Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Sperm Surface Arylsulfatase A in Mouse Sperm-Zona Pellucida Binding1

Abstract We have previously described the zonae pellucidae (ZP) binding ability of a pig sperm surface protein, P68. Our recent results on peptide sequencing of 3 P68 tryptic peptides and molecular cloning of pig testis arylsulfatase A (AS-A) revealed the identity of P68 as AS-A. In this report, we demonstrate the presence of AS-A on the mouse sperm surface and its role in ZP binding. Using anti-AS-A antibody, we have shown by immunoblotting that AS-A was present in a Triton X-100 extract of mouse sperm. The presence of AS-A on the sperm plasma membrane was conclusively demonstrated by indirect immunofluorescence, immunogold electron microscopy, and AS-A's desulfation activity on live mouse sperm. The AS-A remained on the head surface of in vivo capacitated sperm, as revealed by positive immunofluorescent staining of oviductal/uterine sperm. Significantly, the role of mouse sperm surface AS-A on ZP binding was demonstrated by dose-dependent decreases of sperm-ZP binding on sperm pretreatment with anti-AS-A IgG/Fab. Furthermore, Alexa-430 conjugated AS-A bound to mouse ZP of unfertilized eggs but not to fertilized ones, and this level of binding increased and approached saturation with increasing Alexa-430 AS-A concentrations. Moreover, in vivo fertilization was markedly decreased when mouse sperm pretreated with anti-AS-A IgG were artificially inseminated into females. All of these results designated a new function for AS-A in mouse gamete interaction.
High-Level Counterexamples for Probabilistic Automata

Providing compact and understandable counterexamples for violated system properties is an essential task in model checking. Existing works on counterexamples for probabilistic systems so far computed either a large set of system runs or a subset of the system's states, both of which are of limited use in manual debugging. Many probabilistic systems are described in a guarded command language like the one used by the popular model checker PRISM. In this paper we describe how a minimal subset of the commands can be identified which together already make the system erroneous. We additionally show how the selected commands can be further simplified to obtain a well-understandable counterexample.
Impact of interleukin-6 promoter polymorphism and serum interleukin-6 level on the acute inflammation and neovascularization stages of patients with Eales’ disease

Purpose To evaluate the role of interleukin-6 (IL-6) in the inflammatory and proliferative stages of Eales’ disease (ED) and to determine the influence of IL-6–174G/C polymorphism in the IL-6 and IL-6-regulated protein expression, as well as the development of ED. Methods One hundred and twenty-one patients diagnosed with ED, 223 matched healthy controls, and 16 control patients with macular holes were recruited from the eastern Indian population. Serum and vitreous levels of IL-6 and vascular endothelial growth factors (VEGF) were measured by enzyme-linked immunosorbent assay. Serum levels of high-sensitivity C-reactive protein (hsCRP) were measured by enzyme immunoassay. Subjects were genotyped for the IL-6–174G/C polymorphism (rs1800795) by a custom TaqMan single-nucleotide polymorphism (SNP) Genotyping Assays system. Results Serum IL-6 (p<0.0001), hsCRP (p<0.0001), and VEGF (p=0.0031) levels were significantly higher in the inflammatory stage of ED than in healthy controls. Serum IL-6 also significantly correlated with hsCRP (Spearman’s correlation coefficient; r=0.4992, p=0.0009), but not with VEGF in this stage in ED patients. At the proliferative stage of ED, significantly higher levels of vitreous IL-6 (p=<0.0001) and VEGF (p=<0.0001) were found compared with the vitreous of patients with macular holes. A significant correlation was observed between vitreous IL-6 and VEGF in ED patients (Spearman’s correlation coefficient; r=0.5834, p=0.0087). A statistically significant association was found between the −174GG genotype (p=0.006) and occurrence of ED. Mean serum and vitreous concentrations of IL-6 were also higher in the subjects with the GG genotype than in those with the GC or CC genotype in this population. Conclusions IL-6 expression, regulated by the allelic distribution of −174 loci and the enhanced level of IL-6, modulates CRP and VEGF concentration depending respectively on the acute inflammatory stimulation at the initial stage and angiogenic stimulation at the advanced stage of ED.
Helping Schoolchildren Cope with Anger: A Cognitive-Behavioral Intervention. Second Edition.

