gebhart/patrepeval huggingface dataset:
Subnanometer atomic force microscopy of peptide–mineral interactions links clustering and competition to acceleration and catastrophe (2009)

In vitro observations have revealed major effects on the structure, growth, and composition of biomineral phases, including stabilization of amorphous precursors, acceleration and inhibition of kinetics, and alteration of impurity signatures. However, deciphering the mechanistic sources of these effects has been problematic due to a lack of tools to resolve molecular structures on mineral surfaces during growth. Here we report atomic force microscopy investigations using a system designed to maximize resolution while minimizing contact force. By imaging the growth of calcium-oxalate monohydrate under the influence of aspartic-rich peptides at single-molecule resolution, we reveal how the unique interactions of polypeptides with mineral surfaces lead to acceleration, inhibition, and switching of growth between two distinct states. Interaction with the positively charged face of calcium-oxalate monohydrate leads to formation of a peptide film, but the slow adsorption kinetics and gradual relaxation to a well-bound state result in time-dependent effects. These include a positive feedback between peptide adsorption and step inhibition described by a mathematical catastrophe that results in growth hysteresis, characterized by rapid switching from fast to near-zero growth rates for very small reductions in supersaturation. Interactions with the negatively charged face result in formation of peptide clusters that impede step advancement. The result is a competition between accelerated solute attachment and inhibition due to blocking of the steps by the clusters. The findings have implications for control of pathological mineralization and suggest artificial strategies for directing crystallization.
Synergies of VEGF Inhibition and Photodynamic Therapy in the Treatment of Age-Related Macular Degeneration (2007)

The combined use of PDT and of agents targeting angiogenic cytokines may synergistically improve therapeutic outcome after combined treatment in patients with CNV secondary to AMD.
In Situ Gene Expression Analysis of Cancer Using Laser Capture Microdissection, Microarrays and Real Time Quantitative PCR (2002)

The simultaneous development of laser capture microdissection (LCM) and high-throughput mRNA analysis platforms has provided a significant technological advance in the world of cancer biology. The combination of such technologies provides a unique and powerful opportunity to directly assess the in situ molecular genetic events that are associated with initiation and progression of human malignancies. Despite these technological advances, the integration of LCM with high-throughput gene expression analysis has been met with various challenges. The goal of this review is to highlight some of the obstacles that we have faced and continue to face as we try to optimally apply LCM to in situ gene expression analysis.
Modeling and Control Analysis of a 3-PUPU Dual Compliant Parallel Manipulator for Micro Positioning and Active Vibration Isolation (2011)

In recent years, many applications in precision engineering require a careful isolation of the instrument from the vibration sources by adopting active vibration isolation system to achieve a very low remaining vibration level, especially for the very low frequency under 10 Hz vibration signals. This paper presents a 3-PUPU dual parallel manipulator for both rough positioning and active vibration isolation in a wide-range workspace based on our previous research experiences in the systematical modeling and study of parallel robots. The manipulator is designed as a kind of macro/micro hybrid robot. Both the kinematics model for macro motion and dynamics model for micro motion are established by using stiffness equation and the Kane’s method, respectively. An active vibration control strategy is described by using the H2 method. Moreover, numerical simulations on the inverse solution for macro motion, workspace, and the active vibration control effects are performed at the end of this paper.
Branched Chain Amino Acid Uptake and Muscle Free Amino Acid Concentrations Predict Postoperative Muscle Nitrogen Balance (1986)

