gebhart/patrepeval huggingface dataset:
Influence of Fibrillar Collagen Structure on the Mechanisms of Platelet Thrombus Formation Under Flow (1999)

We have used real-time video microscopy to study the mechanisms of platelet adhesion to type I collagen fibrils of distinct structure exposed to flowing blood. Electron microscopy analysis by surface replication demonstrated morphological differences between acid-insoluble fibrils, displaying a regularly repeating striated pattern (banded collagen), and acid-soluble fibrils generated by pepsin treatment of insoluble collagen, smaller in size with a helical configuration (nonbanded collagen). These structural differences proved to be related to the role of platelet integrin alpha(2)beta(1) in stabilizing adhesion to collagen under a variety of flow conditions. Blocking alpha(2)beta(1) function with a monoclonal antibody had no effect on platelet adhesion to insoluble type I collagen coated at high density on a glass surface, whereas there was an absolute dependence of alpha(2)beta(1) function for the initial permanent arrest of platelets and subsequent thrombus formation on pepsin-solubilized type I collagen under the same conditions. In contrast, reconstituted, banded fibrils prepared from pepsin-solubilized type I collagen supported platelet adhesion and thrombus development even when platelet alpha(2)beta(1) function was blocked, a process that was greatly accelerated by pre-exposure of this substrate to autologous plasma under flow. These results implicate a collagen receptor(s) on platelets other than alpha(2)beta(1) that can selectively engage domains in banded, but not nonbanded type I collagen when alpha(2)beta(1) function is blocked. In addition, collagen structure may regulate the extent and affinity of the binding under flow of plasma components such as von Willebrand factor and/or other alpha(IIb)beta(3) ligands.
A Conformationally Restricted Cyclic Phosphate Analogue of Inositol Trisphosphate:  Synthesis and Physicochemical Properties (1998)

The design and total synthesis of dl-6-deoxy-6-(hydroxymethyl)-scyllo-inositol 1:7-cyclic 2,4-trisphosphate (4), a conformationally restricted cyclic phosphate analogue of the second messenger inositol 1,4,5-trisphosphate [Ins(1,4,5)P3], is described. The protected inosose 2,4,6/3,5-pentahydroxy-3,5-bis-O-(p-methoxybenzyl)-2,4,6-O-methylidynecyclohexanone (7) was obtained from myo-inositol orthoformate in two steps, and Wittig methylenation and then hydroboration−oxidation using 9-BBN−H/OH-/H2O2 gave the axial hydroxymethyl derivative 9. A series of protection/deprotection steps provided the diol 13, which was converted into two cyclic phosphate esters 14a and 14b, epimeric at phosphorus, by reaction with (benzyloxy)bis(N,N-diisopropylamino)phosphine /1H-tetrazole followed by m-CPBA. Two other hydroxyl groups were then exposed and phosphorylated, and total deprotection gave racemic 4. NMR studies confirmed that in 4 the phosphate group equivalent to the 4-phosphate of Ins(1,4,5)P3 is held in the positive gauche orientation and that the inositol ring maintains a chair conformation from pH 2 to 12. Investigation of the acid−base properties of 4 using potentiometric and 31P NMR techniques showed that, over the physiological pH range, 4 behaves as a diprotic acid and that the ionization of the phosphate group equivalent to the 5-phosphate of Ins(1,4,5)P3 is enhanced. In biological assays, 4 appears to behave as a weak full agonist at the platelet Ins(1,4,5)P3 receptor, and the possible interpretation of this result is discussed.
Real-time Monitoring of Radiofrequency Ablation and Postablation Assessment: Accuracy of Contrast-enhanced US in Experimental Rat Liver Model (2013)