This book is one of a series of books published by the Guilford Press for a specific readership, the school–based clinician (‘The Guilford School Practitioner Series’). I must confess that I am not currently working as a school–based clinician (though I have done so in past). I chose to review this book because of a desire to learn more about the basis of aggression in children, and because of a long-standing interest in cognitive–behavioral therapy. On the whole, this is a great book for school-based clinicians who are looking for guidance in starting and running an efficacious anger management group for children between the ages of 8 and 12 years. The book is of less practical relevance to mental health clinicians in other settings. I enjoyed the first two chapters, which provided me with a basic understanding of the many issues associated with the development of aggression in children. These chapters outline the guiding theoretical principles underlying the “Anger Coping Program. ” A particular strength of this book is the authors’ relentless focus on the message that “treatment is not only about change, it is about generalization of that change. ” Indeed this generalization is achieved via significant collaboration with teachers, school administrators, and parents (reference chapters 3 – 5). In the 6th chapter, the authors present outcome research results. I found it hard to stay focused while reading this chapter, although the information presented is of direct relevance to the issue at hand. I believe this to be because the chapter itself was written in a less cohesive style than both earlier and subsequent chapters. Chapter 7 contains the complete, session-by-session, treatment manual. It is well written and interesting. The balance between providing adequate structure, and allowing for flexibility in treatment is achieved with skill and grace. A section on ‘frequently asked questions’ is provided in the eighth chapter. A case example is described in the ninth chapter. The book concludes with a chapter that discusses the importance of post-treatment evaluation of group members, booster sessions, additional maintenance and generalization ideas, and insightful comments about the ongoing needs of highly externalizing children after the group sessions are over. In conclusion, the book is a well written, detailed account of an empirically tested school-based group intervention for children manifesting aggressive behavior who are between the ages of eight and twelve years. The theoretical foundations are sound and well elucidated. The importance of collaboration with school personnel and parents is underlined and practical suggestions are made with regard to how to approach staff, administrators and parents. The manual itself is clearly written with specific, practical suggestions and built in flexibility. The book concludes with ten appendices providing sample letters and forms.
Toxicity Issues Related to Biomedical Applications of Carbon Nanotubes

Carbon Nanotubes (CNTs) have emerged as a potential candidate for application in targeted drug delivery, cancer treatment, gene therapy and diagnostics. This review critically evaluates the biomedical potential of CNTs, and possible toxicological implications. Success of CNTs in other fields has not yet been translated to the biomedical field due to the lack of consistent data on toxicity, variation of toxicity due to characteristics such as shape and size along with the method of preparation, and limited control over functionalized CNTs behavior. Thus there is a lack of a predictable toxicity pattern of CNTs. This review summarizes the key findings on the toxicity of CNTs and the role of functionalization with hydrophilic moieties to reduce their toxicity, and increase cell penetrability for drug delivery and gene therapy applications. Caution is urged when handling this ‘wonder material’ but the immense potential for its commercial utilization and clinical trials infuses hope for future biomedical applications.
Fuzzy C-means with a local membership kl distance for medical image segmentation

This paper presents a new technique for incorporating local membership information into the standard fuzzy C-means (FCM) clustering algorithm. In this technique, the objective consists of minimizing the classical FCM function with a unity fuzzifier exponent plus the Kullback-Leibler (KL) information distance acting as a fuzzification and regularization term. The KL distance is proposed to measure the proximity between cluster membership function of a pixel and an average of the cluster membership functions of immediate neighborhood pixels. Therefore, minimizing this KL distance biases the cluster membership of the pixel toward this smoothed membership function of the local neighborhoods. This can provide immunity against noise and results in clustered images with piecewise homogeneous regions. Results of clustering and segmentation of synthetic and real-world medical images are presented to compare the performance of the proposed local membership KL information based FCM (LMKLFCM) and the standard FCM, a local data information based FCM (LDFCM) and a type of local membership information based FCM (LMFCM) algorithms.
Nucleophosmin modulates stability, activity, and nucleolar accumulation of base excision repair proteins

