bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and safety of core-needle biopsy in initially detected thyroid nodules via propensity score analysis
Authors: Suh Chong Hyun , Baek Jung Hwan , Choi Young Jun , Kim Tae Yong , Sung Tae Yon , Song Dong Eun , Lee Jeong Hyun 
Published: August 2017

AbstractWe compared the efficacy and complications of core-needle biopsy (CNB) with those of fine-needle aspiration (FNA) in a large population of patients with initially detected thyroid nodules via a propensity score analysis. Outpatients with initially detected thyroid nodules, who had undergone CNB or FNA between January 2013 and December 2013, were selected. This study included 4,822 thyroid nodules from 4,553 consecutive patients. Adjustments for significant differences in patients’ baseline characteristics were facilitated via propensity score analysis. Subgroup analyses were performed according to nodule sizes ≥ 1 cm. The non-diagnostic result rate, malignancy rate, complication rate, and diagnostic accuracy were compared. A 1:1 matching of 1,615 patients yielded no significant differences between two groups for any covariate. The non-diagnostic result rate was significantly lower in the core-needle biopsy group than in the fine-needle aspiration group (5.2% vs. 12.1%), while the malignancy rate (23.7% vs. 11.8%) and sensitivity (75.9% vs. 55.6%) were significantly higher. However, the specificities were similar (100% and 99.9%, respectively). Propensity score and subgroup analyses showed similar results. The complication rate was similar between groups in matched cohorts. CNB is a promising and safe diagnostic tool for patients with initially detected thyroid nodules.
High-fat diet-induced acceleration of osteoarthritis is associated with a distinct and sustained plasma metabolite signature
Authors: Datta Poulami , Zhang Yue , Parousis Alexa , Sharma Anirudh , Rossomacha Evgeny , Endisha Helal , Wu Brian , Kacprzak Izabela , Mahomed Nizar N. , Gandhi Rajiv , Rockel Jason S. , Kapoor Mohit 
Published: August 2017

AbstractMetabolic changes induced by high fat diet (HFD) that contribute to osteoarthritis (OA) are poorly understood. We investigated longitudinal changes to metabolites and their contribution to OA pathogenesis in response to HFD. HFD-fed mice exhibited acceleration of spontaneous age-related and surgically-induced OA compared to lean diet (LD)-fed mice. Using metabolomics, we identified that HFD-fed mice exhibited a distinct and sustained plasma metabolite signature rich in phosphatidylcholines (PC) and lysophosphatidylcholines (lysoPCs), even after resumption of normal chow diet. Using receiver operator curve analysis and prediction modelling, we showed that the concentration of these identified metabolites could efficiently predict the type of diet and OA risk with an accuracy of 93%. Further, longitudinal evaluation of knee joints of HFD- compared to LD- fed mice showed a greater percentage of leptin-positive chondrocytes. Mechanistic data showed that leptin-treated human OA chondrocytes exhibited enhanced production of lysoPCs and expression of autotaxin and catabolic MMP-13. Leptin-induced increased MMP13 expression was reversed by autotaxin inhibition. Together, this study is the first to describe a distinct and sustained HFD-induced metabolite signature. This study suggests that in addition to increased weight, identified metabolites and local leptin-signaling may also contribute in part, towards the accelerated OA-phenotype observed in HFD mice.
Complete alanine scanning of the Escherichia coli RbsB ribose binding protein reveals residues important for chemoreceptor signaling and periplasmic abundance
Authors: Reimer Artur , Maffenbeier Vitali , Dubey Manupriyam , Sentchilo Vladimir , Tavares Diogo , Gil Manuel Hernandez , Beggah Siham , van der Meer Jan Roelof 
Published: August 2017