Amino acid solutions rich in branched chain amino acids (BCAA) are commonly utilized both clinically and in experimental protocols in an attempt to reduce skeletal muscle and whole body protein catabolism. To investigate the effectiveness of BCAA infusion, amino acid formulas containing varying concentrations of BCAA were given during operation in this study to three groups of dogs undergoing a standard laparotomy and retroperitoneal dissection. A fourth group was given saline alone. With the use of previously described hindquarter flux techniques, individual and total amino acid nitrogen exchange rates were measured and utilized in estimating skeletal muscle protein catabolism. Intracellular free amino acid concentrations were measured in percutaneous muscle biopsy samples. Although there was no relationship with the rate of BCAA infusion, there was a significant correlation between the rate of BCAA uptake by muscle and diminished total nitrogen release from hindquarter skeletal muscle after operation. There was also a significant relationship between muscle nitrogen balance and the postoperative change in the muscle concentration of either total amino acids or the single amino acid glutamine. When combined in a single equation, BCAA uptake and the change in muscle free amino acid concentration predict skeletal muscle nitrogen release with an r = 0.86. Thus, the rate of BCAA uptake and the free glutamine or total amino acid concentration in muscle appear to be independent predictors of muscle nitrogen balance. The nitrogen-sparing effect of BCAA in skeletal muscle is unrelated to infusion concentration or rate of infusion.
Performance of scheduling algorithms for channel reservation (1994)

The performance of scheduling algorithms for a reservation system is investigated. In this system, a user request is characterised by its start time, resource requirement and holding time. Of interest are scheduling algorithms to handle user requests in a loss system where resource requirements may vary. A Markov decision process formulation is used to obtain the optimal scheduling decisions. Two special cases are considered in depth; they correspond to optimal algorithms that minimise the blocking probability and maximise the channel utilisation, respectively. Analytic results are also obtained for the blocking probability and channel utilisation for an arbitrary scheduling algorithm. Using these results, the performance of first come, first served (FCFS) and the two optimal algorithms is compared. We also prove that FCFS is optimal for maximising channel utilisation when the resource requirement follows a uniform distribution.
A Fabrication Process for Microstructured Optical Fibers (2006)

In this paper, a fabrication process is introduced and demonstrated for a square microstructured optical fiber lattice. An existing mathematical model of the manufacturing process of a single-hole capillary tube was modified to identify parameters for the microstructured fiber case. Commercial interests in silica microstructured optical fiber have resulted in the limited documentation of the fabrication process. This work may provide a straightforward technique to produce high-quality novel silica microstructured optical fibers with the potential to serve as a "road map" to future research in the area of micro- and nanostructured fiber development
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage (2003)

We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5' end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.
Transcriptional Profiling Reveals Coordinated Up-Regulation of Oxidative Metabolism Genes in Thyroid Oncocytic Tumors (2004)

Oncocytomas are large cell tumors characterized by an abnormal proliferation of mitochondria. To investigate this phenomenon in thyroid oncocytomas, we determined gene expression profiles of 87 samples using microarrays of 6720 PCR products from cDNA clones. Samples included 29 thyroid oncocytomas and six papillary carcinomas, the remainder representing other thyroid pathologies or mitochondria-rich tumor samples, normal thyroid samples, and two thyroid cell lines. Hierarchical clustering and supervised analysis identified two specific oncocytic clusters and 163 distinctly regulated genes between oncocytoma and normal thyroid. Differential expression of five selected genes (APOD, BCL-2, COX, CTSB, and MAP2) was confirmed by immunohistochemistry. The two specific oncocytic clusters were rich in mitochondrial genes and revealed coordinated expression of nuclear and mitochondrial respiratory chain genes. We also observed the up-regulation of genes involved in mitochondrial biogenesis, such as nuclear respiratory factor 1 and the endothelial nitric oxide synthase. Several oxidative metabolism genes were overexpressed in oncocytomas, including those from the tricarboxylic acid cycle (MDH1) and cytosolic glycolysis (GAPD, ENO1, and GPI). On the contrary, the lactate dehydrogenase A gene, involved in anaerobic metabolism, was down-regulated. Our results suggest that, unlike a large number of solid tumors, thyroid oncocytomas produce energy through an aerobic pathway.
A2 Media Studies (2010)

