gebhart/patrepeval huggingface dataset:
Characterization of local geometry of protein surfaces with the visibility criterion (2007)

Experimentally determined protein tertiary structures are rapidly accumulating in a database, partly due to the structural genomics projects. Included are proteins of unknown function, whose function has not been investigated by experiments and was not able to be predicted by conventional sequence-based search. Those uncharacterized protein structures highlight the urgent need of computational methods for annotating proteins from tertiary structures, which include function annotation methods through characterizing protein local surfaces. Toward structure-based protein annotation, we have developed VisGrid algorithm that uses the visibility criterion to characterize local geometric features of protein surfaces. Unlike existing methods, which only concerns identifying pockets that could be potential ligand-binding sites in proteins, VisGrid is also aimed to identify large protrusions, hollows, and flat regions, which can characterize geometric features of a protein structure. The visibility used in VisGrid is defined as the fraction of visible directions from a target position on a protein surface. A pocket or a hollow is recognized as a cluster of positions with a small visibility. A large protrusion in a protein structure is recognized as a pocket in the negative image of the structure. VisGrid correctly identified 95.0% of ligand-binding sites as one of the three largest pockets in 5616 benchmark proteins. To examine how natural flexibility of proteins affects pocket identification, VisGrid was tested on distorted structures by molecular dynamics simulation. Sensitivity decreased approximately 20% for structures of a root mean square deviation of 2.0 A to the original crystal structure, but specificity was not much affected. Because of its intuitiveness and simplicity, the visibility criterion will lay the foundation for characterization and function annotation of local shape of proteins.
Response: 5-azacytidine induction of human fetal hemoglobin (2008)

We thank Dr Lavelle and his colleagues for their letter. Their comments are related to 2 major conclusions from our paper: that the induction of fetal globin gene expression by 5-azacytidine (5-Aza) is not the result of global DNA hypomethylation and that both transcriptional and posttranscriptional
Automated amplification-free digital RNA detection platform for rapid and sensitive SARS-CoV-2 diagnosis (2022)

In the ongoing COVID-19 pandemic, rapid and sensitive diagnosis of viral infection is a critical deterrent to the spread of SARS-CoV-2. To this end, we developed an automated amplification-free digital RNA detection platform using CRISPR-Cas13a and microchamber device (opn-SATORI), which automatically completes a detection process from sample mixing to RNA quantification in clinical specimens within ~9 min. Using the optimal Cas13a enzyme and magnetic beads technology, opn-SATORI detected SARS-CoV-2 genomic RNA with a LoD of < 6.5 aM (3.9 copies μL<sup>-1</sup>), comparable to RT-qPCR. Additionally, opn-SATORI discriminated between SARS-CoV-2 variants of concern, including alpha, delta, and omicron, with 98% accuracy. Thus, opn-SATORI can serve as a rapid and convenient diagnostic platform for identifying several types of viral infections.
Enhancing semistructured data mediators with document type definitions (1999)

Mediation is an important application of XML. The MIX mediator uses Document Type Definitions (DTDs) to assist the user in query formulation and query processors in running queries more efficiently. We provide an algorithm for inferring the view DTD from the view definition and the source DTDs. We develop a metric of the quality of the inference algorithm's view DTD by formalizing the notions of soundness and tightness. Intuitively, tightness is similar to precision, i.e., it deteriorates when "many" objects described by the view DTD can never appear as content of the view. In addition we show that DTDs have some inherent deficiencies that prevent the development of tight DTDs. We propose "DTDs with specialization" as a way to resolve this problem.
How to Use an Article Reporting a Multiple Treatment Comparison Meta-analysis (2012)