Purpose To examine the accuracy of the unenhanced zone at contrast material–enhanced ultrasonography (US) in predicting coagulative necrosis during and 21 days after radiofrequency (RF) ablation by using radiologic-pathologic comparison. Materials and methods Animal studies were approved by the Institutional Animal Care and Use Committee. The livers of 28 rats underwent US-guided RF ablation. In four animals, contrast-enhanced US was performed during ablation and 2 hours and 2, 7, 14, and 21 days after ablation. The unenhanced zone area on US images was measured. DiI-labeled microbubbles were administered during ablation at 2, 4, and 6 minutes or at 2 hours and 2, 7, 14, and 21 days after ablation in the remaining 24 animals (n = 3 at each time point). One minute later, the animal was euthanized, and the ablated liver was harvested. Tissue samples were imaged to quantify total fluorescence, and NADH staining was performed on the same slice. Hematoxylin-eosin staining was also performed. The findings on fluorescence images, NADH-stained images, and hematoxylin-eosin–stained images were compared. The areas of DiI bubble–negative zones, NADH-negative zones, and lightly NADH-staining zones were measured. Data were analyzed by using one-way analysis of variance. Results The area of the unenhanced zone on contrast-enhanced US images increased during RF ablation and reached a maximum within 2 days after ablation. At histopathologic examination, a transition zone manifested adjacent to the coagulation zone until 2 days after ablation. The DiI-bubble negative zone on fluorescence images and the damaged zone (transition zone plus coagulation zone) on NADH-stained images increased rapidly within 2 hours after ablation, then slowly reached the maximum on day 2. The ratios of the mean areas of these two zones at hour 2 to those at day 2 were 94.6% and 95.6%, respectively. High uniformity between the damaged zone on NADH-stained images and the DiI bubble–negative zone on fluorescence images was noted at all time points. Conclusion The temporary transition zone in NADH staining is partially damaged and should transition to nonviability 2 days after ablation. These results demonstrate that contrast-enhanced US can help delineate the maximum area of cell damage (to within 5% of the maximum) as early as 2 hours after ablation. Contrast-enhanced US may be a simple and accurate tool for monitoring the effects of RF ablation and quantifying the size of thermal damage after treatment. © RSNA, 2013 Online supplemental material is available for this article.
Depletion of essential fatty acids in muscle is associated with shorter survival of cancer patients undergoing surgery-preliminary report (2021)

Emerging studies are reporting associations between skeletal muscle abnormalities and survival in cancer patients. Cancer prognosis is associated with depletion of essential fatty acids in erythrocytes and plasma in humans. However the relationship between skeletal muscle membrane fatty acid composition and survival is unknown. This study investigates the relationship between fatty acid content of phospholipids in skeletal muscle and survival in cancer patients. Rectus abdominis biopsies were collected during cancer surgery from 35 patients diagnosed with cancer. Thin-layer and gas chromatography were used for quantification of phospholipid fatty acids. Cutpoints for survival were defined using optimal stratification. Median survival was between 450 and 500 days when patients had arachidonic acid (AA) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in muscle phospholipid below the cut-point compared to 720-800 days for patients above. Cox regression analysis revealed that low amounts of AA, EPA and DHA are risk factors for death. The risk of death remained significant for AA [HR 3.5 (1.11-10.87), p = 0.03], EPA [HR 3.92 (1.1-14.0), p = 0.04] and DHA [HR 4.08 (1.1-14.6), p = 0.03] when adjusted for sex. Lower amounts of essential fatty acids in skeletal muscle membrane is a predictor of survival in cancer patients. These results warrant investigation to restore bioactive fatty acids in people with cancer.
OdeFS: A File System Interface to an Object-Oriented Database (1994)

OdeFS is a file-like interface to the Ode objectoriented database. OdeFS allows database objects to be accessed and manipulated with standard commands, just like files in a traditional file system. No recompilation is required, so proprietary applications can access Ode objects. OdeFS is implemented as a network file server, using the NFS protocol. This paper describes OdeFS and its implementation.
Threshold voltage instability of amorphous silicon thin-film transistors under constant current stress (2005)

We investigate the time-dependent shift in the threshold voltage of amorphous silicon thin-film transistor stressed with constant drain current. We observe a nonsaturating power-law time dependence, which is in contrast to the conventional stretched exponential that saturates at prolonged stress time. The result is consistent with the carrier-induced defect creation model and corroborates the nonlinear dependence of the rate of defect creation on the band-tail carrier density.
Supplemental Figure 2 from CUE-101, a Novel E7-pHLA-IL2-Fc Fusion Protein, Enhances Tumor Antigen-Specific T-Cell Activation for the Treatment of HPV16-Driven Malignancies (2023)

