bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data
Authors: Lutzmayer Stefan , Enugutti Balaji , Nodine Michael D. 
Published: July 2017

AbstractNormalization of high-throughput small RNA sequencing (sRNA-Seq) data is required to compare sRNA levels across different samples. Commonly used relative normalization approaches can cause erroneous conclusions due to fluctuating small RNA populations between tissues. We developed a set of sRNA spike-in oligonucleotides (sRNA spike-ins) that enable absolute normalization of sRNA-Seq data across independent experiments, as well as the genome-wide estimation of sRNA:mRNA stoichiometries when used together with mRNA spike-in oligonucleotides.
A Practical Model Evaluating Antiviral Cytokines by Natural Killer Cells in Treatment Naïve Patients with Chronic Hepatitis B Virus Infection
Authors: Li Xiaoyan , Gu Yurong , Guo Xiaobo , Gu Lin , Zhou Liang , Wu Xiaojuan , Wang Xueqin , Stamataki Zania , Huang Yuehua 
Published: July 2017

AbstractNatural killer (NK) cells play a major role in anti-viral immunity as first line defense during hepatitis B infection, particularly in untreated patients whose T cells functions are profoundly impaired. Cytokine interferon (IFN)-γ and tumor necrosis factor (TNF)-α produced by NK cells are important anti-viral factors. However, there is lack of a quantifiable model to evaluate cytokine responses by NK cells. In this study, almost half of the patients (47.9%) beyond treatment criteria had high cytokine activity, although it was lower than those recommended for antiviral therapy (78.2%). Moreover, we developed a model that low levels of HBsAg, HBcAb, and albumin and high fibrosis values predicted strong antiviral cytokine production by NK cells. Based on the cut-off score (0.361) obtained from the multivariable model, patients with 67%, 8%, 92%, and 74% in immune-active (IA), immune-tolerant (IT), immune-inactive (IC), and grey zone (GZ), respectively, showed active antiviral cytokines produced by NK cells. These results suggest that those who possess activated cytokine responses beyond the current treatment criteria may have potential implications for the timing of antiviral therapy to achieve better virus control.
Carrier-Mediated and Energy-Dependent Uptake and Efflux of Deoxynivalenol in Mammalian Cells
Authors: Li Xiaoming , Mu Peiqiang , Wen Jikai , Deng Yiqun 
Published: July 2017

AbstractDeoxynivalenol (DON) is one of the most abundant mycotoxins and exerts many adverse effects on humans and animals. To date, the transporting mechanism of DON in mammalian cells remains unclear. In this study, the parallel artificial membrane permeability assay (PAMPA), Transwell models and metabolic inhibitors were used to determine the possible transporting mechanisms of DON in Caco-2, MDCK and HepG2 cells. PAMPA and Transwell models showed reduced passive transport and increased intestinal absorption, indicating a carrier-mediated transporting mechanism. Furthermore, higher unidirectional transport of DON was observed in the basolateral-to-apical direction than in the apical-to-basolateral direction, indicating the existence of efflux proteins. Interestingly, DON was accumulated in the nucleus, and no DON was detected in mitochondria, indicating that the nucleus may be the main target organelle of DON. Moreover, the use of various transporter inhibitors in different cells shows that organic anion transporters, organic cation transporters, and organic anion-transporting polypeptides participate in DON uptake, and P-glycoprotein is the major efflux protein. Importantly, DON uptake is strongly inhibited by metabolic inhibitors and is highly dependent on temperature. In summary, carrier-mediated and energy-dependent uptake and efflux mechanisms for DON in mammalian cells are reported, aiding in improving our understanding of its toxicological mechanisms.
Coherence properties of different light sources and their effect on the image sharpness and speckle of holographic displays
Authors: Deng Yuanbo , Chu Daping 
Published: July 2017