NPM1 is a novel modulator of the BER pathway. NPM1 depletion results in BER protein up-regulation; NPM1 has a stimulatory effect on BER capacity and promotes accumulation of BER proteins within nucleoli. Cisplatin leads to redistribution of NPM1 and BER proteins from nucleoli.
Photonic Crystal Enhanced Silicon Cell Based Thermophotovoltaic Systems References and Links

We report the design, optimization, and experimental results of large area commercial silicon solar cell based thermophotovoltaic (TPV) energy conversion systems. Using global non-linear optimization tools, we demonstrate theoretically a maximum radiative heat-to-electricity efficiency of 6.4% and a corresponding output electrical power density of 0.39 W cm −2 at temperature T = 1660 K when implementing both the optimized two-dimensional (2D) tantalum photonic crystal (PhC) selective emitter, and the optimized 1D tantalum pentoxide – silicon dioxide PhC cold-side selective filter. In addition, we have developed an experimental large area TPV test setup that enables accurate measurement of radiative heat-to-electricity efficiency for any emitter-filter-TPV cell combination of interest. In fact, the experimental results match extremely well with predictions of our numerical models. Our experimental setup achieved a maximum output electrical power density of 0.10 W cm −2 and radiative heat-to-electricity efficiency of 1.18% at T = 1380 K using commercial wafer size back-contacted silicon solar cells. Efficiency and power density potential of combustion-driven thermophotovoltaic systems using GaSb photovoltaic cells, " IEEE Trans. Solar thermophotovoltaic converters based on tungsten emitters, " J. " Greater than 20% radiant heat conversion efficiency of a thermophotovoltaic radiator/module system using reflective spectral control, " IEEE Trans. Toward high-energy-density, high-efficiency, and moderate-temperature chip-scale thermophotovoltaics. Development of a silicon concentrator solar cell based TPV power system, " Energ. A highly efficient NiO-Doped MgO matched emitter for thermophotovoltaic energy conversion, " Mat. Characterisation of rare earth selective emitters for thermophotovoltaic applications, " Sol. Thermal emission and design in one-dimensional periodic metallic photonic crystal slabs, " Phys. Photonic crystal enhanced narrow-band infrared emitters, " Appl. Phys. Thermophotovoltaic generation with selective radiators based on tungsten surface gratings , " Appl. Sharp thermal emission and absorption from conformally coated metallic photonic crystal with triangular lattice, " Appl. All-metallic three-dimensional photonic crystals with a large infrared bandgap, " Nature 417, 52–55 (2002). Three-dimensional photonic-crystal emitter for thermal photovoltaic power generation, " Appl. High-temperature metal coating for modification of photonic band edge position, " J. Tailoring thermal emission via Q-matching of photonic crystal resonances, " Phys. Performance analysis of experimentally viable photonic crystal enhanced thermophotovoltaic systems, " Opt. Large-area fabrication of high aspect ratio tantalum photonic crystals for high-temperature selective emitters, " J. " High-temperature stability and selective thermal emission of polycrystalline tantalum photonic crystals, " Opt. A free electromagnetic solver for layered periodic structures, " Comput. A flexible free-software package for electromagnetic simulations …
Characterization of a Relatively Malignant Form of Osteopetrosis Caused by a Novel Mutation in the PLEKHM1 Gene

Osteopetrosis (OMIM: 611497), literally “stone bone,” is a group of inherited bone disorders characterized by increased skeletal mass due to defective osteoclast function. A patient who reported a history of frequent fractures, weakness and fatigue was admitted to our hospital in 2011. The patient presented with the typical features of osteopetrosis: fractures after minor trauma, early tooth loss, anemia, hepatosplenomegaly, and a generalized increase in bone mineral density (BMD). Aside from his father's complaint of excessive tooth loss, his mother, two sisters, son, and daughter were healthy. Blood samples of the family members were drawn for genetic analyses. The entire coding region and adjacent splice sites of the pleckstrin homology domain–containing family M (with RUN domain) member 1 (PLEKHM1) gene were sequenced. One mutation, a heterozygous deletion mutation in exon 11 (c.3051_3052delCA), was identified in the patient but not in his relatives. The mutation leads to a translation product with a highly impaired Rubicon homology domain. Co‐immunoprecipitation and immunofluorescence analyses using HEK293 cells showed that overexpression of a PLEKHM1 CA‐deletion mutant resulted in a dramatic decrease in the interaction between PLEKHM1 and the small GTPase Rab7 compared to wild‐type PLEKHM1. The normal processes of endocytosis and autophagy were disturbed in cells expressing the mutant (transfected HEK293 and U937 cells), as indicated by epidermal growth factor receptor (EGFR) degradation and an altered LC3‐I/II ratio, respectively, which may lead to a defect in osteoclast function. A four‐year follow‐up study of the patient showed that the PLEKHM1‐dependent osteopetrosis was relatively malignant, with significant symptoms of pancytopenia and hepatosplenomegaly. © 2016 American Society for Bone and Mineral Research.
Oxygen uptake dynamics during high-intensity exercise in children and adults.