Developing key topics in depth and introducing students to the notion of independent study, this full colour, highly illustrated textbook is designed to support students through the transition from AS to A2 and is the perfect guide for the new WJEC A2 Media Studies syllabus. Individual chapters, written by experienced teachers and examiners cover the following key areas: •&nbsp;Introduction: From AS to A2•&nbsp;1. Key Concepts: genre, narrative, representation, audience •&nbsp;2. Developing Textual Analysis •&nbsp;3. Theoretical Perspectives •&nbsp;4.&nbsp; Passing MS4: Text, Industry and Audience•&nbsp;5.&nbsp; Passing MS3: Media Investigation and Production•&nbsp;EpilogueSpecially designed to be user-friendly, A2 Media Studies: The Essential Introduction for&nbsp;WJEC includes activities, key terms, case studies, sample exam questions and over 120 full colour images.
The influence of gestational age and postnatal age on neonatal cerebrospinal fluid parameters (2019)

Objective
To study the influence of gestational age (GA) and postnatal age on neonatal cerebrospinal fluid parameters.


Method
From January 2013 to December 2015, the results of WBC counts, glucose and protein concentrations of cerebro-spinal fluid (CSF) were collected from neonates admitted to neonatal department of our hospitals. The neonates were assigned into different groups according to their GA and postnatal age. The CSF parameters were compared between different groups, and the changes of CSF parameters were analyzed. STATA 12.0 software was used for statistical analysis.


Result
A total of 1 410 infants were included. 516 (36.6%) cases were preterm infants. 1 208 cases (85.7%) received antibiotics before lumbar puncture. WBC counts in CSF between preterm and term infants showed no significant differences (upper reference limit, 12.5×106/L). CSF glucose in term infants (lower reference limit, 1.8 mmol/L) was higher than preterm infants (lower reference limit, 1.6 mmol/L). CSF protein in preterm infants (upper reference limit, 226.6 mg/dl) was significantly higher than term infants (upper reference limit, 140.3 mg/dl). CSF WBC counts decreased with the growth of postnatal age in preterm infants (regression coefficients -0.030, P=0.035). CSF protein also declined significantly with the increase of postnatal age in term infants (regression coefficients -1.254, P<0.001). CSF glucose showed no significant decrease with the increase of postnatal age (regression coefficients -0.009, P=0.012).


Conclusion
GA and postnatal age did not produce an effect on WBC counts of CSF. The preterm infants had lower glucose level and higher protein level in CSF. CSF protein declined significantly with the increase of GA and postnatal age.


Key words: 
Cerebrospinal fluid; Reference values; Lumbar puncture; Influence factor
Conformational Changes of Escherichia coli RNA Polymerase ς70 Factor Induced by Binding to the Core Enzyme (1998)

Mutants of RNA polymerase sigma70 subunit from Escherichia coli with unique cysteine residues engineered into conserved region 1 (autoinhibition domain of sigma70), region 2.4 (-10 DNA element binding domain), region 4.2 (-35 DNA element binding domain), and a nonconserved region between regions 1 and 2 were prepared. The chemical reactivity of the cysteine at each position was determined for free sigma70 and sigma70 in complex with the core polymerase and was used as a measure of a conformational response of a particular region of the protein to an interaction with the core polymerase. Both increases and decreases in cysteine reactivity were observed in the presence of core polymerase at several positions in sigma70, providing direct physical evidence for modulation of sigma70 conformation by the core enzyme. Binding of the core polymerase resulted in increased solvent exposure of DNA binding domains of sigma70 and in more complex changes in the autoinhibition domain (region 1). Similar conformational changes in sigma70 were detected using fluorescence probes covalently attached to cysteine residues engineered into sigma70. Thus, the results obtained provided physical evidence supporting a model in which core enzyme allosterically regulates DNA binding activity of sigma70 by "unmasking" its DNA binding domains.
Uptake of Botulinum Neurotoxin into Cultured Neurons (2003)