AbstractCoherence properties of different light sources and how they affect the image quality of holographic display are investigated. Temporal coherence is related to the intrinsic spectrum bandwidth of the light source, while spatial coherence can be affected by the size of the light source and propagation distance in use. These two coherence properties are measured for various light sources of diode-pumped solid-state (DPSS) laser, laser diode (LD), light emitting diode (LED), super luminescent light emitting diode (sLED) and micro light emitting diode (mLED) in different settings, together with the quality of the holographic reconstructed images. Although the image sharpness and speckle are related to both coherence parameters, our results and subsequent analysis show that the spatial coherence can be linked directly to the image sharpness and the temporal coherence to the speckle. This will provide a quantitative way not only to optimize the image quality between uniformity and sharpness but also to determine the safety power level for different light sources when viewing the produced images by human eyes directly.
Marker-trait association analysis of frost tolerance of 672 worldwide pea (Pisum sativum L.) collections
Authors: Liu Rong , Fang Li , Yang Tao , Zhang Xiaoyan , Hu Jinguo , Zhang Hongyan , Han Wenliang , Hua Zeke , Hao Junjie , Zong Xuxiao 
Published: July 2017

AbstractFrost stress is one of the major abiotic stresses causing seedling death and yield reduction in winter pea. To improve the frost tolerance of pea, field evaluation of frost tolerance was conducted on 672 diverse pea accessions at three locations in Northern China in three growing seasons from 2013 to 2016 and marker-trait association analysis of frost tolerance were performed with 267 informative SSR markers in this study. Sixteen accessions were identified as the most winter-hardy for their ability to survive in all nine field experiments with a mean survival rate of 0.57, ranging from 0.41 to 0.75. Population structure analysis revealed a structured population of two sub-populations plus some admixtures in the 672 accessions. Association analysis detected seven markers that repeatedly had associations with frost tolerance in at least two different environments with two different statistical models. One of the markers is the functional marker EST1109 on LG VI which was predicted to co-localize with a gene involved in the metabolism of glycoproteins in response to chilling stress and may provide a novel mechanism of frost tolerance in pea. These winter-hardy germplasms and frost tolerance associated markers will play a vital role in marker-assisted breeding for winter-hardy pea cultivar.
Full-color, large area, transmissive holograms enabled by multi-level diffractive optics
Authors: Mohammad Nabil , Meem Monjurul , Wan Xiaowen , Menon Rajesh 
Published: July 2017

AbstractWe show that multi-level diffractive microstructures can enable broadband, on-axis transmissive holograms that can project complex full-color images, which are invariant to viewing angle. Compared to alternatives like metaholograms, diffractive holograms utilize much larger minimum features (>10 µm), much smaller aspect ratios (<0.2) and thereby, can be fabricated in a single lithography step over relatively large areas (>30 mm ×30 mm). We designed, fabricated and characterized holograms that encode various full-color images. Our devices demonstrate absolute transmission efficiencies of >86% across the visible spectrum from 405 nm to 633 nm (peak value of about 92%), and excellent color fidelity. Furthermore, these devices do not exhibit polarization dependence. Finally, we emphasize that our devices exhibit negligible absorption and are phase-only holograms with high diffraction efficiency.
Efficient generation of single domain antibodies with high affinities and enhanced thermal stabilities
Authors: Shinozaki Naoya , Hashimoto Ryuji , Fukui Kiichi , Uchiyama Susumu 
Published: July 2017

AbstractSingle domain antibodies (sdAbs), made of natural single variable regions of camelid or cartilaginous fish antibodies, or unpaired variable regions of mouse or human IgGs, are some of the more promising biologic modalities. However, such conventional sdAbs have difficulties of either using unwieldy animals for immunization or having high affinity deficiencies. Herein, we offer a versatile method to generate rabbit variable domain of heavy chain (rVH) derived sdAbs with high affinities (KD values of single digit nM or less) and enhanced thermal stabilities (equal to or even higher than those of camelid derived sdAbs). It was found that a variety of rVH binders, including those with high affinities, were efficiently acquired using an rVH-displaying phage library produced at a low temperature of 16 °C. By a simple method to introduce an additional disulfide bond, their unfolding temperatures were increased by more than 20 °C without severe loss of binding affinity. Differential scanning calorimetry analysis suggested that this highly efficient thermal stabilization was mainly attributed to the entropic contribution and unique thermodynamic character of the rVHs.
Bovine milk-derived exosomes from colostrum are enriched with proteins implicated in immune response and growth
Authors: Samuel Monisha , Chisanga David , Liem Michael , Keerthikumar Shivakumar , Anand Sushma , Ang Ching-Seng , Adda Christopher G. , Versteegen Ellen , Jois Markandeya , Mathivanan Suresh 
Published: July 2017

