gebhart/patrepeval huggingface dataset:
Formatting and ligating biopolymers using adjustable nanoconfinement (2016)

Sensitive visualization and conformational control of long, delicate biopolymers present critical challenges to emerging biotechnologies and biophysical studies. Next-generation nanofluidic manipulation platforms strive to maintain the structural integrity of genomic DNA prior to analysis but can face challenges in device clogging, molecular breakage, and single-label detection. We address these challenges by integrating the Convex Lens-induced Confinement (CLiC) technique with a suite of nanotopographies embedded within thin-glass nanofluidic chambers. We gently load DNA polymers into open-face nanogrooves in linear, concentric circular, and ring array formats and perform imaging with single-fluorophore sensitivity. We use ring-shaped nanogrooves to access and visualize confinement-enhanced self-ligation of long DNA polymers. We use concentric circular nanogrooves to enable hour-long observations of polymers at constant confinement in a geometry which eliminates the confinement gradient which causes drift and can alter molecular conformations and interactions. Taken together, this work opens doors to myriad biophysical studies and biotechnologies which operate on the nanoscale.
A coding unit classification based AVC-to-HEVC transcoding with background modeling for surveillance videos (2013)

To save the storage and transmission cost, it is applicable now to develop fast and efficient methods to transcode the perennial surveillance videos to HEVC ones, since HEVC has doubled the compression ratio. Considering the long-time static background characteristic of surveillance videos, this paper presents a coding unit (CU) classification based AVC-to-HEVC transcoding method with background modeling. In our method, the background frame modeled from originally decoded frames is firstly transcoded into HEVC stream as long-term reference to enhance the prediction efficiency. Afterwards, a CU classification algorithm which employs decoded motion vectors and the modeled background frame as input is proposed to divide the decoded data into background, foreground and hybrid CUs. Following this, different transcoding strategies of CU partition termination, prediction unit candidate selection and motion estimation simplification are adopted for different CU categories to reduce the complexity. Experimental results show our method can achieve 45% bit saving and 50% complexity reduction against traditional AVC-to-HEVC transcoding.
Performance Characteristics of Flush Angle-of-Attack Measurement System Integrated on a Pitot Tube (2010)

:In this paper the performance characteristics of a pressure based flush angle-of-attack measurement system, integrated on a Pitot-Static tube, is presented. The non-dimensional pressure difference between two static pressure ports located on the upper and lower surface of the conical interface, with half-cone-angle of 20°, of the Pitot tube shows linear behavior (desirable) with angle-of-attack in the subsonic regime while in the supersonic regime it has non-linear behavior (undesirable). This non-linear behavior is attributed to shockwave induced flow separation just upstream of the conical interface. The undesirable non-linear trend can be eliminated by reducing the half-cone-angle of the conical interface from 20° to 12°. The reduction in half-cone-angle eliminates the upstream shockwave induced flow separation in the supersonic regime thereby restoring the linear behavior between nondimensional pressure difference and angle-of-attack. However, reducing the conical interface half-cone-angle also reduces the sensitivity of the angle-of-attack measurement system in the subsonic regime by 18%. Computational Fluid Dynamics tools have been used in the analysis and refinement of flush angle-of-attack measurement system. The complete Mach number regime (Mach<2) has been computationally analyzed for the two conical interfaces. The results presented in this study have been validated by subsequent wind tunnel tests.
Clinical evaluation of aortic diseases using nonenhanced MRA with ECG‐triggered 3D half‐Fourier FSE (2001)

The efficacy of the nonenhanced magnetic resonance angiography (MRA) technique known as fresh-blood imaging (FBI), using electrocardiograph (ECG)-triggered 3D half-Fourier fast spin-echo (FSE), was evaluated for the detection and characterization of aortic diseases. Seventy-five consecutive patients with aortic disease underwent the FBI examination on a 1.5-T clinical imager. The results showed that the FBI technique permits clear visualization of aortic diseases, and the vessel branches and their relationship, which provides valuable information. Therefore, the nonenhanced FBI technique is appropriate to use for screening purposes.
Bone Formation on Synthetic Precursors of Hydroxyapatite. (1991)