AbstractThe Escherichia coli RbsB ribose binding protein has been used as a scaffold for predicting new ligand binding functions through in silico modeling, yet with limited success and reproducibility. In order to possibly improve the success of predictive modeling on RbsB, we study here the influence of individual residues on RbsB-mediated signaling in a near complete library of alanine-substituted RbsB mutants. Among a total of 232 tested mutants, we found 10 which no longer activated GFPmut2 reporter expression in E. coli from a ribose-RbsB hybrid receptor signaling chain, and 13 with significantly lower GFPmut2 induction than wild-type. Quantitative mass spectrometry abundance measurements of 25 mutants and wild-type RbsB in periplasmic space showed four categories of effects. Some (such as D89A) seem correctly produced and translocated but fail to be induced with ribose. Others (such as N190A) show lower induction probably as a result of less efficient production, folding and translocation. The third (such as N41A or K29A) have defects in both induction and abundance. The fourth category consists of semi-constitutive mutants with increased periplasmic abundance but maintenance of ribose induction. Our data show how RbsB modeling should include ligand-binding as well as folding, translocation and receptor binding.
From metabolome to phenotype: GC-MS metabolomics of developing mutant barley seeds reveals effects of growth, temperature and genotype
Authors: Khakimov Bekzod , Rasmussen Morten Arendt , Kannangara Rubini Maya , Jespersen Birthe Møller , Munck Lars , Engelsen Søren Balling 
Published: August 2017

AbstractThe development of crop varieties tolerant to growth temperature fluctuations and improved nutritional value is crucial due to climate change and global population growth. This study investigated the metabolite patterns of developing barley seed as a function of genotype and growth temperature for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS). The lys3.a mutation disrupts a regulator gene, causing an increase in proteins rich in the essential amino acid lysine, while lys5.f carries a mutation in an ADP-glucose transporter gene leading to a significant increase in production of mixed-linkage β-glucan at the expense of α-glucan. Unique metabolic patterns associated with the tricarboxylic acid cycle, shikimate-phenylpropanoid pathway, mevalonate, lipid and carbohydrate metabolism were observed for the barley mutants, whereas growth temperature primarily affected shikimate-phenylpropanoid and lipid metabolism. The study applied recently developed GC-MS metabolomics methods and demonstrated their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production.
Lacrimal Gland Repair after Short-term Obstruction of Excretory Duct in Rabbits
Authors: Lin Hui , Liu Ying , He Hong , Botsford Benjamin , Yiu Samuel 
Published: August 2017

AbstractAqueous tear-deficient dry eye is a multifactorial chronic disorder in which the lacrimal glands fail to produce enough tears to maintain a healthy ocular surface. The existence of lacrimal gland stem/progenitor cells was proposed in several species, yet their origin and characteristics are not very clear. Here, we investigated the presence of resident progenitor cells and their regenerative potential in a rabbit model with lacrimal gland main excretory duct ligation-induced injury. The ligation-injured lacrimal glands temporarily decreased in weight and had impaired tear secretion. Protein expression profiles and transcriptional profiles were obtained from injured tissue. Isolated lacrimal gland progenitor cells were tested and characterized by stem cell-related marker evaluation, single cell clonal assay and three-dimensional (3-D) culture. The results of our study indicate that lacrimal glands are capable of tissue repair after duct ligation-induced injury, likely involving resident stem/progenitor cells and epithelial-mesenchymal transitions. Lacrimal gland progenitor cells isolated from ligated tissue can differentiate in 3-D culture. The results provide further insights into lacrimal gland stem/progenitor cell physiology and their potential for treating severe cases of tear deficiency.
IgE Trimers Drive SPE-7 Cytokinergic Activity
Authors: Bax Heather J. , Bowen Holly , Beavil Rebecca L. , Chung Raymond , Ward Malcolm , Davies Anna M. , Dodev Tihomir S. , McDonnell James M. , Beavil Andrew J. , Sutton Brian J. , Gould Hannah J. 
Published: August 2017

AbstractDegranulation of mast cells and basophils, with release of agents of the allergic response, ensues when multivalent antigens bind to and cross-link the cells’ receptor-bound IgE antibodies. A widely used commercial monoclonal IgE antibody, SPE-7 IgE from Sigma, was found to possess the radically anomalous property, termed “cytokinergic”, of inducing basophil degranulation without the intervention of an antigen. We show here that the IgE monomer, freed of protein contaminants, is devoid of this activity, and that the source of the anomaly is a trace impurity, identified as a dissociation-resistant IgE trimer. Possible models for the formation of IgE trimers and the manner in which they cross-link cell surface receptors are suggested herein.
Pupil Size Tracks Attentional Performance In Attention-Deficit/Hyperactivity Disorder
Authors: Wainstein G. , Rojas-Líbano D. , Crossley N. A. , Carrasco X. , Aboitiz F. , Ossandón T. 
Published: August 2017

