bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic biology of polyketide synthases
Authors: Yuzawa Satoshi , Backman Tyler W H , Keasling Jay D , Katz Leonard 
Published: February 2018

Abstract
Complex reduced polyketides represent the largest class of natural products that have applications in medicine, agriculture, and animal health. This structurally diverse class of compounds shares a common methodology of biosynthesis employing modular enzyme systems called polyketide synthases (PKSs). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we describe the chassis (hosts) that are used to assemble, express, and engineer the parts and devices to produce polyketides. We describe a recently developed software tool to design PKS system and provide an example of its use. Finally, we provide perspectives of what needs to be accomplished to fully realize the potential that synthetic biology approaches bring to this class of molecules.
Soil moisture and salt ionic composition effects on species distribution and diversity in semiarid inland saline habitats, northwestern China
Authors: Zhang Dong‐mei , Zhao Wen‐zhi , Zhang Ge‐fei 
Published: February 2018

AbstractSalinization is one of the main types causing land desertification in arid and semi‐arid regions. Little is known about the impacts of salinization on the distribution and diversity of plant species, especially in semiarid inland saline habitats. We established a total of 40 sampling plots to determine plant community (floristic composition, species abundance, cover, frequency, and aboveground biomass) and soil characteristics (moisture, pH, electrical conductivity (EC), and the contents of Na+, K+, Ca2+, Mg2+, Cl−, SO42− and HCO3−). The TWINSPAN method was used to distinguish plant communities, by which three plant communities (I, II, III) were identified, namely Artemisia scoparia + Agropyron cristatum + Sophora alopecuroides (I), Kalidium gracile + Atriplex centralasiatica (II), and Salicornia europaea + Suaeda salsa (III). From I to III, the indices reflecting species diversity all decreased except for Pielou's index of evenness, while the aboveground biomass and cover increased; the characteristic indices of soil moisture, EC, the contents of Na+, K+, Ca2+, Mg2+, Cl−, SO42− and total dissolved salts (TDS) significantly increased, while the Ca2+/Na+, K+/Na+ ratios and HCO3− content significantly decreased. Canonical correspondence analysis (CCA) showed that the most important environmental factors influencing species distribution were: soil moisture, SO42−, K+/Na+ and pH. Stepwise multiple‐regression analysis indicated that species richness was correlated mainly with TDS and moisture. These results also suggested that vegetation can be used as a proxy indicating soil salt conditions, and their relationships can further provide important information for the improvement of salt‐affected soil's management and salt‐tolerant species utilization in environmental restoration.
Enterovesical fistula caused by ileal primary adenocarcinoma
Authors: Corrêa Romualdo da Silva , Salviano Fellipe Alexandre Macena , Melo Luís Felipe Revorêdo Antunes de , Dantas Junior José Manoel , Pereira Brandão Igor Rafael Guedes , Pinheiro Thiago Barros 
Published: February 2018

Abstract
Introduction Small bowel neoplasms are rare entities, with only 3.2% of gastrointestinal tumors localized in this segment. Adenocarcinoma is the second most common histologic type among small bowel neoplasms. The disease's symptoms are non-specific, with abdominal pain being the most common. Among the complications, fistulas are a far rare condition.
Case report We present the case of an 86-year-old woman, hypertensive, diabetic, and former smoker, with lower abdominal pain, hematuria, fecaluria and fever associated with weight loss. Upon physical examination presented pale mucous membranes. Magnetic resonance imaging of the abdomen showed parietal thickening in the distal ileum segment with an anterior wall bladder fistula. Absence of metastases.Subjected to transurethral endoscopic biopsy of the bladder lesion, which anatomopathological study was compatible with invasive mucinous adenocarcinoma. An enterectomy was performed with primary enteroanastomosis, associated with partial cystectomy by videolaparoscopy. Anatomopathological study of the surgical specimens concluded mucinous adenocarcinoma with signet ring cells located in the small bowel and bladder. Immunohistochemical exam has identified findings compatible with mucinous adenocarcinoma of origin in the small bowel. The patient evolved well, being discharged, and returned to postoperative follow-up without signs of relapse of the disease.
Conclusion The relative inaccessibility of the small bowel and the malignant neoplasms’ non-specific symptoms make an early diagnosis difficult. Discovery of the disease, often only at an advanced stage, results in complications and less effective therapy. The laparoscopic approach might be advantageous and effective in the treatment of advanced small bowel cancer with invasion of adjacent structures.
Artrodese lombar intersomática anterior multinível combinada com estabilização posterior em discopatia—Análise clínico-funcional prospectiva
Authors: Moura Diogo Lino , Lawrence David , Gabriel Josué Pereira 
Published: February 2018

