gebhart/patrepeval huggingface dataset:
Crystallographic Study of a Site-Specifically Cross-Linked Protein Complex with a Genetically Incorporated Photoreactive Amino Acid, (2010)

The benzophenone photophore is widely used to photo-cross-link macromolecules. Recent developments in genetic code expansion have allowed the biosynthesis of proteins with p-benzoyl-L-phenylalanine (pBpa) at defined sites, for covalent bonding with interacting proteins. However, the structure of a photo-cross-linked protein complex had not been revealed, and thus neither the actual structure of the "photobridge" in a complex nor the influence of this covalent bridge on the overall complex structure was known. In this study, we determine the crystal structure of the cross-linked complex of the liver oncoprotein gankyrin and the C-terminal domain of S6 proteasomal protein (S6C), at 2.05 Å resolution. First, the photoreactive amino acid was separately incorporated into gankyrin at 16 sites on the protein surface, and two variants that efficiently formed a covalent bond with S6C were found. The yield of one of the cross-linked products, with pBpa in place of Arg85 in gankyrin, was maximized for crystallization via optimization of the duration of complex exposure to 365 nm light. The structure revealed that the carbonyl group of the benzophenone of pBpa85 formed a covalent bond exclusively with the Cγ atom of Glu356 in S6C, showing the high selectivity of formation of cross-links by pBpa. In addition, the cross-linked structure exhibited little structural distortion from the native complex structure. Our results demonstrated that cross-linking with site-specifically incorporated pBpa preserves the native binding mode and is useful for probing protein-protein interactions.
Text line segmentation and word recognition in a system for general writer independent handwriting recognition (2002)

We present a system for recognizing unconstrained English handwritten text based on a large vocabulary. We describe the three main components of the system, which are preprocessing, feature extraction and recognition. In the preprocessing phase the handwritten texts are first segmented into lines. Then each line of text is normalized with respect to of skew, slant, vertical position and width. After these steps, text lines are segmented into single words. For this purpose distances between connected components are measured. Using a threshold, the distances are divided into distances within a word and distances between different words. A line of text is segmented at positions where the distances are larger than the chosen threshold. From each image representing a single word, a sequence of features is extracted. These features are input to a recognition procedure which is based on hidden Markov models. To investigate the stability of the segmentation algorithm the threshold that separates intra- and inter-word distances from each other is varied. If the threshold is small many errors are caused by over-segmentation, while for large thresholds under-segmentation errors occur. The best segmentation performance is 95.56% correctly segmented words, tested on 541 text lines containing 3899 words. Given a correct segmentation rate of 95.56%, a recognition rate of 73.45% on the word level is achieved.
ChemInform Abstract: SYNTHESIS OF ALL POSSIBLE STEREOISOMERS OF POLYGODIAL (1984)

Abstract Der nach bekannten Verfahren über Diels‐Alder‐Reaktion zugängliche Diester (I) wird mit I)BU zu (II) isomerisiert und dann zu (III) hydriert, aus dem mit Lithiumalanat das Diol (IV) erhalten wird.
Patterns of Anticoagulation Use and Cardioembolic Risk After Catheter Ablation for Atrial Fibrillation (2015)

The overall risk of stroke in postablation patients is low; however, OAC discontinuation after ablation is common and is associated with increased risk of cardioembolism for all patients within the first 3 months and for high-risk patients in the long term. Continuing OAC for at least 3 months in all patients and indefinitely in high-risk patients appears to be the safest strategy.
Biosynthesis of an Elastin‐Mimetic Polypeptide with Two Different Chemical Functional Groups within the Repetitive Elastin Fragment (2005)