AbstractAttention-deficit/hyperactivity disorder (ADHD) diagnosis is based on reported symptoms, which carries the potential risk of over- or under-diagnosis. A biological marker that helps to objectively define the disorder, providing information about its pathophysiology, is needed. A promising marker of cognitive states in humans is pupil size, which reflects the activity of an ‘arousal’ network, related to the norepinephrine system. We monitored pupil size from ADHD and control subjects, during a visuo-spatial working memory task. A sub group of ADHD children performed the task twice, with and without methylphenidate, a norepinephrine–dopamine reuptake inhibitor. Off-medication patients showed a decreased pupil diameter during the task. This difference was no longer present when patients were on-medication. Pupil size correlated with the subjects’ performance and reaction time variability, two vastly studied indicators of attention. Furthermore, this effect was modulated by medication. Through pupil size, we provide evidence of an involvement of the noradrenergic system during an attentional task. Our results suggest that pupil size could serve as a biomarker in ADHD.
Transcription factor ZNF148 is a negative regulator of human muscle differentiation
Authors: Bakke Jesse , Wright William C. , Zamora Anthony E. , Ong Su Sien , Wang Yue-Ming , Hoyer Jessica D. , Brewer Christopher T. , Thomas Paul G. , Chen Taosheng 
Published: August 2017

AbstractMuscle differentiation is a complex process in which muscle progenitor cells undergo determination and eventually cellular fusion. This process is heavily regulated by such master transcription factors as MYOD and members of the MEF2 family. Here, we show that the transcription factor ZNF148 plays a direct role in human muscle cell differentiation. Downregulation of ZNF148 drives the formation of a muscle phenotype with rapid expression of myosin heavy chain, even in proliferative conditions. This phenotype was most likely mediated by the robust and swift upregulation of MYOD and MEF2C.
Multimerization is required for antigen binding activity of an engineered IgM/IgG chimeric antibody recognizing a skin-related antigen
Authors: Teye Kwesi , Hashimoto Koji , Numata Sanae , Ohta Kunihiro , Haftek Marek , Hashimoto Takashi 
Published: August 2017

AbstractMonoclonal antibodies offer great tools for research. We encountered a potentially useful mouse IgM monoclonal antibody whose antigen is expressed in normal skin but lost in human skin cancer. Because IgM is difficult to work with and the antigen was unknown, we decided to convert the IgM (µ) to IgG (γ) version. After cDNA for the antibody was obtained by RACE PCR, we made a series of molecules with different combinations of IgM and IgG domains. Whereas VH-Cµ1-Cµ2-Cγ3 and VH-Cµ1-Cµ2-Hinge-Cγ2-Cγ3 functionally bound to the antigen, VH-Cγ1-Hinge-Cγ2-Cγ3, VH-Cµ1-Hinge-Cγ2-Cγ3, and VH-Cµ1-Cµ2-Cγ2-Cγ3 did not. Gel filtration analyses revealed that the functional molecules tend to form multimers and the multimeric forms retained antigen binding activity. Furthermore, the mutation of amino acid residue p.309Q > C of mouse IgG and addition of IgM tailpiece to the C-terminus of the molecules induced multimer formation, dramatically enhanced antibody functionality and all non-functional molecules became strongly functional. The functional molecules could be bound by protein A/protein G and other IgG specific reagents and therefore should be useful for further characterization of the antigen. Our study revealed that multimerization of converted IgM is functionally important for antigen binding activity of engineered IgM/IgG chimeric antibodies.
Complementarity among natural enemies enhances pest suppression
Authors: Dainese Matteo , Schneider Gudrun , Krauss Jochen , Steffan-Dewenter Ingolf 
Published: August 2017