The aim of this study was to investigate the reaction of skeletal tissue to various synthetic calcium phosphate (Ca-P) compounds in vivo. Five synthetic Ca-P compounds were implanted into the subperiosteal area of the calvaria of 7-week-old BALB/c mice for one to 15 weeks. Synthetic compounds were dicalcium phosphate (DCP), octacalcium phosphate (OCP), amorphous calcium phosphate (ACP), Ca-deficient hydroxyapatite and hydroxyapatile (HA). Implanted DCP, OCP and ACP were found to be converted to apatitic phase by x-ray microdiffraction analysis using undecalcified specimens. Structure of bone was found out on all of Ca-P compounds eventually at late stage under the light microscope, but the rate of bone formation calculated from a number of experiments varied on respective synthetic Ca-P compound. It was high as 80% for DCP, OCP and ACP, but was low as 5.6% for Ca-deficient HA, and no reaction was found for HA at the stage of 3 weeks. Fine filaments and granular materials in the newly formed bone matrix were detected at 7 days around the remnants of OCP particles which already converted to apatitic phase by ultrastructural study of decalcified specimens. These structures were very similar to the components of bone nodules seen in intramembranous osteogenesis. It is postulated that the precursors of HA have an important role in intramembranous osteogenesis.
Nuclear Magnetic Resonance Spectroscopy of Organo-Clay Complexes (2001)

Nuclear magnetic resonance (NMR) spectroscopy has been used successfully in the study of clay minerals and clay organic interactions, providing information on both structural and dynamic aspects. This chapter is concerned with clayorganic interactions, but due to the complexity of these reactions in which are involved simultaneously the silicate substrate, inorganic cations, water and the organic species, references to the NMR study of phyllosilicate structure, localiza­ tion, and mobility of exchangeable inorganic cations and water have also been included.
Orthogonality of exponential transients (1988)

It is shown that simple orthogonal representations exist for signals which are of a decaying, rather than purely sinusoidal nature. This orthogonality is expressed in terms of a weighting function. It is shown that alternate, nonuniform sampling techniques for representation and processing of these signals are appropriate. Using this nonuniform sampling scheme, a simple discrete representation, very much like the discrete Fourier transform, can be derived. Hence, it is pointed out that traditional, frequency-spectrum-based techniques for signal analysis may be replaced by methods that are better suited for the specific decaying signal type.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Comparative functional analysis of lymphocytes and monocytes from plateletapheresis (1983)

Large numbers (2.9 +/- 1.2 X 10(9)) of mononuclear cells can be obtained from incidental samples collected during routine plateletapheresis. We conducted studies comparing characteristics and functions of mononuclear cells derived from venous blood samples and from routine plateletapheresis in the same normal donors. Cell viability was similar in both samples (96 +/- 1% plateletapheresis vs 97 +/- 2% venous blood). Higher concentration of monocytes were observed in the plateletapheresis samples (32.3 +/- 6%) than in the venous blood (14.3 +/- 4%). The procedure of plateletapheresis does not seem to alter lymphocyte or monocyte function. Thus, the functional integrity of these cell populations was demonstrated in terms of natural killer cell activity, blastogenic response to mitogens, local graft-versus-host reactions, monocyte-mediated antibody-dependent cellular cytotoxicity against human red cells, monocyte-mediated tumor cell cytotoxicity, latex phagocytosis, and monocyte-dependent lymphocyte blastogenesis. We conclude that monocytes and lymphocytes obtained during routine plateletapheresis are functionally intact.
ZBTB7A Mediates the Transcriptional Repression Activity of the Androgen Receptor in Prostate Cancer (2019)