A new protein engineering strategy was utilized to synthesize an elastin-mimetic polypeptide. The primary structure represents an elastic motif composed of thirty amino acids with one lysine and one glutamic acid per repeat unit EMM = (VPGVG VPGKG VGPVG VPGVG VPGEG VPGIG). The gene was constructed using a Seamless Cloning method by generating three DNA cassettes which all encoded the EMM repeat unit, but with different flanking restriction recognition sites. The DNA cassettes were assembled to yield a gene that could be directly cloned into the multiple cloning site of pBluescript II SK+. The resulting gene (EMM)(7) with approximately 650 base pairs in length was further cloned into the expression vector pET-28b. Protein biosynthesis in E. coli strain BLR(DE3) resulted in the 21.5 kDa repeating polypeptide His(6)-(EMM)(7) yielding up to 50 mg . L(-1) of cell culture. Secondary structure analysis by far UV circular dichroism revealed a minimum at 197 nm and a shoulder at 218 nm indicative for a random coil with some type II beta-turn conformation content. Lower critical solution temperature (LCST) behavior strongly depends on salt and polypeptide concentration. Importantly, first cross-linking experiments indicate successful hydrogel formation with a surface structure reminiscent to natural elastin as visualized by SEM micrographs.
Optical pyrometer temperature measurement in metal-casting operations (1989)

The Oak Ridge Y-12 Plant in Oak Ridge, Tennessee, produces a variety of weapons-related components for the US Department of Defense. In recent years the Y-12 Plant has been undergoing renovations and process improvements as part of an overall modernization effort. Part of this work includes the automation of temperature control in a number of metal-casting operations. This paper relates the experience of implementing an automatic temperature measurement system for the metal casters, especially the two-color optical pyrometers eventually selected as the primary temperature sensor. 2 refs., 2 figs., 1 tab.
Abstract 6129: The proapoptotic peptide PEP-010 is efficient on several models of different tumor origins and it can be monitored by pharmacodynamic biomarker candidates in clinical practice (2023)

Abstract In cancer cells, the proapoptotic proteins caspase-9 and PP2A interaction prevents them to play their role in apoptosis. PEP-010, a drug candidate developed by PEP-Therapy, a French Biotech company, is a proapoptotic peptide targeting and disrupting this interaction leading to restoration of the apoptotic cascade. PEP-010 is an innovative bifunctional peptide. It penetrates into cells thanks to its cell penetrating part and specifically disrupts the caspase-9/PP2A interaction thanks to its interfering part. PEP-010 is currently in Phase I a/b multicenter clinical trial for the treatment of advanced solid tumors.To the aim of screening different potential therapeutic targets, to investigate the molecular mechanism-of-action of PEP-010 and to identify potential pharmacodynamic biomarkers, we have tested PEP-010 efficacy on several cell models of different tumor origins. By the Annexin V/Propidium Iodide staining and flow cytometry analysis, we found that PEP-010 induces apoptosis in most of the tested models. One possible mechanism-of-action is an involvement of the PP2A which, once released by PEP-010, could regulate expression and/or activity of different intracellular factors leading to caspases activation and cell death.The identification of the major molecular features involved in PEP-010 mechanism-of-action, were instrumental to identify different pharmacodynamic biomarker candidates (e.g. active caspase-3). Hence, such biomarkers could be useful in clinical practice to monitor the effect of PEP-010 at molecular level. We have compared specific features related to the mechanism-of-action of PEP-010 in sensitive (MDA-MB-231, IGROV1) and not sensitive cell models of different tumor origins and in tissue sections derived from Patient-Derived Xenografts models of breast cancer treated or not with PEP-010. Widely used techniques as immunofluorescent staining and immunohistochemistry were employed, making these results easily transferable in clinical routine.Taken together, our pre-clinical data showed the potential of PEP-010 as an anti-cancer peptide on a wide variety of malignancies and enabled the identification of pharmacodynamic biomarker candidates, important to ease the clinical development. Citation Format: Rayan Farhat, Laura Dadon, F Nemati, A Rebollo, D Decaudin, Joelle Wiels, Catherine Brenner, Diego Germini. The proapoptotic peptide PEP-010 is efficient on several models of different tumor origins and it can be monitored by pharmacodynamic biomarker candidates in clinical practice. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6129.
Second international symposium on information interaction in context (2009)