AbstractNatural enemies have been shown to be effective agents for controlling insect pests in crops. However, it remains unclear how different natural enemy guilds contribute to the regulation of pests and how this might be modulated by landscape context. In a field exclusion experiment in oilseed rape (OSR), we found that parasitoids and ground-dwelling predators acted in a complementary way to suppress pollen beetles, suggesting that pest control by multiple enemies attacking a pest during different periods of its occurrence in the field improves biological control efficacy. The density of pollen beetle significantly decreased with an increased proportion of non-crop habitats in the landscape. Parasitism had a strong effect on pollen beetle numbers in landscapes with a low or intermediate proportion of non-crop habitats, but not in complex landscapes. Our results underline the importance of different natural enemy guilds to pest regulation in crops, and demonstrate how biological control can be strengthened by complementarity among natural enemies. The optimization of natural pest control by adoption of specific management practices at local and landscape scales, such as establishing non-crop areas, low-impact tillage, and temporal crop rotation, could significantly reduce dependence on pesticides and foster yield stability through ecological intensification in agriculture.
Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism
Authors: Seki Motohide , Ohara Takayuki , Hearn Timothy J. , Frank Alexander , da Silva Viviane C. H. , Caldana Camila , Webb Alex A. R. , Satake Akiko 
Published: August 2017

AbstractArabidopsis plants store part of the carbon fixed by photosynthesis as starch to sustain growth at night. Two competing hypotheses have been proposed to explain this diel starch turnover based on either the measurement of starch abundance with respect to circadian time, or the sensing of sugars to feedback to the circadian oscillator to dynamically adjust the timing of starch turnover. We report a phase oscillator model that permitted derivation of the ideal responses of the circadian regulation of starch breakdown to maintain sucrose homeostasis. Testing the model predictions using a sugar-unresponsive mutant of Arabidopsis demonstrated that the dynamics of starch turnover arise from the circadian clock measuring and responding to the rate of change of cellular sucrose. Our theory and experiments suggest that starch turnover is controlled by the circadian clock acting as a dynamic homeostat responding to sucrose signals to maintain carbon homeostasis.
Intraoperative Parathyroid Localization with Near-Infrared Fluorescence Imaging Using Indocyanine Green during Total Parathyroidectomy for Secondary Hyperparathyroidism
Authors: Cui Le , Gao Yang , Yu Heping , Li Min , Wang Birong , Zhou Tao , Hu Qinggang 
Published: August 2017

AbstractThe detection of all glands during total parathyroidectomy (TPTX) in secondary hyperparathyroidism (SHPT) patients is often difficult due to their variability in number and location. The objective of this study was to evaluate the feasibility of near-infrared fluorescence (NIRF) imaging using indocyanine green (ICG) for intraoperative parathyroid gland (PTG) localization in SHPT patients. Twenty-nine patients with SHPT were divided into two groups with or without intraoperative NIRF imaging. ICG was administered in patients undergoing intraoperative imaging, and the fluorescence of PTGs was assessed. Clinical and histopathologic variables were analyzed to determine factors associated with ICG uptake. Comparisons between NIRF and preoperative imaging, as well as differences between groups with or without NIRF imaging, were carried out to evaluate the efficacy of this technique. Most PTGs could be clearly identified, including one ectopic gland. The sensitivity of NIRF imaging is 91.1% in contrast to 81.82% for ultrasonography (US), 62.34% for 99mTc-MIBI and 85.71% for computed tomography (CT). In addition, intraoperative NIRF imaging can reduce the operation time and improve the complete resection rate compared with the group not using it. Intraoperative NIRF imaging using ICG during TPTX is technically feasible and reliable for assisting surgeons in detecting and confirming PTGs.
Structure-based cross-docking analysis of antibody–antigen interactions
Authors: Kilambi Krishna Praneeth , Gray Jeffrey J. 
Published: August 2017

AbstractAntibody–antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody–antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody–antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes. Using the Rosetta interface score as a classifier, the cognate pair was the top-ranked model in 80% (14/17) of the antigen targets using bound monomer structures in docking, 35% (6/17) when using unbound, and 12% (2/17) when using the homology-modeled backbones to generate the complexes. Increasing rigid-body diversity of the models using RosettaDock’s local dock routine lowers the discrimination accuracy with the cognate antibody–antigen pair ranking in bound and unbound models but recovers additional top-ranked cognate complexes when using homology models. The study is the first structure-based cross-docking attempt aimed at distinguishing antibody–antigen binders from non-binders and demonstrates the challenges to address for the methods to be widely applicable to supplement high-throughput experimental antibody sequencing workflows.
Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells
Authors: Pardo Mercedes , Yu Lu , Shen Shihpei , Tate Peri , Bode Daniel , Letney Blake L. , Quelle Dawn E. , Skarnes William , Choudhary Jyoti S. 
Published: August 2017