Loss of expression of context-specific tumor suppressors is a critical event that facilitates the development of prostate cancer. Zinc finger and BTB domain containing transcriptional repressors, such as ZBTB7A and ZBTB16, have been recently identified as tumor suppressors that play important roles in preventing prostate cancer progression. In this study, we used combined ChIP-seq and RNA-seq analyses of prostate cancer cells to identify direct ZBTB7A-repressed genes, which are enriched for transcriptional targets of E2F, and identified that the androgen receptor (AR) played a critical role in the transcriptional suppression of these E2F targets. AR recruitment of the retinoblastoma protein (Rb) was required to strengthen the E2F-Rb transcriptional repression complex. In addition, ZBTB7A was rapidly recruited to the E2F-Rb binding sites by AR and negatively regulated the transcriptional activity of E2F1 on DNA replication genes. Finally, ZBTB7A suppressed the growth of castration-resistant prostate cancer (CRPC) <i>in vitro</i> and <i>in vivo</i>, and overexpression of ZBTB7A acted in synergy with high-dose testosterone treatment to effectively prevent the recurrence of CRPC. Overall, this study provides novel molecular insights of the role of ZBTB7A in CRPC cells and demonstrates globally its critical role in mediating the transcriptional repression activity of AR. SIGNIFICANCE: ZBTB7A is recruited to the E2F-Rb binding sites by AR and negatively regulates the transcriptional activity of E2F1 on DNA replication genes.
Effect of regularization in the migration of time-lapse data (2006)

With 4D seismic studies the aim is to look at signal changes in the reservoir which can improve our understanding of the dynamic reservoir system and enable us to optimize production. For a successful study, noise must be minimized as the magnitude of the signal related to the 4D effect is generally weak and the same order of magnitude as the noise. There are many sources of non-repeatability in marine 4D seismic studies from differences in acquisition parameters, differences in environmental factors, and also from data processing effects. When we compare time-lapse datasets, this nonrepeatable noise will remain and impede the interpretation of the data. Pre-stack Kirchhoff Time Migration (PreSTM) is a processing technique utilized in seismic exploration and reservoir monitoring. Such a migration scheme is attractive as it allows the implementation of spatially and temporally varying velocity fields to migrate the data. It is only suitable for datasets with smooth velocity contrasts as any sharp velocity changes (e.g., shallow surface heterogeneities) would leave residual energy visible as a migration smile. Even with smooth velocity variations, another form of migration noise comes from the sub-optimal interference of the migration operator. As the PreSTM implementation uses a symmetrical operator (not the case for Pre-stack Depth Migration), the best possible constructive and destructive interference requires square bins with the midpoint position of the traces at the bin centre. In addition, the traces in a single offset volume should be mono-azimuth (or contain an equally distributed azimuth content for each bin) and mono-offset. When this is not the case residual migration noise will remain as an imprint of the acquisition pattern. In a 4D study where each dataset has slightly different acquisition parameters, each vintage will also have its own pattern of migration noise. This noise is uncorrelated between vintages and appears as energy on the difference section. The use of weighting schemes inside the PreSTM algorithm can help reduce noise by normalizing the migration output. However, regularizing the data on input optimizes the constructive and destructive interference, this handles amplitudes on seismic events as well as attenuating migration smiles. In this paper we consider the level of migration noise from sub-optimal recording positions in a constant velocity medium for a Kirchhoff PreSTM algorithm. In addition, we outline some processing techniques to reduce the level of migration noise.
On hardware implementation of radix 3 and radix 5 FFT kernels for LTE systems (2011)

This paper treats the hardware architecture and implementation of mixed radix FFTs with cores of radix 3 and radix 5 in addition to the standard radix 2 core. The implementation flow graphs of the higher radix cores are presented together with a description of how these cores affect a pipelined FFT implementation. It is shown that the mixed radix FFT is more expensive than the radix 2 implementation - a mixed radix FFT of 1200 points require 36 real multipliers in a pipelined implementation whereas a 2048 radix 2 FFT needs 30 real multipliers. However, half of the multipliers in the mixed radix case can be constant. Therefore it is still feasible to use the mixed radix FFT if an algorithm calls for it.
Henoch–Schonlein purpura and stroke: Antiphosphatidyl-ethanolamine antibody in CSF and serum (2000)