&lt;p&gt;Supplementary Figure 2. Flow cytometric characterization of PBMC expansion cultures.&lt;/p&gt;
The AT-Hook motif as a versatile minor groove anchor for promoting DNA binding of transcription factor fragments (2015)

We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.
Le génie des procédés en France : Quelles réponses du Génie des Procédés pour un renouveau industriel ? (2017)

LIVRE BLANC - LE GÉNIE DES PROCÉDÉS EN FRANCE -2017
Remediation of Cellular Hypoxic Damage by Pharmacological Agents (2005)

Many known pathological conditions lead to decreases in oxygen supply to various cells. When secondary cellular hypoxia becomes severe, it causes additional cellular damage, aggravating the primary disorder and leading to cell death. Therefore, remediation of secondary hypoxic damage should significantly increase the efficacy of the treatment of primary disease and prevent extensive cellular damage. Analysis of the literature and our experimental data show that the main mechanisms of secondary hypoxic cellular damage include lactate acidosis (lactic acidosis), the boost in free radical processes and the activation of apoptosis and necrosis. These factors result in damage to cellular membranes which in turn further limits oxygen supply leading to augmented hypoxic cellular damage. Therefore, to effectively break this vicious cycle of cellular hypoxia, antihypoxic therapy should simultaneously: (1) mitigate existing cellular hypoxic damage; (2) increase cellular ability to utilize available oxygen; (3) amplify the power of cellular antioxidant defense and (4) prevent hypoxic activation of apoptosis and necrosis. It is clear that such complex task cannot be fulfilled by a single pharmacological agent. Therefore, a complex multi component antihypoxic drug delivery system should be designed to address all the four desiderata indicated above. This review will examine existing pharmaceutical antihypoxic preparations and evaluate the new methods for the pharmacological remediation of cellular hypoxic damage and propose future directions for the design of the needed drug delivery systems.
Macroscopic Wall Number Analysis of Single-Walled, Double-Walled, and Few-Walled Carbon Nanotubes by X-ray Diffraction (2011)

The layer number is of great importance for nanocarbon materials, such as carbon nanotubes (CNTs) and graphene. While simple optical methods exist to evaluate few-layer graphene, equivalent analysis for CNTs is limited to transmission electron microscopy. We present a simple macroscopic method based on the (002) X-ray diffraction peak to evaluate the average wall number of CNTs in the range from single- to few-walled. The key was the finding that the (002) peak could be decomposed into two basic components: the intertube structure (outer-wall contacts) and the intratube structure (concentric shells). Decomposition of the peaks revealed a linear relationship between the average wall number and the ratio of the intertube and intratube contributions to the (002) peak. Good agreement with CNTs having average wall numbers ranging from 1 to ∼5 demonstrated this as a macroscopic method for average wall number analysis.
A High-content Imaging Workflow to Study Grb2 Signaling Complexes by Expression Cloning (2012)

Signal transduction by growth factor receptors is essential for cells to maintain proliferation and differentiation and requires tight control. Signal transduction is initiated by binding of an external ligand to a transmembrane receptor and activation of downstream signaling cascades. A key regulator of mitogenic signaling is Grb2, a modular protein composed of an internal SH2 (Src Homology 2) domain flanked by two SH3 domains that lacks enzymatic activity. Grb2 is constitutively associated with the GTPase Son-Of-Sevenless (SOS) via its N-terminal SH3 domain. The SH2 domain of Grb2 binds to growth factor receptors at phosphorylated tyrosine residues thus coupling receptor activation to the SOS-Ras-MAP kinase signaling cascade. In addition, other roles for Grb2 as a positive or negative regulator of signaling and receptor endocytosis have been described. The modular composition of Grb2 suggests that it can dock to a variety of receptors and transduce signals along a multitude of different pathways(1-3). Described here is a simple microscopy assay that monitors recruitment of Grb2 to the plasma membrane. It is adapted from an assay that measures changes in sub-cellular localization of green-fluorescent protein (GFP)-tagged Grb2 in response to a stimulus(4-6). Plasma membrane receptors that bind Grb2 such as activated Epidermal Growth Factor Receptor (EGFR) recruit GFP-Grb2 to the plasma membrane upon cDNA expression and subsequently relocate to endosomal compartments in the cell. In order to identify in vivo protein complexes of Grb2, this technique can be used to perform a genome-wide high-content screen based on changes in Grb2 sub-cellular localization. The preparation of cDNA expression clones, transfection and image acquisition are described in detail below. Compared to other genomic methods used to identify protein interaction partners, such as yeast-two-hybrid, this technique allows the visualization of protein complexes in mammalian cells at the sub-cellular site of interaction by a simple microscopy-based assay. Hence both qualitative features, such as patterns of localization can be assessed, as well as the quantitative strength of the interaction.
Supplementary Figure 3 from A687V EZH2 Is a Driver of Histone H3 Lysine 27 (H3K27) Hypertrimethylation (2023)