We hypothesized that the O2 uptake (Vo2) response to high-intensity exercise would be different in children than in adults. To test this hypothesis, 22 children (6-12 yr old) and 7 adults (27-40 yr old) performed 6 min of constant-work-rate cycle-ergometer exercise. Sixteen children performed a single test above their anaerobic threshold (AT). In a separate protocol, six children and all adults exercised at low and high intensity. Low-intensity exercise corresponded to the work rate at 80% of each subject's AT. High-intensity exercise (above the AT) was determined first by calculating the difference in work rate between the AT and the maximal Vo2 (delta). Twenty-five, 50, and 75% of this difference were added to the work rate at the subject's AT, and these work rates were referred to as 25% delta, 50% delta, and 75% delta. For exercise at 50% delta and 75% delta, Vo2 increased throughout exercise (O2 drift, linear regression slope of Vo2 as a function of time from 3 to 6 min) in all the adults, and the magnitude of the drift was correlated with increasing work rates in the above-AT range (r = 0.91, P less than 0.0001). In contrast, no O2 drift was observed in over half of the children during above-AT exercise. The O2 drifts were much higher in adults (1.76 +/- 0.63 ml O2.kg-1.min-2 at 75% delta) than in children (0.20 +/- 0.42, P less than 0.01). (ABSTRACT TRUNCATED AT 250 WORDS)
The 2005 Music Information retrieval Evaluation Exchange (MIREX 2005): Preliminary Overview

This paper is an extended abstract which provides a brief preliminary overview of the 2005 Music Information Retrieval Evaluation eXchange (MIREX 2005). The MIREX organizational framework and infrastructure are outlined. Summary data concerning the 10 evaluation contests is provided. Key issues affecting future MIR evaluations are identified and discussed. The paper concludes with a listing of targets items to be undertaken before MIREX 2006 to ensure the ongoing success of the MIREX framework.
Insights into associative long-term potentiation from computational models of NMDA receptor-mediated calcium influx and intracellular calcium concentration changes.

1. Because induction of associative long-term potentiation (LTP) in the dentate gyrus is thought to depend on Ca2+ influx through channels controlled by N-methyl-D-aspartate (NMDA) receptors, quantitative modeling was performed of synaptically mediated Ca2+ influx as a function of synaptic coactivation. The goal was to determine whether Ca2+ influx through NMDA-receptor channels was, by itself, sufficient to explain associative LTP, including control experiments and the temporal requirements of LTP. 2. Ca2+ influx through NMDA-receptor channels was modeled at a synapse on a dendritic spine of a reconstructed hippocampal dentate granule cell when 1-115 synapses on spines at different dendritic locations were activated eight times at frequencies of 10-800 Hz. The resulting change in [Ca2+] in the spine head was estimated from the Ca2+ influx with the use of a model of a dendritic spine that included Ca2+ buffers, pumps, and diffusion. 3. To use a compelling model of synaptic activation, we developed quantitative descriptions of the NMDA and non-NMDA receptor-mediated conductances consistent with available experimental data. The experimental data reported for NMDA and non-NMDA receptor-channel properties and data from other non-LTP experiments that separated the NMDA and non-NMDA receptor-mediated components of synaptic events proved to be limiting for particular synaptic variables. Relative to the non-NMDA glutamate-type receptors, 1) the unbinding of transmitter from NMDA receptors had to be slow, 2) the transition from the bound NMDA receptor-transmitter complex to the open channel state had to be even slower, and 3) the average number of NMDA-receptor channels at a single activated synapse on a single spine head that were open and conducting at a given moment in time had to be very small (usually less than 1). 4. With the use of these quantitative synaptic conductance descriptions. Ca2+ influx through NMDA-receptor channels at a synapse was computed for a variety of conditions. For a constant number of pulses, Ca2+ influx was calculated as a function of input frequency and the number of coactivated synapses. When few synapses were coactivated, Ca2+ influx was small, even for high-frequency activation. However, with larger numbers of coactivated synapses, there was a steep increase in Ca2+ influx with increasing input frequency because of the voltage-dependent nature of the NMDA receptor-mediated conductance. Nevertheless, total Ca2+ influx was never increased more than fourfold by increasing input frequency or the number of coactivated synapses. (ABSTRACT TRUNCATED AT 400 WORDS)
Proceedings of Detc00 2000 Asme Design Engineering Technical Conferences Layered Manufacturing of Thin-walled Parts