AbstractMYST histone acetyltransferases have crucial functions in transcription, replication and DNA repair and are hence implicated in development and cancer. Here we characterise Myst2/Kat7/Hbo1 protein interactions in mouse embryonic stem cells by affinity purification coupled to mass spectrometry. This study confirms that in embryonic stem cells Myst2 is part of H3 and H4 histone acetylation complexes similar to those described in somatic cells. We identify a novel Myst2-associated protein, the tumour suppressor protein Niam (Nuclear Interactor of ARF and Mdm2). Human NIAM is involved in chromosome segregation, p53 regulation and cell proliferation in somatic cells, but its role in embryonic stem cells is unknown. We describe the first Niam embryonic stem cell interactome, which includes proteins with roles in DNA replication and repair, transcription, splicing and ribosome biogenesis. Many of Myst2 and Niam binding partners are required for correct embryonic development, implicating Myst2 and Niam in the cooperative regulation of this process and suggesting a novel role for Niam in embryonic biology. The data provides a useful resource for exploring Myst2 and Niam essential cellular functions and should contribute to deeper understanding of organism early development and survival as well as cancer. Data are available via ProteomeXchange with identifier PXD005987.
Association between fasting glucose and all-cause mortality according to sex and age: a prospective cohort study
Authors: Yi Sang-Wook , Park Sangkyu , Lee Yong-ho , Park Hyang-Jeong , Balkau Beverley , Yi Jee-Jeon 
Published: August 2017

AbstractThe association of fasting glucose with the risk of death according to sex and age remains unclear, and insufficient information is available on sex- and age-specific glucose concentrations within ethnic groups. This study analyzed a sample of 12,455,361 Korean adults who participated in health examinations during 2001–2004, and were followed up until 2013. Men had 3.0 mg/dL (0.167 mmol/L) higher mean glucose concentrations than women (94.7 vs. 91.7 mg/dL), although women over 73 years had higher levels. For glucose levels of 100–199 mg/dL, each 18 mg/dL (1 mmol/L) increase in fasting glucose increased mortality by 13% (HR = 1.13, [95% CI 1.12 to 1.13], p < 0.001). In individuals with fasting glucose levels of 100–125 mg/dL, each 18 mg/dL increase in fasting glucose was associated with a 30% increase in the risk for mortality (1.30, [1.18 to 1.43]) in those aged 18–34 years, a 32% increase (1.32, [1.26 to 1.39]) in those aged 35–44 years, and a 10% increase (1.10, [1.02 to 1.19]) in those aged 75–99 years. The fasting glucose levels associated with the lowest mortality were 80–94 mg/dL regardless of sex and age. Prediabetes (100–125 mg/dL) was associated with higher mortality. The associations of hyperglycemia with mortality were stronger at younger ages.
Nano metamaterials for ultrasensitive Terahertz biosensing
Authors: Lee Dong-Kyu , Kang Ji-Hun , Kwon Junghoon , Lee Jun-Seok , Lee Seok , Woo Deok Ha , Kim Jae Hun , Song Chang-Seon , Park Q-Han , Seo Minah 
Published: August 2017

AbstractAs a candidate for a rapid detection of biomaterials, terahertz (THz) spectroscopy system can be considered with some advantage in non-destructive, label-free, and non-contact manner. Because protein-ligand binding energy is in the THz range, especially, most important conformational information in molecular interactions can be captured by THz electromagnetic wave. Based on the THz time-domain spectroscopy system, THz nano-metamaterial sensing chips were prepared for great enhancing of detection sensitivity. A metamaterial sensing chip was designed for increasing of absorption cross section of the target sample, related to the transmitted THz near field enhancement via the composition of metamaterial. The measured THz optical properties were then analyzed in terms of refractive index and absorption coefficient, and compared with simulation results. Also, virus quantification regarding various concentrations of the viruses was performed, showing a clear linearity. The proposed sensitive and selective THz detection method can provide abundant information of detected biomaterials to help deep understanding of fundamental optical characteristics of them, suggesting rapid diagnosis way especially useful for such dangerous and time-sensitive target biomaterials.