AbstractExosomes are extracellular vesicles secreted by multiple cell types into the extracellular space. They contain cell-state specific cargos which often reflects the (patho)physiological condition of the cells/organism. Milk contains high amounts of exosomes and it is unclear whether their cargo is altered based on the lactation stage of the organism. Here, we isolated exosomes from bovine milk that were obtained at various stages of lactation and examined the content by quantitative proteomics. Exosomes were isolated by OptiPrep density gradient centrifugation from milk obtained from cow after 24, 48 and 72 h post calving. As control, exosomes were also isolated from cows during mid-lactation period which has been referred to as mature milk (MM). Biochemical and biophysical characterization of exosomes revealed the high abundance of exosomes in colostrum and MM samples. Quantitative proteomics analysis highlighted the change in the proteomic cargo of exosomes based on the lactation state of the cow. Functional enrichment analysis revealed that exosomes from colostrum are significantly enriched with proteins that can potentially regulate the immune response and growth. This study highlights the importance of exosomes in colostrum and hence opens up new avenues to exploit these vesicles in the regulation of the immune response and growth.
Effects of exogenous thymosin β4 on carbon tetrachloride-induced liver injury and fibrosis
Authors: Li Xiankui , Wang Lei , Chen Cai 
Published: July 2017

AbstractThe present study investigated the effects of exogenous thymosin β4 (TB4) on carbon tetrachloride (CCl4)-induced acute liver injury and fibrosis in rodent animals. Results showed that both in mice and rats CCl4 rendered significant increases in serum alanine aminotransferase and aspartate aminotransferase, hepatic malondialdehyde formation, decreases in antioxidants including superoxide dismutase and glutathione, and up-regulated expressions of transforming growth factor-β1, α-smooth muscle actin, tumor necrosis factor-α and interleukin-1β in the liver tissues. Hydroxyproline contents in the rat livers were increased by CCl4. Histopathological examinations indicated that CCl4 induced extensive necrosis in mice livers and pseudo-lobule formations, collagen deposition in rats livers. However, all these changes in mice and rats were significantly attenuated by exogenous TB4 treatment. Furthermore, up-regulations of nuclear factor-κB p65 protein expression by CCl4 treatment in mice and rats livers were also remarkably reduced by exogenous TB4 administration. Taken together, findings in this study suggested that exogenous TB4 might prevent CCl4-induced acute liver injury and subsequent fibrosis through alleviating oxidative stress and inflammation.
Alternatives to mineral oil adjuvants in vaccines against Aeromonas salmonicida subsp. salmonicida in rainbow trout offer reductions in adverse effects
Authors: Villumsen Kasper Rømer , Koppang Erling Olaf , Christensen Dennis , Bojesen Anders Miki 
Published: July 2017

AbstractIn an effort to reduce the frequency and severity of adverse reactions seen from the use of mineral oil adjuvants in salmonid fish, the effects of two alternative adjuvants were assessed, focusing on the induction of adverse effects as well as protection. Using rainbow trout (Oncorhynchus mykiss) as recipients, injection vaccines based on formalin-inactivatedAeromonas salmonicidasubspeciessalmonicidawere formulated with CpG oligodeoxynucleotides, the liposomal cationic adjuvant formulation 01 (CAF01) or with Freund’s incomplete adjuvant and administered intraperitoneally. Control groups of unvaccinated, Tris-buffered saline-injected or bacterin-injected individuals were included, and each group included in the study held a total number of 240 individuals. Subsequently, individuals from each group were examined for differences in Fulton’s condition factor, macro- and microscopic pathological changes, as well as protection against experimental infection withA. salmonicida. While adverse effects were not eliminated, reductions in microscopic and macroscopic adverse effects, in particular, were seen for both the nucleotide- and liposome-based vaccine formulations. Furthermore, the induced protection appears similar to that of the benchmark formulation, thus introducing viable, potential alternative types of adjuvants for use in future fish vaccines.
Nitrogen-doped Carbon Dots Mediated Fluorescent on-off Assay for Rapid and Highly Sensitive Pyrophosphate and Alkaline Phosphatase Detection
Authors: Hu Yalei , Geng Xin , Zhang Lin , Huang Zhongming , Ge Jia , Li Zhaohui 
Published: July 2017