Multiple treatment comparison (MTC) meta-analysis uses both direct (head-to-head) randomized clinical trial (RCT) evidence as well as indirect evidence from RCTs to compare the relative effectiveness of all included interventions. The methodological quality of MTCs may be difficult for clinicians to interpret because the number of interventions evaluated may be large and the methodological approaches may be complex. Clinicians and others evaluating an MTC should be aware of the potential biases that can affect the interpretation of these analyses. Readers should consider whether the primary studies are sufficiently homogeneous to combine; whether the different interventions are sufficiently similar in their populations, study designs, and outcomes; and whether the direct evidence is sufficiently similar to the indirect evidence to consider combining. This article uses the existing Users' Guides format to address study validity, interpretation of results, and application to a patient scenario.
Oral nanoparticle-based antituberculosis drug delivery to the brain in an experimental model (2006)

Polymeric nanoparticles bear significant potential for ATD delivery to the brain.
Trustworthy whole-system provenance for the Linux kernel (2015)

In a provenance-aware system, mechanisms gather and report metadata that describes the history of each object being processed on the system, allowing users to understand how data objects came to exist in their present state. However, while past work has demonstrated the usefulness of provenance, less attention has been given to securing provenance-aware systems. Provenance itself is a ripe attack vector, and its authenticity and integrity must be guaranteed before it can be put to use.

We present Linux Provenance Modules (LPM), the first general framework for the development of provenance-aware systems. We demonstrate that LPM creates a trusted provenance-aware execution environment, collecting complete whole-system provenance while imposing as little as 2.7% performance overhead on normal system operation. LPM introduces new mechanisms for secure provenance layering and authenticated communication between provenance-aware hosts, and also interoperates with existing mechanisms to provide strong security assurances. To demonstrate the potential uses of LPM, we design a Provenance-Based Data Loss Prevention (PB-DLP) system. We implement PBDLP as a file transfer application that blocks the transmission of files derived from sensitive ancestors while imposing just tens of milliseconds overhead. LPM is the first step towards widespread deployment of trustworthy provenance-aware applications.
Effects of interleukin-6 on fetal hematopoietic progenitors (1990)

Effects of interleukin-6 (IL-6) on cycling status and clonogenic maturation of human fetal (cord blood) and adult hematopoietic progenitors were compared. Adult marrow cells were incubated for various lengths of time with various concentrations of IL-6, in a serum- free system, after which tritiated thymidine suicide studies were performed. After incubation of 2 to 5 x 10(6) cells/mL for 4 hours in 5.0 ng IL-6/mL, increased thymidine suicide rates were observed for multipotent progenitors (CFU-Mix), granulocyte-macrophage progenitors (CFU-GM), and erythroid burst-forming units (BFU-E). Similar incubations of fetal cells in IL-6 resulted in similar increases in tritiated thymidine suicide rates. In other studies, IL-6 used alone did not support colony formation from adult progenitors. However, it did support colony formation from fetal CFU-Mix (P less than .05), CFU- GM (P less than .001), and BFU-E (P less than .05). In cultures of adult progenitors, IL-6 acted synergistically with IL-3 to support CFU- Mix colony formation (P less than .001), but synergistic actions on CFU- GM and BFU-E were not seen. In contrast, IL-6 acted synergistically with IL-3 and with GM-CSF to support colony formation by fetal CFU-Mix, CFU-GM, and BFU-E. Thus, IL-6 appears to have a wider spectrum of action on fetal progenitors from cord blood than on adult progenitors; including not only the induction of cycling, but also the support of clonogenic maturation of CFU-Mix, CFU-GM, and BFU-E.
Topical treatment with thiazolidinediones, activators of peroxisome proliferator‐activated receptor‐γ, normalizes epidermal homeostasis in a murine hyperproliferative disease model (2006)