A 15-year-old girl with features of Henoch-Schönlein purpura and brain infarct had a transient IgA antiphosphatidylethanolamine antibody (aPE) in her serum and CSF that disappeared 5 months after presentation. Serum aPE is known to be associated with thrombotic events. The authors found no aPE in the CSF of two control individuals or in the serum of two patients with active Henoch-Schönlein purpura without neurologic involvement. The patient may represent a variant of antiphospholipid antibody syndrome.
An analysis of the performance of a vertically oriented, gas loaded, variable conductance heat pipe (1986)

An analysis of steady state operation of a vertically oriented, variable conductance heat pipe is presented. The effects of binary mass diffusion, axial pipe wall conduction, and gravitational effects, caused by the difference in molecular weight of the non-condensible gas and the working fluid are incorporated. Analytical expressions for the conservation of mass, momentum, and energy are combined along with equations of state to describe steady state operation of the heat pipe. These expressions are combined to form a system of three differential equations with three unknowns; working fluid vapor velocity, mass fraction, and temperature. These equations are nondimensionalized and an iteration scheme for numerical solution of the equations is presented .
Expression of vascular endothelial growth factor (VEGF) and association with microvessel density in benign prostatic hyperplasia and prostate cancer. (2004)

Our data showed that angiogenesis was more prominent in carcinomas than in BPH. Furthermore, increased MVC was significantly associated with high-grade carcinomas. Angiogenesis was correlated with VEGF expression and it was, at least in part, mediated by the latter. Thus, prostate adenocarcinoma may represent a suitable neoplasm for antiangiogenic treatment in combination with conventional therapies.
Cryopreserving Human Peripheral Blood Progenitor Cells (2006)

5% DMSO is the optimal concentration for cryopreserving human PBPC in vitro. Consequently, some hospitals have started using 5% DMSO as cryoprotectant for the autologous PBPC as a standard procedure.
A fingertip detection and tracking system as a virtual mouse, a signature input device and an application selector (2008)

This paper presents vision-based fingertip detection and tracking system on a 2D plane using a camera as an input interface to the computer. An intensity based approach is used to detect the arbitrary shaped, uniform colored 2D area on which the hand operates, and then the fingertip is effectively detected and tracked using the sampled hand contour. Grid sampling approach is used for a fast implementation. The system achieves speeds of up to 30 fps. Tip pointers such as a stylus or a pen can be used in place of the fingertip, making the device user-friendly. The system is used to implement a virtual mouse, a signature input device and an application selector.
Practical Approaches to Remote Asymmetric Induction in Steroidal Side-Chains Utilizing Oxazaborolidine Reagents (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTPractical Approaches to Remote Asymmetric Induction in Steroidal Side-Chains Utilizing Oxazaborolidine ReagentsMeenakshi N. Rao, Melissa A. McGuigan, Xuehai Zhang, Ze'ev Shaked, William A. Kinney, Michel Bulliard, Blandine Laboue, and Nancy E. LeeView Author Information Magainin Pharmaceuticals, 5110 Campus Drive, Plymouth Meeting, Pennsylvania 19462, Sipsy Chemical Co., Route de Beaucouzé - B.P. 79, 49242 Avrillé Cedex, France, and Department of Chemistry, Simmons College, 300 The Fenway, Boston, Massachusetts 02115 Cite this: J. Org. Chem. 1997, 62, 13, 4541–4545Publication Date (Web):June 27, 1997Publication History Received7 February 1997Published online27 June 1997Published inissue 1 June 1997https://doi.org/10.1021/jo970227lCopyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views507Altmetric-Citations26LEARN 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 InReddit Read OnlinePDF (205 KB) Get e-AlertsSUBJECTS:Alcohols,Aldehydes,Reagents,Redox reactions,Steroids Get e-Alerts
Construction of a prokaryotic expression system of<i>vacA</i>gene and detection of<i>vacA</i>gene, VacA protein in<i>Helicobacter pylori</i>isolates and ant-VacA antibody in patients’ sera (2004)