Resumo
Objetivo Estudo prospectivo controlado em pacientes com discopatia degenerativa submetidos a artrodese intersomática lombar anterior instrumentada combinada com estabilização posterior.
Métodos Amostra com 64 pacientes consecutivos operados pelos mesmos cirurgiões ao longo de quatro anos. Metade das artrodeses intersomática lombar anterior foi efetuada em dois níveis, 43,8% em três níveis e 6,25% em um nível. Foram usadas caixas intersomáticas com parafusos integrados preenchidas com matriz óssea e proteína morfogenética óssea 2.
Resultados Metade da amostra apresentava cirurgias prévias à coluna lombar, 75% listeses degenerativas associadas e 62,5% patologia compressiva posterior da coluna lombar. Aproximadamente 56% da amostra apresentavam pelo menos um fator de risco de não união da artrodese. O índice Oswestry passou de 71,81 ± 7,22 no pré-operatório para 24,75 ± 7,82 na avaliação no fim do tempo de seguimento, enquanto a escala visual analógica da dor passou de 7,88 ± 0,70 para 2,44 ± 0,87 (p < 0,001). A melhoria clínico-funcional foi crescente de acordo com a intervenção num número superior de níveis, o que comprova a eficácia da artrodese intersomática lombar anterior multinível, aplicada em 93,75% da amostra. A taxa global de complicações foi de 7,82% e de complicações major de 0%. Não se identificou qualquer caso de não união.
Conclusão A artrodese intersomática lombar anterior instrumentada combinada com estabilização posterior é uma opção de sucesso na discopatia degenerativa uni ou multinível dos segmentos de L3 a S1, mesmo em presença significativa de fatores de risco de não união e cirurgias prévias da coluna lombar, garante resultados clínico-funcionais e radiográficos muito satisfatórios e reduzida taxa de complicações em médio prazo.
Efeito do ácido zoledrônico e do alendronato no edema ósseo e dor na osteonecrose espontânea do joelho: Um novo paradigma no manejo
Authors: Agarwala Sanjay , Sharoff Lokesh , Jagani Naeem 
Published: February 2018

Resumo
Objetivo Determinar o efeito do tratamento combinado de ácido zoledrônico e alendronato no edema ósseo e na dor no joelho em casos de osteonecrose espontânea do joelho. A experiência dos autores com este tratamento é relatada.
Métodos Série de casos retrospectiva, incluindo 11 pacientes com osteonecrose espontânea do joelho confirmada por ressonância magnética. Os pacientes foram tratados com uma dose intravenosa única de 5 mg de ácido zoledrônico combinada com 35 mg de alendronato oral, 2 vezes por semana, por 16 semanas. Os escores da escala visual analógica foram aferidos antes do começo do tratamento, em 8 semanas e em 16 semanas de acompanhamento. O tamanho do edema da medula óssea adjacente à lesão foi medido em imagens de ressonância magnética coronal ponderadas em T2 no início do tratamento e em 16 semanas.
Resultados O escore médio da escala visual analógica em 0 semanas foi de 7,72, contra 0,81 em 16 semanas de tratamento, uma diferença estatisticamente significativa (p = 0,03). O envolvimento médio da medula óssea em 0 semanas foi de 80%, e foi reduzido para 11,81% em 16 semanas de tratamento, uma diferença também estatisticamente significativa (p = 0,03).
Conclusão Os dados mostram que a terapia combinada proporciona alívio da dor inicial e redução do edema ósseo, sendo segura, eﬁcaz e bem tolerada em uma enfermidade dolorosa como a osteonecrose espontânea do joelho.
Temozolomide–perillyl alcohol conjugate downregulates O6-methylguanin DNA methltransferase via inducing ubiquitination-dependent proteolysis in non-small cell lung cancer
Authors: Song Xingguo , Xie Li , Chang Minghui , Geng Xinran , Wang Xingwu , Chen Thomas C. , Song Xianrang 
Published: February 2018