In a murine model of epidermal hyperplasia reproducing some of the abnormalities of several common skin disorders, we previously demonstrated the antiproliferative and pro-differentiating effects of peroxisome proliferator-activated receptor (PPAR)alpha, PPARbeta/delta, and liver X receptor activators. Unlike other subgroups of PPAR activators, thiazolidinediones (TZDs), a family of PPARgamma ligands, did not inhibit keratinocyte proliferation in normal murine skin. Here, we studied the effects of two TZDs, namely ciglitazone (10 mM) and troglitazone (1 mM), in the same murine model where epidermal hyperproliferation was reproduced by repeated barrier abrogation with tape stripping. Topical treatment with ciglitazone and troglitazone resulted in a marked and significant decrease in epidermal thickness. Furthermore, in all TZD-treated groups, we observed a significant decrease in keratinocyte proliferation using proliferating cell nuclear antigen, 5-bromo-2'-deoxyuridine, and tritiated thymidine incorporation. However, using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling assay, we found no difference in apoptosis between different treatments, emphasizing that it is the antiproliferative role of these activators that accounts for the decrease of epidermal thickness. Finally, using immunohistochemical methods, we determined the effects of ciglitazone on keratinocyte differentiation in this hyperproliferative model. We observed an increased expression of involucrin and filaggrin following ciglitazone treatment, suggesting a pro-differentiating action of TZDs in this model. In summary, topical TZDs significantly reduce epidermal keratinocyte proliferation while promoting differentiation in a murine model of hyperproliferative epidermis. Together, these results suggest that in addition to their metabolic effects currently in use in the treatment of type 2 diabetes, topical TZDs could be considered as potential alternative therapeutic agents in hyperproliferative skin diseases such as psoriasis.
Charge transport of ion pumps on lipid bilayer membranes (1993)

Ion pumps create ion gradients across cell membranes while consuming light energy or chemical energy. The ion gradients are used by the corresponding cell types for passive-ion transport via ion channels or carriers or for accumulation of nutrients like sugar or amino acids via cotransport systems or antiporters.
Track-Following High Frequency Lateral Motion of Flexible Magnetic Media With Sub-100 nm Positioning Error (2011)

Lateral motion of the magnetic tape in data storage applications misaligns the flexible medium relative to the recording head and reduces the potential for decreasing data track width and spacing, and thereby the achievable data storage density. In order to reduce the effect of misalignment between the tape and the recording head, the head is mounted on a track-following actuator that can compensate for the position error up to a frequency that is governed partly by its mechanical resonances; this bandwidth is typically 1 kHz or less for conventional voice coil-based actuators. This paper introduces the design and implementation of a track-following actuator that is piezo-electrically actuated in order to potentially achieve a significant increase of bandwidth and positioning precision. A proof-of-concept is prototyped and experimental results are presented. An H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> controller is designed and implemented to compensate for typical disturbances such as periodic runout of packs and rollers, or non-periodic flange impacts. Preliminary closed loop experimental results with an experimental low lateral motion tape path, and conventional servo format and media demonstrate a reduction in positioning error standard deviation to 74.5 nm, with simulations indicating a potential for further improvement to 20.6 nm with the use of improved media and servo format.
The Quantum Yield of Photolysis of Water on TiO<sub>2</sub> Electrodes (1975)

Abstract The quantum yield of the photo‐currents in the electrochemical cell, n‐TiO 2 /electrolyte/Pt, was measured under monochromatic illumination of TiO 2 at various electrode potentials. It has been found that the quantum yield is very small (10 −3 ) in case where no voltage was applied from outside, getting smaller with illumination intensity. The results of measurements of the quantum yield, together with those of the electrode potential of TiO 2 , at various conditions are explained from the energy level scheme of the semi‐conductor and redox potentials in the solution. The very small efficiency of this photo‐galvanic cell as a light energy converter has been attributed to the small difference between the flat‐band potential of the TiO 2 electrode and the reduction potential of H + .
Eyelid movements. Mechanisms and normal data. (1991)

This study provides a comprehensive description of upper eyelid movement in normal human subjects. Using the magnetic search coil technique to monitor lid position and modified skin electrodes to record orbicularis oculi electromyographic (EMG) activity, the authors found that the basic eyelid movements, blinks, and saccadic lid movements, can be uniquely and reliably characterized by their amplitude-maximum velocity relationships. The data show that similar increases in levator palpebrae activity produce the upward lid movements that accompany upward saccadic eye movements as well as the upward phase of a blink. The lid movements that accompany downward saccadic eye movements arise almost exclusively from the passive downward forces and relaxation of the levator palpebrae muscle. In contrast, active orbicularis oculi contraction and the passive downward forces act together to generate lid closure with a blink. These normative data and techniques provide the basis for the clinical analysis of lid motility by which abnormal lid movements can be compared with normal lid kinematics.
Conformability of Wet Pulp Fibres at Small Length Scales (2001)