&lt;p&gt;Supplementary Figure 3: Biochemical activity of PRC2 complexes containing WT, A687V, Y641N, or A677G EZH2 using a library of histone H3 peptides containing H3K27&lt;/p&gt;
Expression and Regulation of the Prokineticins (Endocrine Gland-Derived Vascular Endothelial Growth Factor and Bv8) and Their Receptors in the Human Endometrium across the Menstrual Cycle (2004)

This study investigated the possible role of the newly discovered endocrine gland-derived vascular endothelial growth factors and their cognate receptors in the human endometrium during the menstrual cycle. Endocrine gland-derived vascular endothelial growth factors are also known as prokineticin (PK) 1 and PK2 and their receptors as PKR1 and PKR2. Expression of PK1 was elevated in the secretory compared with the proliferative phase of the menstrual cycle (P < 0.05). There was no temporal variation in expression of PK2, PKR1, or PKR2. PK1 and PK2 and their receptors were localized to multiple cellular compartments, including glandular epithelial, stromal, and endothelial cells in the endometrium and endothelial and smooth muscle cells in the myometrium. The elevation in PK1 expression in the secretory phase of the menstrual cycle indicated potential regulation of PK1 by progesterone. To investigate this, endometrial tissue was treated with 1 microM (micromol/liter(-1)) progesterone for 24 h, and PK1 expression was assessed by quantitative RT-PCR. Treatment with 1 microM ( micromol/liter(-1)) progesterone resulted in 2.91 +/- 0.75-fold elevation in PK1 expression, compared with controls (P < 0.05). These data identify a paracrine role for the PKs and their receptors in endometrial vascular function.
Polysubstance abuse and traumatic brain injury: Quantitative magnetic resonance imaging and neuropsychological outcome in older adolescents and young adults (1999)

Few studies have examined the consequences of alcohol and drug abuse on TBI though they commonly co-occur. Both TBI and substance abuse independently result in neuropathological changes in the brain such as ventricular enlargement and cortical atrophy, thus it is reasonable to hypothesize that the combination of the two would result in more significant cerebral damage. In this study, 3 groups of patients--traumatically brain injured (TBI) with substance abuse (N = 19), TBI without substance abuse (N = 19), and substance abuse with no TBI (N = 16)--were compared with normal controls (N = 20) on several quantitative MRI (QMRI) measures. Since TBI most frequently occurs in older adolescents and young men, we examined only male participants between 16 and 30 years of age. Comparing young substance abusers to controls resulted in no QMRI differences. When controlling for head injury severity, the effects of substance abuse in combination with TBI resulted in greater atrophic changes than seen in any other group. TBI and substance abuse patients' neuropsychological test performances also were examined, and no differences were found among patient groups on any measures. These findings have implications for the deleterious interaction of substance abuse combining with TBI to result in greater neuropathological changes that can be detected by QMRI techniques.
Introducing sensing into future wireless communication systems (2022)