AbstractThe DNA repair enzyme O6-methylguanin-DNA-methltransferase (MGMT) is able to remove products of alkylating agent such as O6-meG and emerges as a central determinant of cancer resistance to temozolomide (TMZ). Temozolomide–perillyl alcohol conjugate (TMZ–POH), a novel TMZ analog developed based on the conjugation of TMZ and POH, displayed strong anticancer potency in multiple cancer types, but seemed not to experience the chemoresistance even in cells with high MGMT expression unlike TMZ and other alkylating agents. In this study, we demonstrated TMZ–POH inhibited MGMT dependent on proteasomal pathway and this inhibition is a significant factor in its toxic effect in the non-small cell lung cancer (NSCLC) cells.
CD1d-dependent immune suppression mediated by regulatory B cells through modulations of iNKT cells
Authors: Oleinika K. , Rosser E. C. , Matei D. E. , Nistala K. , Bosma A. , Drozdov I. , Mauri C. 
Published: February 2018

AbstractRegulatory B cells (Breg) express high levels of CD1d that presents lipid antigens to invariant natural killer T (iNKT) cells. The function of CD1d in Breg biology and iNKT cell activity during inflammation remains unclear. Here we show, using chimeric mice, cell depletion and adoptive cell transfer, that CD1d–lipid presentation by Bregs induces iNKT cells to secrete interferon (IFN)-γ to contribute, partially, to the downregulation of T helper (Th)1 and Th17-adaptive immune responses and ameliorate experimental arthritis. Mice lacking CD1d-expressing B cells develop exacerbated disease compared to wild-type mice, and fail to respond to treatment with the prototypical iNKT cell agonist α-galactosylceramide. The absence of lipid presentation by B cells alters iNKT cell activation with disruption of metabolism regulation and cytokine responses. Thus, we identify a mechanism by which Bregs restrain excessive inflammation via lipid presentation.
Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure
Authors: Bates Kieran A. , Clare Frances C. , O’Hanlon Simon , Bosch Jaime , Brookes Lola , Hopkins Kevin , McLaughlin Emilia J. , Daniel Olivia , Garner Trenton W. J. , Fisher Matthew C. , Harrison Xavier A. 
Published: February 2018

AbstractHost-associated microbes are vital for combatting infections and maintaining health. In amphibians, certain skin-associated bacteria inhibit the fungal pathogenBatrachochytrium dendrobatidis(Bd), yet our understanding of host microbial ecology and its role in disease outbreaks is limited. We sampled skin-associated bacteria andBdfrom Pyrenean midwife toad populations exhibiting enzootic or epizootic disease dynamics. We demonstrate that bacterial communities differ between life stages with few shared taxa, indicative of restructuring at metamorphosis. We detected a significant effect of infection history on metamorph skin microbiota, with reduced bacterial diversity in epizootic populations and differences in community structure and predicted function. Genome sequencing ofBdisolates supports a single introduction to the Pyrenees and reveals no association between pathogen genetics and epidemiological trends. Our findings provide an ecologically relevant insight into the microbial ecology of amphibian skin and highlight the relative importance of host microbiota and pathogen genetics in predicting disease outcome.
Observationally quantified reconnection providing a viable mechanism for active region coronal heating
Authors: Yang Kai E. , Longcope Dana W. , Ding M. D. , Guo Yang 
Published: February 2018

AbstractThe heating of the Sun’s corona has been explained by several different mechanisms including wave dissipation and magnetic reconnection. While both have been shown capable of supplying the requisite power, neither has been used in a quantitative model of observations fed by measured inputs. Here we show that impulsive reconnection is capable of producing an active region corona agreeing both qualitatively and quantitatively with extreme-ultraviolet observations. We calculate the heating power proportional to the velocity difference between magnetic footpoints and the photospheric plasma, called the non-ideal velocity. The length scale of flux elements reconnected in the corona is found to be around 160 km. The differential emission measure of the model corona agrees with that derived using multi-wavelength images. Synthesized extreme-ultraviolet images resemble observations both in their loop-dominated appearance and their intensity histograms. This work provides compelling evidence that impulsive reconnection events are a viable mechanism for heating the corona.
Systematic analysis of protein turnover in primary cells
Authors: Mathieson Toby , Franken Holger , Kosinski Jan , Kurzawa Nils , Zinn Nico , Sweetman Gavain , Poeckel Daniel , Ratnu Vikram S. , Schramm Maike , Becher Isabelle , Steidel Michael , Noh Kyung-Min , Bergamini Giovanna , Beck Martin , Bantscheff Marcus , Savitski Mikhail M. 
Published: February 2018

