MCSs for a given target reaction.ResultsWe compare MCS2 to the method of Ballerstein et al. and two other existing methods. We show that MCS2 succeeds in calculating the full set of MCSs in many models where other approaches cannot finish within a reasonable amount of time. Thus, in addition to its theoretical novelty, our approach provides a practical advantage over existing methods.AvailabilityMCS2 is freely available at https://github.com/RezaMash/MCS under the GNU 3.0 license.
A Novel Melatonergic Signature Predicts Reccurence Risk and Therapeutic Response in Breast Cancer Patients
Authors: Tran Hoa Quynh , Luu Phuc Loi , Than Van Thai , Clarke Declan , Lam Hanh Ngoc , Nguyen Dinh Truong , Thi Le Kim Van , Nguyen Trung Viet , Le Minh Thong , Hoang Xuan The , Duy Phan Q. , Tran Huyen , Nguyen Minh Nam 
Published: November 2018

AbstractASMT is a key determinant of the levels of released melatonin. Though melatonin has been shown to exhibit anti-cancer activity and prevents endocrine resistance in breast cancer, the role of ASMT in breast cancer progression remains unclear. In this retrospective study, we analyzed gene expression profiles from thousands of patients and found thatASMTexpression was significantly lower in breast cancer tumors relative to healthy tissue. Among cancer patients, those with greater expression had better relapse-free survival outcomes and longer metastasis-free survival times, and they also experienced longer periods before relapse or distance recurrence following tamoxifen treatment. Administration of melatonin, in combination with tamoxifen, further promoted cancer cell death by promoting apoptosis. Motivated by these results, we devised an ASMT gene signature that identifies low-risk cases with great accuracy. This signature was validated using both mRNA array and RNAseq datasets. Intriguingly, patients who are classified as high-risk benefit from adjuvant chemotherapy, and those with grade II tumors who are classified as low-risk exhibit improved overall survival and distance relapse-free outcomes following endocrine therapy. Our findings more clearly elucidate the roles ofASMT,provide strategies for improving the efficacy of tamoxifen treatment, and help to identify those patients who may maximally benefit from adjuvant or endocrine therapies.
A high‐quality chromosome‐level genome assembly of a generalist herbivore, Trichoplusia ni
Authors: Chen Wenbo , Yang Xiaowei , Tetreau Guillaume , Song Xiaozhao , Coutu Cathy , Hegedus Dwayne , Blissard Gary , Fei Zhangjun , Wang Ping 
Published: November 2018

AbstractThe cabbage looper, Trichoplusia ni, is a globally distributed highly polyphagous herbivore and an important agricultural pest. T. ni has evolved resistance to various chemical insecticides, and is one of the only two insect species that have evolved resistance to the biopesticide Bacillus thuringiensis (Bt) in agricultural systems and has been selected for resistance to baculovirus infections. We report a 333‐Mb high‐quality T. ni genome assembly, which has N50 lengths of scaffolds and contigs of 4.6 Mb and 140 Kb, respectively, and contains 14,384 protein‐coding genes. High‐density genetic maps were constructed to anchor 305 Mb (91.7%) of the assembly to 31 chromosomes. Comparative genomic analysis of T. ni with Bombyx mori showed enrichment of tandemly duplicated genes in T. ni in families involved in detoxification and digestion, consistent with the broad host range of T. ni. High levels of genome synteny were found between T. ni and other sequenced lepidopterans. However, genome synteny analysis of T. ni and the T. ni derived cell line High Five (Hi5) indicated extensive genome rearrangements in the cell line. These results provided the first genomic evidence revealing the high instability of chromosomes in lepidopteran cell lines known from karyotypic observations. The high‐quality T. ni genome sequence provides a valuable resource for research in a broad range of areas including fundamental insect biology, insect‐plant interactions and co‐evolution, mechanisms and evolution of insect resistance to chemical and biological pesticides, and technology development for insect pest management.
A niche for ecosystem multifunctionality in global change research
Authors: Giling Darren P. , Beaumelle Léa , Phillips Helen R. P. , Cesarz Simone , Eisenhauer Nico , Ferlian Olga , Gottschall Felix , Guerra Carlos , Hines Jes , Sendek Agnieszka , Siebert Julia , Thakur Madhav P. , Barnes Andrew D. 
Published: November 2018

AbstractConcern about human modification of Earth's ecosystems has recently motivated ecologists to address how global change drivers will impact the simultaneous provisioning of multiple functions, termed ecosystem multifunctionality (EMF). However, metrics of EMF have often been applied in global change studies with little consideration of the information they provide beyond single functions, or how and why EMF may respond to global change drivers. Here, we critically review the current state of this rapidly expanding field and provide a conceptual framework to guide the effective incorporation of EMF in global change research. In particular, we emphasize the need for a priori identification and explicit testing of the biotic and abiotic mechanisms through which global change drivers impact EMF, as well as assessing correlations among multiple single functions because these patterns underlie shifts in EMF. While the role of biodiversity in mediating global change effects on EMF has justifiably received much attention, empirical support for effects via other biotic and physicochemical mechanisms are also needed. Studies also frequently stated the importance of measuring EMF responses to global change drivers to understand the potential consequences for multiple ecosystem services, but explicit links between measured functions and ecosystem services were missing from many such studies. While there is clear potential for EMF to provide novel insights to global change research, predictive understanding will be greatly improved by insuring future research is strongly hypothesis‐driven, is designed to explicitly test multiple abiotic and biotic mechanisms, and assesses how single functions and their covariation drive emergent EMF responses to global change drivers.