Joint communication and sensing is emerging as a potential extension to the existing wireless communication systems. In this paper, we present an overview of sensing using a primarily wireless communication network and investigate different design aspects such as hardware implications, spectrum requirements and multiplexing of communication and sensing signals. Also, we present sensing signal design based on the required sensing accuracies for an OFDM-based communication system and show the corresponding detection performance. One interesting finding is the large difference between transmission power of sensing compared to transmission power used for communication. We will discuss how this impacts the design, including duplex direction as well as waveform that is used for sensing. Finally, we discuss some tradeoffs between sensing accuracy and the overhead of sensing signal and solutions to reduce the overhead in a joint communication and sensing system.
Selected papers from the 9th International Workshop on Micro and Nanotechnology for Power Generation and Energy Conversion Applications (PowerMEMS 2009) (2010)

This special section of the Journal of Micromechanics and Microengineering presents papers selected from the 9th International Workshop on Micro and Nanotechnology for Power Generation and Energy Conversion Applications (PowerMEMS 2009), which was held in Washington DC, USA from 1–4 December 2009.
Cooperative Manipulation by Autonomous Intelligent Robots (1996)

Cooperative manipulation by autonomous intelligent robots promises fertile potential for improving the ability of robotic manipulation and expanding the domain where robots may be used. This paper focuses on the method for calculating the optimal force of each robot based on local sensor feedback and high-level communication. First, we propose adaptive force direction control, which is useful for monitoring the state of force equilibrium, and then describe the theoretical background of this control method. Second, we describe the strategy to find the proper force using our proposed control method. We also describe a control system architecture which is suitable for these operations. In this control system, each manipulator motion function, each sensor function, and each message-passing operation are programmed as primitive tasks which run in parallel. Third, we illustrate the usefulness of our proposed method with some experiments such as tumbling operation by two autonomous robots.
Anomeric oxygen to carbon rearrangements of alkynyl tributylstannane derivatives of furanyl (γ)- and pyranyl (δ)-lactols (2004)

Tetrahydropyran and tetrahydrofuran containing natural products, drugs and agrochemicals often possess carbon-carbon bonds adjacent to the heteroatom. Consequently, new methods for the construction of anomeric carbon-carbon bonds are of considerable importance. We have devised a new strategy to access these systems that requires the treatment of O-glycoside alkynyl tributylstannane derivatives of furanyl and pyranyl lactols with Lewis acid to effect oxygen to carbon rearrangements. This leads to the formation of the corresponding carbon linked alkynol products that can be further manipulated to produce key structural motifs and building blocks for the assembly of complex molecules.
Steganalysis for LSB Matching in Images with High-frequency Noise (2007)

Considerable progress has been made in the detection of steganographic algorithms based on replacement of the least significant bit (LSB) plane. However, if LSB matching, also known as -1 embedding, is used, the detection rates are considerably reduced. In particular, since LSB embedding is modeled as an additive noise process, detection is especially poor for images that exhibit high-frequency noise - the high-frequency noise is often incorrectly thought to be indicative of a hidden message. To overcome this, we propose a targeted steganalysis algorithm that exploits the fact that after LSB matching, the local maxima of an images graylevel or color histogram decrease and the local minima increase. Consequently, the sum of the absolute differences between local extrema and their neighbors in the intensity histogram of stego images will be smaller than for cover images. Experimental results on two datasets, each of 2000 images, demonstrate that this method has superior results compared with other recently proposed algorithms when the images contain high-frequency noise, e.g. never-compressed imagery such as high-resolution scans of photographs and video. However, the method is inferior to the prior art when applied to decompressed imagery with little or no high-frequency noise.
Estimating the Quality of Postings in the Real-time Web (2010)

Millions of users are posting their status updates, interesting findings, news, ideas and observations in real-time on microblogging services such as Twitter, Jaiku and Plurk. This real-time Web can be a great resource of valuable timely information. Since the real-time Web is completely open and decentralized and anyone may post information at whim, distinguishing interesting and popular postings from the mundane ones is a challenging task. In this paper we study the problem of estimating the quality (or “interestingness”) of postings in the real-time Web. We identify several important factors that are indicative of the quality of postings, and present metrics that capture these factors. To showcase the promise of our approach, we present early experimental results on Twitter. 1.