review-article Share on Second international symposium on information interaction in context Authors: Mounia Lalmas University of Glasgow, Glasgow, UK University of Glasgow, Glasgow, UKView Profile , Anastasios Tombros Queen Mary University of London, London, UK Queen Mary University of London, London, UKView Profile , Pia Borlund Royal School of LIS, Aalborg, Denmark Royal School of LIS, Aalborg, DenmarkView Profile , Jesper W. Schneider Royal School of LIS, Aalborg, Denmark Royal School of LIS, Aalborg, DenmarkView Profile Authors Info & Claims ACM SIGIR ForumVolume 43Issue 1June 2009pp 59–62https://doi.org/10.1145/1670598.1670610Published:25 June 2009Publication History 1citation61DownloadsMetricsTotal Citations1Total Downloads61Last 12 Months0Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Publisher SiteGet Access
ChemInform Abstract: Improved Procedure for the Solution Phase Preparation of 1,4‐Benzodiazepine‐2,5‐dione Libraries via Armstrong′s Convertible Isonitrile and the Ugi Reaction. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Kinase Inhibitors for CNS Diseases: An Analysis of the Recent Patent Literature (2012)

Protein kinases (PKs), as members of an important target class in current pharmaceutical research, have been mostly exploited so far in therapeutic areas such as oncology and inflammation. However, basic research on some PKs as key components of molecular mechanisms underlying neurodegeneration and neuroprotection may translate into new medicines for CNS diseases in the next few years. This review is an account of recent patents dealing with kinase inhibitors primarily designed for CNS indications. CNS-directed patents on kinase modulators published after 2008 were surveyed using SciFinder(®) and public patent search engines. Some PK targets, such as GSK-3β, CDK5, ROCK and p38α MAPK, continue to attract interest even though a clinical proof-of-concept is yet to be attained in a CNS setting. Less established PKs such as LRRK2, MLK, PAK and DAPK-1 hold promise as valuable targets of the future.
ChemInform Abstract: Catalytic Enantioselective Protoboration of Disubstituted Allenes. Access to Alkenylboron Compounds in High Enantiomeric Purity. (2015)

Abstract Optimized reaction conditions are developed for the proto‐boryl addition of (Bpin) 2 up to 1,1‐disubstituted allenes to afford alkenyl boronic esters in good site selectivity.
Nanosized biligated metal–organic framework systems for enhanced cellular and mitochondrial sequential targeting of hepatic carcinoma (2021)

Mitochondria are reported to play a paramount role in tumorigenesis which positions them as an instrumental druggable target. However, selective drug delivery to cancer-localized mitochondria remains challenging. Herein, we report for the first time, the design, development and evaluation of a hepatic cancer-specific mitochondria-targeted dual ligated nanoscale metal-organic framework (NMOF) for cellular and mitochondrial sequential drug delivery. Surface functionalization was performed through covalent-linking of folic acid and triphenylphosphonium moieties to the aminated Zr-based MOF, NH<sub>2</sub>-UiO-66. The characterization of the dual-ligated NMOFs using XRD, FTIR, DSC and BET analysis proved the successful conjugation process. Assessment of the drug loading and release profiling of doxorubicin (DOX)-loaded NMOF confirmed the proper retention of the drug within the NMOF porous structure alongside enhanced release in the tumor acidic environment. Furthermore, biological evaluation of the anti-tumor activity of the DOX-loaded dual-ligated NMOF on hepatocellular carcinoma affirmed the superiority of the developed system in killing the cancerous cells <i>via</i> apoptosis induction and halting cell cycle progression. This study attempts to underscore the promising potential of surface functionalized NMOFs in developing anticancer drug delivery systems to achieve targeted therapy.
Successfully Unlocking New Deep Reserves and Overcoming High-Temperature Environment Using Novel Advanced Hostile Wireline Formation Tester in North Malay Basin, Malaysia-Thailand Joint Development Area (2017)