A prokaryotic expression system of H pylori vacA gene was successfully constructed. The expressed rVacA can be used to detect specific anti-VacA antibody in human and to prepare antiserum in animals. The high frequency of vacA gene in H pylori isolates, but with a low frequency of VacA expression and specific anti-VacA antibody in H pylori infected patients implies that VacA is not an ideal antigen for H pylori vaccine.
ALCAM/CD166 is overexpressed in colorectal carcinoma and correlates with shortened patient survival (2004)

ALCAM is frequently upregulated in colorectal cancer and is a new independent prognostic marker, underscoring the importance of ALCAM in tumour progression in this disease.
An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis (2008)

We study the problem of domain transfer for a supervised classification task in\nmRNA splicing. We consider a number of recent domain transfer methods from\nmachine learning, including some that are novel, and evaluate them on genomic\nsequence data from model organisms of varying evolutionary distance. We find\nthat in cases where the organisms are not closely related, the use of domain adap-\ntation methods can help improve classification performance.
Studies on the Binding of a 32K Rat Epididymal Protein to Rat Epididymal Spermatozoa (1982)

A glycoprotein of molecular weight 32K has been isolated and purified from the rat caudal epididymal fluid by gel filtration, ion-exchange and affinity chromatography. The highly purified protein was labeled with radioactive iodine and the binding of the 125I-labeled 32K rat epididymal protein (REP) to washed rat caudal epididymal sperm was studied under various conditions. Scatchard plots of the binding data revealed two binding kinetics. One bound with high affinity (KD = 2.6 X 10(-10) ) but low capacity. The other bound with lower affinity (KD = 2.2 X 10(-9)M) but high capacity. The rate of binding of the labeled protein to sperm was dependent on the temperature of the incubation medium. At the scrotal temperature of 33 degrees C, maximal binding was obtained after 40 min. However, at 22 degrees C equilibrium state was reached after 90 min and at 0 degrees C, the equilibrium rate was not reached even after 120 min of incubation. Binding showed dependence on extracellular pH (optimal pH at 4) and ionic strength of the incubation medium. High ionic strength was found to inhibit binding of the 125I-labeled 32K REP to rat caudal epididymal sperm. Specific binding was abolished by 100-fold molar excess unlabeled 32K REP or by native rat caudal epididymal fluid proteins, but not by albumin or ovalbumin. This indicates high specificity of binding. This study has provided direct evidence for the interaction of an epididymal protein with epididymal spermatozoa.
Is movement of mannose 6-phosphate-specific receptor triggered by binding of lysosomal enzymes? (1987)

Mannose 6-phosphate-specific receptors with an apparent molecular mass of 215,000 are present in fibroblasts at the cell surface and in intracellular membranes. The cell surface receptors mediate endocytosis of exogenous lysosomal enzymes and exchange with the intracellular receptors, which function in the sorting of endogenous lysosomal enzymes. In the present study, several methods independent of receptor ligands were designed in order to examine the exchange of receptors under conditions where receptor-ligand complexes do not dissociate (weak bases and monensin) or where receptor-ligand complexes are not formed due to absence of endogenous ligands as a result of inhibition of protein synthesis. Weak bases and monensin reduce the concentration of receptors at the cell surface by 20-30% and free cell surface receptors were replaced by occupied receptors. The latter continued to be exchanged with internal ligand-occupied receptors and the rates of the exchange were similar to the control values. The exchange of receptors between the cell surface and internal membranes was also not affected when the receptor ligands were depleted from the transport compartments by treating the cells with cycloheximide for up to 10 h. We conclude from these results that movement of mannose 6-phosphate-specific receptors along the endocytosis and sorting pathways is constitutive and not triggered by binding or dissociation of ligands.
Pericyclic Cascade Reactions of (Bicyclo[1.1.0]butylmethyl)amines (2006)

Direct access: Phase-transfer N-allylation and N-propargylation of (bicyclo[1.1.0]butylmethyl)amines initiate diastereoselective pericyclic cascade reactions that culminate in novel spirocyclic and tricyclic pyrrolidine heterocycles through formal ene or [2+2] pathways. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z600723_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.