Botulinum neurotoxins (BoNTs) act within the synaptic terminal to block neurotransmitter release. The toxin enters the neuron by binding to neuronal membrane receptor(s), being taken up into an endosome-like compartment, and penetrating the endosome membrane via a pH-dependent translocation process. Once within the synaptic cytoplasm, BoNT serotypes A and E cleave separate sites on the C-terminus of the neuronal protein SNAP-25, one of the SNARE proteins required for synaptic vesicle fusion. In this study, we measured the effect of brief toxin exposure on SNAP-25 proteolysis in neuronal cell cultures as an indicator of toxin translocation. The results indicate that (1) uptake of both BoNT-A and -E is enhanced with synaptic activity induced by K+ depolarization in the presence of Ca2+ and (2) translocation of BoNT-A from the acidic endosomal compartment is slow relative to that of BoNT-E. Polyclonal antisera against each toxin protect cells when applied with the toxin during stimulation but has no effect when added immediately after toxin exposure, indicating that toxin endocytosis occurs with synaptic activity. Both serotypes cleave SNAP-25 at concentrations between 50 pM and 4 nM. IC50 values for SNAP-25 cleavage are approximately 0.5 nM for both serotypes. Inhibition of the pH-dependent translocation process by pretreating cultures with concanamycin A (Con A) prevents cleavage of SNAP-25 with IC50 values of approximately 25 nM. Addition of Con A at times up to 15 min after toxin exposure abrogated BoNT-A action; however, addition of Con A after 40 min was no longer protective. In contrast, Con A inhibited, but did not prevent, translocation of BoNT-E even when added immediately after toxin exposure, indicating that pH-dependent translocation of BoNT-E is rapid relative to that of BoNT-A. This study demonstrates that uptake of both BoNT-A and -E is enhanced with synaptic activity and that translocation of the toxin catalytic moiety into the cytosol occurs at different rates for these two serotypes.
Thin‐film silicon solar cell technology (2004)

Abstract This paper describes the use, within p – i – n ‐ and n – i – p ‐type solar cells, of hydrogenated amorphous silicon (a‐Si:H) and hydrogenated microcrystalline silicon (μc‐Si:H) thin films (layers), both deposited at low temperatures (200°C) by plasma‐assisted chemical vapour deposition (PECVD), from a mixture of silane and hydrogen. Optical and electrical properties of the i ‐layers are described. These properties are linked to the microstructure and hence to the i ‐layer deposition rate, that in turn, affects throughput in production. The importance of contact and reflection layers in achieving low electrical and optical losses is explained, particularly for the superstrate case. Especially the required properties for the transparent conductive oxide (TCO) need to be well balanced in order to provide, at the same time, for high electrical conductivity (preferably by high electron mobility), low optical absorption and surface texture (for low optical losses and pronounced light trapping). Single‐junction amorphous and microcrystalline p – i – n ‐type solar cells, as fabricated so far, are compared in their key parameters ( J sc , FF, V oc ) with the [theoretical] limiting values. Tandem and multijunction cells are introduced; the μc‐Si: H/a‐Si: H or [micromorph] tandem solar cell concept is explained in detail, and recent results obtained here are listed and commented. Factors governing the mass‐production of thin‐film silicon modules are determined both by inherent technical reasons, described in detail, and by economic considerations. The cumulative effect of these factors results in distinct efficiency reductions from values of record laboratory cells to statistical averages of production modules. Finally, applications of thin‐film silicon PV modules, especially in building‐integrated PV (BIPV) are shown. In this context, the energy yields of thin‐film silicon modules emerge as a valuable gauge for module performance, and compare very favourably with those of other PV technologies. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Nucleic acid related compounds. 12. Facileand high yield stannous chloride catalyzed monomethylation of the cis glycol system of nucleosides by diazomethane (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleic acid related compounds. 12. Facileand high yield stannous chloride catalyzed monomethylation of the cis glycol system of nucleosides by diazomethaneMorris J. Robins, S. R. Naik, and Alan S. K. LeeCite this: J. Org. Chem. 1974, 39, 13, 1891–1899Publication Date (Print):June 1, 1974Publication History Published online1 May 2002Published inissue 1 June 1974https://pubs.acs.org/doi/10.1021/jo00927a022https://doi.org/10.1021/jo00927a022research-articleACS PublicationsRequest reuse permissionsArticle Views453Altmetric-Citations71LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Treatment of Lymphangiomas in Children: An Update of Picibanil (OK‐432) Sclerotherapy (1999)