Abstract Gas fields in a Malaysia-Thailand joint development area (MTJDA) are well-known to have the presence of high CO2 concentration and high-temperature reservoir characteristics. Sophisticated tools are necessary to measures important data to support further development and reservoir management of this field. Thus, reservoir data, such as pressure and fluid type, become crucial in terms of achieving production targets. Fields operated by this operator are located in the North Malay Basin, a few hundred kilometers from the onshore border of Malaysia and Thailand. High bottom hole temperatures (BHTs) limits data gathering runs and challenges associated with fresh water made it more crucial to identify and qualify fluid types for further field development. The extensive wireline formation pressure testing and sampling (WFPT&amp;S) program is mandatory to evaluate the viability of field development. Additional challenges included low porosity-low mobility reservoirs where fluid collection at low contamination in reservoirs with elevated temperatures of approximately 410°F (210°C) is considered a necessity. This operator pioneers the use of novel hostile wireline formation testers globally. Reliable pressure and downhole fluid analysis data should lead to production optimization. The ability of fluid characterization using a pump-out formation tester coupled with downhole fluid identification has been introduced to help improve decision making and provide real-time data and the capability to pump out high-temperature formation fluid and acquire samples that meet expected contamination levels. As a result, fluid contact, formation pressure, fluid type, reservoir mobility, and CO2 content, which are the primary drivers of production optimization and field development are able to be determined successfully. In addition, new deep reserves could potentially be discovered in the MTJDA concession that are economically accessible with extreme high-temperature tools. This paper discusses the use of a novel hostile wireline formation tester to collect low contamination samples at a predetermined level in hostile reservoir conditions with elevated temperature of 410°F (210°C). Challenges, considerations, and results are detailed. This novel tool has proven lower CO2 content than expected in deeper reservoirs with elevated temperature up to 410°F (210 °C). This is the deepest well ever drilled by this operator in a development drilling campaign.
Pick-up systems for vibrating sample magnetometers-a theoretical discussion based on magnetic multipole expansions (1994)

It is quantitatively analysed how the voltage induced in a pick-up coil is related to arbitrarily (i.e. non-uniformly) magnetized samples, arbitrarily large vibration amplitude and arbitrary direction of vibration. The influence of errors in the position and in the vibration direction of the sample on the measured magnetization is discussed, and a well known criterion, commonly used to minimize sample position errors, is generalized. The authors propose compensated coil pairs, which are insensitive to either spurious vibrations or to power line pick-up. They also outline a system which realizes a true vector measurement of the three dipole moments as well as a measurement of three of the five quadrupole moments.
TTL Procedures for SR-TE Paths in Label Switched Path Traceroute Mechanisms (2019)

Segment routing supports the creation of explicit paths using
adjacency-sids, node-sids, and anycast-sids. The SR-TE paths are built
by stacking the labels that represent the nodes and links in the
explicit path. A very useful Operations And Maintenance requirement is
to be able to trace these paths as defined in [RFC8029]. This document
specifies a uniform mechanism to support MPLS traceroute for the SR-TE
paths when the nodes in the network are following uniform mode or
short-pipe mode [RFC3443].
Noninvasive in Vivo Measurement of Venous Blood pH during Exercise Using Near-Infrared Reflectance Spectroscopy (2007)

Blood pH is an important indicator of anaerobic metabolism in exercising muscle. This paper demonstrates multivariate calibration techniques that can be used to produce a general pH model that can be applied to spectra from any new subject without significant prediction error. Tissue spectra (725 approximately 880 nm) were acquired through the skin overlying the flexor digitorum profundus muscle on the forearms of eight healthy subjects during repetitive hand-grip exercise and referenced to the pH of venous blood drawn from a catheter placed in a vein close to the muscle. Calibration models were developed using multi-subject partial least squares (PLS) and validated using subject-out cross-validation after the subject-to-subject spectral variations were corrected by mathematical preprocessing methods. A combination of standard normal variate (SNV) scaling and principal component analysis loading correction (PCALC) successfully removed most of the subject-to-subject variations and provided the most accurate prediction results.
Project GeoTV: a three-screen service (2009)