AbstractIn this report, a novel fluorescent sensing platform using nitrogen-doped carbon dots (N-CDs) as probes for fluorescence signal transmission has been designed for the detection of significant biomolecules pyrophosphate (PPi) and alkaline phosphatase (ALP). The high fluorescent N-CDs could be selectively quenched by Cu2+, and recovered by the addition of PPi because PPi preferentially binds to Cu2+. Once ALP was introduced into the system, ALP can specifically hydrolyze PPi into Pi, the intense fluorescence of N-CDs could be quenched again due to the recombination of the as-released Cu2+ with N-CDs. So, fluorescence of N-CDs is regulated by an ALP-triggered reaction. Based on this strategy, we demonstrated that N-CDs could serve as a very effective fluorescent sensing platform for label-free, sensitive and selective detection of PPi and ALP with low detection limit of 0.16 μM and 0.4 U/L for PPi and ALP, respectively. Moreover, the assay time is just around 0.5 min for PPi and 30 min for ALP. This developed strategy shows remarkable advantages including sensitive, rapid, simple, convenient, and low-cost and so forth. Furthermore, this method was also successfully applied to monitor ALP in human serum, which indicates its great potential for practical applications in biological and clinical diagnosis.
Improvement in the production of the human recombinant enzyme N-acetylgalactosamine-6-sulfatase (rhGALNS) in Escherichia coli using synthetic biology approaches
Authors: Reyes Luis H. , Cardona Carolina , Pimentel Luisa , Rodríguez-López Alexander , Alméciga-Díaz Carlos J. 
Published: July 2017

AbstractPreviously, we demonstrated production of an active recombinant human N-acetylgalactosamine-6-sulfatase (rhGALNS) enzyme in Escherichia coli as a potential therapeutic alternative for mucopolysaccharidosis IVA. However, most of the rhGALNS produced was present as protein aggregates. Here, several methods were investigated to improve production and activity of rhGALNS. These methods involved the use of physiologically-regulated promoters and alternatives to improve protein folding including global stress responses (osmotic shock), overexpression of native chaperones, and enhancement of cytoplasmic disulfide bond formation. Increase of rhGALNS activity was obtained when a promoter regulated under σ
s
was implemented. Additionally, improvements were observed when osmotic shock was applied. Noteworthy, overexpression of chaperones did not have any effect on rhGALNS activity, suggesting that the effect of osmotic shock was probably due to a general stress response and not to the action of an individual chaperone. Finally, it was observed that high concentrations of sucrose in conjunction with the physiological-regulated promoter proU
mod
significantly increased the rhGALNS production and activity. Together, these results describe advances in the current knowledge on the production of human recombinant enzymes in a prokaryotic system such as E. coli, and could have a significant impact on the development of enzyme replacement therapies for lysosomal storage diseases.
Pycnodysostosis: Novel Variants in CTSK and Occurrence of Giant Cell Tumor
Authors: Shah Hitesh , Nair Mohandas , Sharan Krishna , Jin Dong-Kyu , Cho Sung , Mathew Mary , Shukla Anju , Shambhavi Arya , Salian Smrithi , Girisha Katta 
Published: July 2017

AbstractPycnodysostosis is an autosomal recessive skeletal dysplasia caused by pathogenic variants in the cathepsin K (CTSK) gene. We report seven patients from four unrelated families with this condition in whom we have identified three novel pathogenic variants, c.120 + 1G > T in intron 2, c.399 + 1G > A in intron 4, and c.148T > G (p.W50G) in exon 2, and a known variant, c.568C > T (p.Q190*) in exon 5 of CTSK. We present the clinical, radiographic, and molecular findings of all individuals with molecularly proven pycnodysostosis from the present cohort. We also report the occurrence of giant cell tumor in the skull of a patient with this condition.
Neuromuscular Adaptations to Combined Strength and Endurance Training: Order and Time-of-Day
Authors: Küüsmaa-Schildt Maria , Eklund Daniela , Avela Janne , Rytkönen Tuomas , Newton Robert , Izquierdo Mikel , Häkkinen Keijo 
Published: July 2017