The conformability of wet pulp fibres has long been recognized as a key factor in the papermaking process. In order for fibres to bond in the sheet, their surfaces must be brought into contact. The conformability of wet pulp fibre surfaces at extremely low forces (nN) and displacements (nm) was investigated by micro-indentation measurements with a standard AFM tip and cantilever. Force-distance curves were measured as the tip impacted wet sulphate softwood fibre surfaces. The surface stiffness showed a large variability, even at different locations on the same fibre surface. Rough estimates of the local apparent elastic modulus of the wet fibres gave low values in the 0.01 GPa range.
Joint inversion of P- and PS-waves in orthorhombic media; theory and a physical modeling study (1999)

Abstract Reflection traveltimes recorded over azimuthally anisotropic fractured media can provide valuable information for reservoir characterization. As recently shown by Grechka and Tsvankin, normal moveout (NMO) velocity of any pure (unconverted) mode depends on only three medium parameters and usually has an elliptical shape in the horizontal plane. Because of the limited information contained in the NMO ellipse of P-waves, it is advantageous to use moveout velocities of shear or converted modes in attempts to resolve the coefficients of realistic orthorhombic or lower-symmetry fractured models. Joint inversion of P and PS traveltimes is especially attractive because it does not require shear-wave excitation. Here, we show that for models composed of horizontal layers with a horizontal symmetry plane, the traveltime of converted waves is reciprocal with respect to the source and receiver positions (i.e., it remains the same if we interchange the source and receiver) and can be adequately described by NMO velocity on conventional-length spreads. The azimuthal dependence of converted-wave NMO velocity has the same form as for pure modes but requires the spatial derivatives of two-way traveltime for its determination. Using the generalized Dix equation of Grechka, Tsvankin, and Cohen, we derive a simple relationship between the NMO ellipses of pure and converted waves that provides a basis for obtaining shear-wave information from P and PS data. For orthorhombic models, the combination of the reflection traveltimes of the P-wave and two split PS-waves makes it possible to reconstruct the azimuthally dependent NMO velocities of the pure shear modes and to find the anisotropic parameters that cannot be determined from P-wave data alone. The method is applied to a physical modeling data set acquired over a block of orthorhombic material--Phenolite XX-324. The inversion of conventional-spread P and PS moveout data allowed us to obtain the orientation of the vertical symmetry planes and eight (out of nine) elastic parameters of the medium (the reflector depth was known). The remaining coefficient (c 12 or delta (super (3)) in Tsvankin's notation) is found from the direct P-wave arrival in the horizontal plane. The inversion results accurately predict moveout curves of the pure S-waves and are in excellent agreement with direct measurements of the horizontal velocities.
Intravascular Stent Therapy for Coarctation of the Aorta (2014)

Intravascular stent therapy is considered a primary therapeutic option for most adults and adolescents with coarctation of the aorta. This review highlights the indications, technical considerations, procedural aspects, and limited long-term outcome data when using this intervention. Stent technology has continued to evolve with potential for further modifications since its inception in the early 1990s. The best therapeutic approach, e.g., stenting versus surgery, in the treatment of native coarctation continues to be debated due to the paucity of long-term clinical and imaging data in both groups.
Design/process learning from electrical test (2005)

Modern design-for-test (DFT) practices not only simplify test generation but also make it much easier to diagnose problems uncovered in electrical test. In fact, many diagnostics steps can be automated enough to enable batch processing of large quantities of fail data captured during production test. Hidden in these fail data is very valuable information about the product design, manufacturing process, and interactions between the two. The embedded tutorial provides an overview of some of the analysis methods that are being used and/or prototyped in the industry, as well as the underlying data sharing between the design and manufacturing areas that is required for and enabled by the analyses.
MicroRNA-221 and -222 pathway controls melanoma progression (2008)