GeoTV is a project that explores seamless integration of mobile phones, HDTV sets, and computers in the living room to enrich the user experience of existing services. The three-screen service allows a user to navigate a world map on a smart phone to track geo-located media RSS content that matches her personal interests. The user can show a matching video clip on her phone or direct a nearby HDTV set to play the video. In addition, the user can bring up a world map on a nearby computer screen to navigate areas of interest related to the video clip. GeoTV allows all three screens to be used for what they are best for: HDTV for high resolution video, computer screen for browsing a world map, and a smart phone for personalized control at hand to select media of interest.
Simvastatin regulates CXC chemokine formation in streptococcal M1 protein-induced neutrophil infiltration in the lung (2011)

Streptococcus pyogenes of the M1 serotype can cause streptococcal toxic shock syndrome and acute lung injury. Statins exert beneficial effects in septic patients although the mechanisms remain elusive. This study examined effects of simvastatin on M1 protein-provoked pulmonary inflammation and tissue injury. Male C57BL/6 mice were pretreated with simvastatin or a CXCR2 antagonist before M1 protein challenge. Bronchoalveolar fluid and lung tissue were harvested for determination of neutrophil infiltration, formation of edema, and CXC chemokines. Flow cytometry was used to determine Mac-1 expression on neutrophils. Gene expression of CXC chemokines was determined in alveolar macrophages by using quantitative RT-PCR. M1 protein challenge caused massive infiltration of neutrophils, edema formation, and production of CXC chemokines in the lung as well as upregulation of Mac-1 on circulating neutrophils. Simvastatin reduced M1 protein-induced infiltration of neutrophils and edema in the lung. In addition, M1 protein-induced Mac-1 expression on neutrophils was abolished by simvastatin. Furthermore, simvastatin markedly decreased pulmonary formation of CXC chemokines and gene expression of CXC chemokines in alveolar macrophages. Moreover, the CXCR2 antagonist reduced M1 protein-induced neutrophil expression of Mac-1 and accumulation of neutrophils as well as edema formation in the lung. These novel findings indicate that simvastatin is a powerful inhibitor of neutrophil infiltration in acute lung damage triggered by streptococcal M1 protein. The inhibitory effect of simvastatin on M1 protein-induced neutrophil recruitment appears related to reduced pulmonary generation of CXC chemokines. Thus, simvastatin may be a useful tool to ameliorate acute lung injury in streptococcal infections.
Advantages and application of label-free detection assays in drug screening (2008)

Microplate-based optical biosensors are enabling a variety of cell-based assays, inhibition assays, protein-protein binding assays and protein-small molecule binding assays to be performed with high-throughput and high sensitivity.
Incorporation of Pentraxin 3 into Hyaluronan Matrices Is Tightly Regulated and Promotes Matrix Cross-linking (2014)

Mammalian oocytes are surrounded by a highly hydrated hyaluronan (HA)-rich extracellular matrix with embedded cumulus cells, forming the cumulus cell·oocyte complex (COC) matrix. The correct assembly, stability, and mechanical properties of this matrix, which are crucial for successful ovulation, transport of the COC to the oviduct, and its fertilization, depend on the interaction between HA and specific HA-organizing proteins. Although the proteins inter-α-inhibitor (IαI), pentraxin 3 (PTX3), and TNF-stimulated gene-6 (TSG-6) have been identified as being critical for COC matrix formation, its supramolecular organization and the molecular mechanism of COC matrix stabilization remain unknown. Here we used films of end-grafted HA as a model system to investigate the molecular interactions involved in the formation and stabilization of HA matrices containing TSG-6, IαI, and PTX3. We found that PTX3 binds neither to HA alone nor to HA films containing TSG-6. This long pentraxin also failed to bind to products of the interaction between IαI, TSG-6, and HA, among which are the covalent heavy chain (HC)·HA and HC·TSG-6 complexes, despite the fact that both IαI and TSG-6 are ligands of PTX3. Interestingly, prior encounter with IαI was required for effective incorporation of PTX3 into TSG-6-loaded HA films. Moreover, we demonstrated that this ternary protein mixture made of IαI, PTX3, and TSG-6 is sufficient to promote formation of a stable (i.e. cross-linked) yet highly hydrated HA matrix. We propose that this mechanism is essential for correct assembly of the COC matrix and may also have general implications in other inflammatory processes that are associated with HA cross-linking.