Picibanil (OK‐432) is a sclerosing agent derived from a low‐virulence strain of Streptococcus pyogenes that induces regression of macrocystic lymphangiomas. This report describes a prospective, nonrandomized trial to evaluate the efficacy of Picibanil in the treatment of 13 affected children ranging in age from 1 to 94 months. On average, 4.1 fluoroscopically guided intracystic injections were performed per child, with an average total dose of 0.56 mg of Picibanil. As judged by physical examination and radiographic studies, 5 children (42%) showed a complete or substantial response, and 2 children (16%) showed an intermediate response. No response was seen in 5 children (42%), 2 of whom had massive craniofacial lymphangioma. Factors that contribute to failure with Picibanil sclerotherapy are the presence of a significant micro‐cystic component to the lesion, massive craniofacial involvement, and previous surgical resection. Macrocystic lymphangiomas of the infratemporal fossa or cervical area have the best response to therapy.
Role of the human Y box-binding protein YB-1 in cellular sensitivity to the DNA-damaging agents cisplatin, mitomycin C, and ultraviolet light. (1996)

The Y box-binding protein (YB-1) binds to DNA sequences, present in the control regions of many genes, that contain an inverted CCAAT box. The binding activity of a nuclear factor, designated MDR-NF1, to an inverted CCAAT box in the promoter of the multidrug resistance 1 (MDR1) gene has previously been shown to be increased in nuclear extracts of cells exposed to UV radiation or various anticancer agents. The MDR-NF1 cDNA has now been cloned by screening a human colon library with an active fragment of the MDR1 promoter. The amino acid sequence encoded by the cloned cDNA was identical to that of YB-1. Northern blot analysis revealed that YB-1 mRNA was present in all human tissues examined. Rabbit antibodies were generated against synthetic peptides corresponding to YB-1, and indirect immunofluorescence microscopy with these antibodies showed that the concentration of YB-1 in all cisplatin-resistant cell lines examined was higher than that in the respective drug-sensitive parental cells. Transfection of human epidermoid cancer KB cells with a YB-1 antisense construct established two cell lines with reduced concentrations of YB-1. These transfectants showed increased sensitivity to cisplatin, mitomycin C, and UV radiation but not to vincristine, doxorubicin, camptothecin, or etoposide. Thus, YB-1 may protect cells from the cytotoxic effects of agents that induce cross-linking of DNA, suggesting a novel function of this ancestor DNA-binding protein.
Expression of Insulin-Like Growth Factor II mRNA-Binding Protein 3 in Human Esophageal Adenocarcinoma and Its Precursor Lesions (2011)

This study suggests that IMP3 may play a role in the carcinogenesis of EAC and has diagnostic utility in differentiating neoplastic and nonneoplastic lesions of the esophagus.
Learning to Fuse Things and Stuff (2018)

We propose an end-to-end learning approach for panoptic segmentation, a novel task unifying instance (things) and semantic (stuff) segmentation. Our model, TASCNet, uses feature maps from a shared backbone network to predict in a single feed-forward pass both things and stuff segmentations. We explicitly constrain these two output distributions through a global things and stuff binary mask to enforce cross-task consistency. Our proposed unified network is competitive with the state of the art on several benchmarks for panoptic segmentation as well as on the individual semantic and instance segmentation tasks.