AbstractA better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h. We identified 4000–6000 proteins in several non-dividing cell types, corresponding to 9699 unique protein identifications over the entire data set. We observed similar protein half-lives in B-cells, natural killer cells and monocytes, whereas hepatocytes and mouse embryonic neurons show substantial differences. Our data set extends and statistically validates the previous observation that subunits of protein complexes tend to have coherent turnover. Moreover, analysis of different proteasome and nuclear pore complex assemblies suggests that their turnover rate is architecture dependent. These results illustrate that our approach allows investigating protein turnover and its implications in various cell types.
Quality and learning aspects of the first 9000 spirometries of the LifeGene study
Authors: Qvarfordt Mikaela , Anderson Martin , Svartengren Magnus 
Published: February 2018

AbstractSpirometry requires the patient to cooperate and do the manoeuvre 'right' for reliable results. Algorithms to assess test quality as well as educational recommendations for personnel are defined in guidelines. We compared the quality of forced spirometry tests performed by spirometry technicians with little or no previous experience of spirometry using spirometry systems with different modes of feedback. In both cases, the spirometry technician received general feedback on the screen based on ATS/ERS guidelines, such as 'exhale faster' and 'exhale longer'. The major difference was whether quality grading system of the complete session was available simultaneously on screen, or in the printed report afterwards. Two parts of the same population-based study (LifeGene), the pilot (LG1) and the first part (LG2) of the subsequent study, were compared retrospectively. In LG1 (on-screen grading) approved examination quality was achieved for 88% of the 10 first subjects for each spirometry technician compared to 70% in LG2 (printed grading afterwards). The corresponding values after 40 subjects was 94 % in LG1, compared to 73% in LG2, and after the first ten subjects there was no apparent quality improvement in either LG1 or LG2. The quality for LG1 is among the highest reported in the literature even though the spirometry technician were relatively inexperienced. We conclude that on-screen grading in addition to general technical quality feedback is powerful in enhancing the spirometry test session quality.
Ultrasound beam steering of oxygen nanobubbles for enhanced bladder cancer therapy
Authors: Bhandari Pushpak , Novikova Gloriia , Goergen Craig J. , Irudayaraj Joseph 
Published: February 2018

AbstractNew intravesical treatment approaches for bladder cancer are needed as currently approved treatments show several side effects and high tumor recurrence rate. Our study used MB49 murine urothelial carcinoma model to evaluate oxygen encapsulated cellulosic nanobubbles as a novel agent for imaging and ultrasound guided drug delivery. In this study, we show that oxygen nanobubbles (ONB) can be propelled (up to 40 mm/s) and precisely guided in vivo to the tumor by an ultrasound beam. Nanobubble velocity can be controlled by altering the power of the ultrasound Doppler beam, while nanobubble direction can be adjusted to different desired angles by altering the angle of the beam. Precise ultrasound beam steering of oxygen nanobubbles was shown to enhance the efficacy of mitomycin-C, resulting in significantly lower tumor progression rates while using a 50% lower concentration of chemotherapeutic drug. Further, dark field imaging was utilized to visualize and quantify the ONB ex vivo. ONBs were found to localize up to 500 µm inside the tumor using beam steering. These results demonstrate the potential of an oxygen nanobubble drug encapsulated system to become a promising strategy for targeted drug delivery because of its multimodal (imaging and oxygen delivery) and multifunctional (targeting and hypoxia programming) properties.
Polygonum aviculare L. extract and quercetin attenuate contraction in airway smooth muscle
Authors: Luo Xi , Xue Lu , Xu Hao , Zhao Qing-Yang , Wang Qian , She Yu-Shan , Zang Dun-An , Shen Jinhua , Peng Yong-Bo , Zhao Ping , Yu Meng-Fei , Chen Weiwei , Ma Li-Qun , Chen Shu , Chen Shanshan , Fu Xiangning , Hu Sheng , Nie Xiaowei , Shen Chenyou , Zou Chunbin , Qin Gangjian , Dai Jiapei , Ji Guangju , Su Yunchao , Hu Shen , Chen Jingyu , Liu Qing-Hua 
Published: February 2018