AbstractThe present study examined the effects of 24 weeks of morning vs. evening same-session combined strength (S) and endurance (E) training on neuromuscular and endurance performance. Fifty-one men were assigned to the morning (m) or evening (e) training group, where S preceded E or vice versa (SEm, ESm, SEe and ESe), or to the control group. Isometric force, voluntary activation, EMG and peak wattage during the maximal cycling test were measured. Training time did not significantly affect the adaptations. Therefore, data are presented for SEm+e (SEm+SEe) and ESm+e (ESm+ESe). In the morning, no order specific gains were observed in neuromuscular performance. In the evening, the changes in isometric force (SEm+e 15.9±16.7%, p=0.001; ESm+e 4.1±12.2%, p=0.615) and EMG (SEm+e 38.3±31.7%, p=0.001; ESm+e 14.67±36.44%, p=0.486) were larger (p=0.014) in SEm+e than in ESm+e and in voluntary activation larger (p=0.026) in SEm+e compared to controls. Peak wattage increased in the morning (SEm+e 15.9±9.2%, ESm+e 22.0±7.0%; p<0.001) and evening (SEm+e 16.3±7.2%, ESm+e 21.0±9.0%; p<0.001) but were larger (p<0.05) in ESm+e. The current training program led to greater neuromuscular adaptations when SE-training was performed in the evening, whereas the ES-training provided more optimal conditions for endurance performance adaptations both in the morning and evening.
Validity and Reliability of a New Device (WIMU®) for Measuring Hamstring Muscle Extensibility
Authors: Muyor José 
Published: July 2017

AbstractThe aims of the current study were 1) to evaluate the validity of the WIMU® system for measuring hamstring muscle extensibility in the passive straight leg raise (PSLR) test using an inclinometer for the criterion and 2) to determine the test-retest reliability of the WIMU® system to measure hamstring muscle extensibility during the PSLR test. 55 subjects were evaluated on 2 separate occasions. Data from a Unilever inclinometer and WIMU® system were collected simultaneously. Intraclass correlation coefficients (ICCs) for the validity were very high (0.983–1); a very low systematic bias (−0.21°–−0.42°), random error (0.05°–0.04°) and standard error of the estimate (0.43°–0.34°) were observed (left–right leg, respectively) between the 2 devices (inclinometer and the WIMU® system). The R2 between the devices was 0.999 (p<0.001) in both the left and right legs. The test-retest reliability of the WIMU® system was excellent, with ICCs ranging from 0.972–0.995, low coefficients of variation (0.01%), and a low standard error of the estimate (0.19–0.31°). The WIMU® system showed strong concurrent validity and excellent test-retest reliability for the evaluation of hamstring muscle extensibility in the PSLR test.
Pregnancy and Tumor Outcomes in Women with Prolactinoma
Authors: Araujo Bárbara , Belo Sandra , Carvalho Davide 
Published: July 2017

Abstract
Context Management of prolactinomas during pregnancy has always been a challenge. There is a concern about the risk of tumor growth, as well as the effects of the treatment on the developing fetus. Another issue that has been less studied is the outcome of women with prolactinoma after pregnancy and lactation.
Objectives To evaluate remission of hyperprolactinaemia after pregnancy and lactation in women with prolactinoma. To describe the safety of dopamine agonists for the fetus and pregnancy outcomes.
Methods A retrospective study of 32 pregnancies in women with prolactinoma was conducted in a single-centre. Other causes of hyperprolactinemia were excluded. Prolactin level was recorded at the time of diagnosis, during treatment, and during follow-up.
Results The pregnancies resulted in one spontaneous abortion (3.1%) and 31 live births (96.9%). No stillbirths, multiple or ectopic pregnancies or trophoblastic disease were recorded. There was only one malformation (club foot) recorded (3.1%) and normalisation of prolactin after pregnancy without medical treatment occurred in 12% of patients.
Conclusions Fetal exposure to bromocriptine or cabergoline during pregnancy is not associated with an increased risk of adverse neonatal or pregnancy disclosures. There is considerable diversity among endocrinologists in the management of prolactinomas during pregnancy and after birth, which indicates that there is a need for better consensus and for carefully drawn-up guidelines to follow.
An unbiased estimator for the ellipticity from image moments
Authors: Tessore Nicolas 
Published: July 2017

Abstract
An unbiased estimator for the ellipticity of an object in a noisy image is given in terms of the image moments. Three assumptions are made: (i) the pixel noise is normally distributed, although with arbitrary covariance matrix; (ii) the image moments are taken about a fixed centre; and (iii) the point spread function is known. The relevant combinations of image moments are then jointly normal and their covariance matrix can be computed. A particular estimator for the ratio of the means of jointly normal variates is constructed and used to provide the unbiased estimator for the ellipticity. Furthermore, an unbiased estimate of the covariance of the new estimator is also given.