We describe a new algorithm we have developed for making partially hollow layered parts with thin, dense walls of approximately uniform thickness, for faster build times and reduced material usage. We have implemented our algorithm on a fused deposition modeling (FDM) machine, using separate build volumes for a loosely filled interior and a thin, solid, exterior wall. The build volumes are derived as simple boolean combinations of slice contours and their offsets. We make use of an efficient algorithm for computing the Voronoi diagram of a general polygon as part of the process of creating offset contours. Our algorithm guarantees that the surface of the final part will be dense while still allowing an efficient build. INTRODUCTION Designers who want to make prototypes of solid three-dimensional parts directly from CAD descriptions are increasingly turning to a class of technologies collectively referred to as layered manufacturing or solid freeform fabrication (SFF). These technologies include stereolithography (SLA), 3-D printing , fused deposition modeling (FDM), selective laser sintering (SLS), and laminated object manufacturing (LOM)(4). In all these processes, a triangulated boundary representation (b-rep) of the CAD model of the part in STL format (1) is sliced into horizontal , 2.5-D layers of uniform thickness. Each cross sectional layer is successively deposited, hardened, fused, or cut, depend
DairyMod : a biophysical simulation model of the Australian dairy system

Abstract DairyMod is a biophysical simulation model of the dairy pasture system. It has been designed to explore dairy pasture management and incorporates the principal rotational grazing management strategies that are used in Australia. It also includes full treatment of the fluxes of water and nutrients in the grazing system, and therefore it also has utility in analyzing changes in resource condition in response to management and/or environmental variation. A principal feature of the model is its ease of use and intuitive, informative, interface.
NS-187 (INNO-406), a Bcr-Abl/Lyn Dual Tyrosine Kinase Inhibitor

Protein kinases catalyze the transfer of the γ-phosphoryl group of adenosine triphosphate (ATP) to the hydroxyl groups of protein side chains, and they play critical roles in regulating cellular signal transduction and other biochemical processes. They are attractive targets for today’s drug discovery and development, and many pharmaceutical companies are intensively developing various kinds of protein kinase inhibitors. A good example is the recent success with the Bcr-Abl tyrosine kinase inhibitor imatinib mesylate (Gleevec™) in the treatment of chronic myeloid leukemia. Though imatinib has dramatically improved the treatment of Bcr-Abl-positive chronic myeloid leukemia, resistance is often found in patients with advanced-stage disease. Several mechanisms have been proposed to explain this resistance, including point mutations within the Abl kinase domain, amplification of the bcr-abl gene, overexpression of the corresponding mRNA, increased drug efflux mediated by P-glycoprotein, and activation of the Src-family kinase (SFK) Lyn. We set out to develop a novel drug whose affinity for Abl is higher than that of imatinib and whose specificity in inhibiting Lyn is higher than that of SFK/Abl inhibitors such as dasatinib (Sprycel™) or bosutinib (SKI-606). Our work has led to the development of NS-187 (INNO-406), a novel Abl/Lyn dual tyrosine kinase inhibitor with clinical prospects. To provide an overview of how a selective kinase inhibitor has been developed, this review presents chemical-modification studies carried out with the guidance of molecular modeling, the structural basis for the high potency and selectivity of NS-187 based on the X-ray structure of the NS-187/Abl complex, and the biological profiling of NS-187, including site-directed mutagenesis experiments.