AbstractBecause of the serious side effects of the currently used bronchodilators, new compounds with similar functions must be developed. We screened several herbs and found that Polygonum aviculare L. contains ingredients that inhibit the precontraction of mouse and human airway smooth muscle (ASM). High K+-induced precontraction in ASM was completely inhibited by nifedipine, a selective blocker of L-type voltage-dependent Ca2+ channels (LVDCCs). However, nifedipine only partially reduced the precontraction induced by acetylcholine chloride (ACH). Additionally, the ACH-induced precontraction was partly reduced by pyrazole-3 (Pyr3), a selective blocker of TRPC3 and stromal interaction molecule (STIM)/Orai channels. These channel-mediated currents were inhibited by the compounds present in P. aviculare extracts, suggesting that this inhibition was mediated by LVDCCs, TRPC3 and/or STIM/Orai channels. Moreover, these channel-mediated currents were inhibited by quercetin, which is present in P. aviculare extracts. Furthermore, quercetin inhibited ACH-induced precontraction in ASM. Overall, our data indicate that the ethyl acetate fraction of P. aviculare and quercetin can inhibit Ca2+-permeant LVDCCs, TRPC3 and STIM/Orai channels, which inhibits the precontraction of ASM. These findings suggest that P. aviculare could be used to develop new bronchodilators to treat obstructive lung diseases such as asthma and chronic obstructive pulmonary disease.
Dyslipidemia and risk of renal replacement therapy or death in incident pre-dialysis patients
Authors: Voskamp Pauline W. M. , van Diepen Merel , Dekker Friedo W. , Hoogeveen Ellen K. 
Published: February 2018

AbstractGlobally the number of patients on renal replacement therapy (RRT) is rising. Dyslipidemia is a potential modifiable cardiovascular risk factor, but its effect on risk of RRT or death in pre-dialysis patients is unclear. The aim of this study was to assess the association between dyslipidemia and risk of RRT or death among patients with CKD stage 4–5 receiving specialized pre-dialysis care, an often under represented group in clinical trials. Of the 502 incident pre-dialysis patients (>18 y) in the Dutch PREPARE-2 study, lipid levels were available in 284 patients and imputed for the other patients. During follow up 376 (75%) patients started RRT and 47 (9%) patients died. Dyslipidemia was defined as total cholesterol ≥5.00 mmol/L, LDL cholesterol ≥2.50 mmol/L, HDL cholesterol <1.00 mmol/L, HDL/LDL ratio <0.4, or triglycerides (TG) ≥2.25 mmol/L, and was present in 181 patients and absent in 93 patients. After multivariable adjustment Cox regression analyses showed a HR (95% CI) for the combined endpoint for dyslipidemia of 1.12 (0.85–1.47), and for high LDL of 1.20 (0.89–1.61). All other HRs were smaller. In conclusion, we did not find an association between dyslipidemia or the separate lipid levels and RRT or death in CKD patients on specialized pre-dialysis care.
Seismic waveform simulation for models with fluctuating interfaces
Authors: Rao Ying , Wang Yanghua 
Published: February 2018

AbstractThe contrast of elastic properties across a subsurface interface imposes a dominant influence on the seismic wavefield, which includes transmitted and reflected waves from the interface. Therefore, for an accurate waveform simulation, it is necessary to have an accurate representation of the subsurface interfaces within the numerical model. Accordingly, body-fitted gridding is used to partition subsurface models so that the grids coincide well with both the irregular surface and fluctuating interfaces of the Earth. However, non-rectangular meshes inevitably exist across fluctuating interfaces. This non-orthogonality degrades the accuracy of the waveform simulation when using a conventional finite-difference method. Here, we find that a summation-by-parts (SBP) finite-difference method can be used for models with non-rectangular meshes across fluctuating interfaces, and can achieve desirable simulation accuracy. The acute angle of non-rectangular meshes can be relaxed to as low as 47°. The cell size rate of change between neighbouring grids can be relaxed to as much as 30%. Because the non-orthogonality of grids has a much smaller impact on the waveform simulation accuracy, the model discretisation can be relatively flexible for fitting fluctuating boundaries within any complex problem. Consequently, seismic waveform inversion can explicitly include fluctuating interfaces within a subsurface velocity model.