MicroRNAs (miRNAs) represent a new family of small noncoding RNAs that negatively regulate gene expression. Recent studies demonstrated miRNA involvement in all the main biological processes, including tumor development as a consequence of an aberrant deregulated expression. Growing evidence is showing the capability of miRNA expression profiles to unequivocally distinguish between normal and neoplastic tissues, leading to the identification of new diagnostic and/or prognostic molecular markers. In addition, miRNAs might eventually represent new targets to aim at as innovative therapeutic approaches, particularly relevant in those types of cancer, such as melanoma, which are still lacking effective traditional therapies. In particular, the inhibition of miRNA-221 and -222, which are abnormally expressed in melanoma and favor the induction of the malignant phenotype by downregulating c-KIT receptor and p27Kip, might in the future represent an efficient treatment for translation into the clinical setting.
Enhanced Osteogenesis by a Biomimic Pseudo‐Periosteum‐Involved Tissue Engineering Strategy (2013)

Elaborating a bone replacement using tissue-engineering strategies for bone repair seems to be a promising remedy. However, previous platforms are limited in constructing three-dimensional porous scaffolds and neglected the critical importance of periosteum (a pivotal source of osteogenic cells for bone regeneration). We report here an innovative method using the periosteum as a template to replicate its exquisite morphologies onto the surfaces of biomaterials. The precise topographic cues (grooved micropatterns) on the surface of collagen membrane inherited from the periosteum effectively directed cell alignment as the way of natural periosteum. Besides, we placed the stem-cell and endothelial-cell-laden collagen membrane (pseudo-periosteum) onto a three-dimensional porous scaffold. The pseudo-periosteum-covered scaffolds showed remarkable osteogenesis when compared with the pseudo-periosteum-free scaffolds, indicating the significant importance of pseudo-periosteum on bone regeneration. This study gives a novel concept for the construction of bone tissue engineering scaffold and may provide new insight for periosteum research.
Measurement of Hemostatic Indexes in Conjunction With Transcranial Doppler Sonography in Patients With Ventricular Assist Devices (1999)

Although no significant relation between MES and TE in VAD patients was found, the data support the hypothesis that MES are related to increased hemostatic activity in this patient group despite aggressive anticoagulant therapy.
Synthesis of Self-Assembling Resorcin[4]arene Tetrasulfide Adsorbates (1995)

The synthesis of a new type of host adsorbate possessing a large resorcin[4]arene headgroup and four di-n-decyl sulfide chains underneath is described. The cross-sectional area of the alkyl chains is equal or larger than that of the headgroups which makes these resorcin[4]arene tetrasulfides suitable for self-assembly onto gold surfaces to form well-packed monolayers of which the outer interface is composed of receptor sites and the alkyl chains underneath the cavity headgroups passivate the gold surface. Resorcin[4]arene tetrasulfides with the following functionalities at the resorcin[4]arene headgroup were synthesized: methylene ether (the so-called cavitand), methyl ether, 2-fluoroethyl, several carboxyl esters, N-propylacetamide and hydroxy. New receptor adsorbates for self-assembling monolayers are described.
Lane-level positioning system based on RFID and vision (2016)

Intelligent and connected vehicle traffic makes it possible to achieve active safety applications and self-driving more efficiently and cheaply, but only when accurate vehicle positioning is accessible. Therefore, to remedy the defects of current GPS positioning technology, a new positioning system based on RFID and vision is proposed. This system aims at lane-level positioning even in various environments. In this system, vehicle positioning is divided into two processes: judging the specific lane the vehicle is occupying (i.e.the lateral position), and obtaining the absolute position or relative position to other vehicles. The method of lane judging with RFID and vision is described in detail, and then proved feasible on a real road. Supported by lane judging, lane-level positioning can be achieved by GPS/DGPS, or V-I communications&ranging. Relative positions of vehicles can also be acquired using lane judging and V-V communications&ranging.