gebhart/patrepeval huggingface dataset:
A functional network of gastric-cancer-associated splicing events controlled by dysregulated splicing factors (2020)

Comprehensive understanding of aberrant splicing in gastric cancer is lacking. We RNA-sequenced 19 gastric tumor-normal pairs and identified 118 high-confidence tumor-associated (TA) alternative splicing events (ASEs) based on high-coverage sequencing and stringent filtering, and also identified 8 differentially expressed splicing factors (SFs). The TA ASEs occurred in genes primarily involved in cytoskeletal organization. We constructed a correlative network between TA ASE splicing ratios and SF expression, replicated it in independent gastric cancer data from The Cancer Genome Atlas and experimentally validated it by knockdown of the nodal SFs (<i>PTBP1</i>, <i>ESRP2</i> and <i>MBNL1</i>). Each SF knockdown drove splicing alterations in several corresponding TA ASEs and led to alterations in cellular migration consistent with the role of TA ASEs in cytoskeletal organization. We have therefore established a robust network of dysregulated splicing associated with tumor invasion in gastric cancer. Our work is a resource for identifying oncogenic splice forms, SFs and splicing-generated tumor antigens as biomarkers and therapeutic targets.
Decreased Effective Connectivity from Cortices to the Right Parahippocampal Gyrus in Alzheimer's Disease Subjects (2014)

The purpose of this study was to detect effective connectivity (EC) changes in the default mode network and hippocampus network in 20 patients with Alzheimer's disease (AD) and 20 cognitively normal (CN) subjects, using multivariate Granger causality. The authors used the maximum coefficients in the multivariate autoregression model to quantitatively measure the different EC strength levels between the CN and AD groups. It was demonstrated that the EC strength difference can classify AD from CN subjects. Further, the right parahippocampal gyrus (PHP_R) showed imbalanced bidirectional EC connections. The PHP_R received weaker input connections from the neocortices, but its output connections were significantly increased in AD. These findings may provide neural physiological mechanisms for interpreting AD subjects' memory deficits during the encoding processes.
Detektionsrate der [68Ga]PSMA I&T PET/CT bei Patienten mit biochemischen Prostatakarzinomrezidiv und Vergleich mit publizierten Detektionsraten von [68Ga]PSMA HBED-CC (2017)

Bestimmung der Detektionsrate der [68Ga]PSMA I&T PET/CT bei biochemischen Prostatakarzinomrezidiv und Vergleich mit publizierten Detektionsraten der [68Ga]PSMA HBED-CC PET/CT.
Species-Specific Inactivation of Triosephosphate Isomerase from Trypanosoma brucei: Kinetic and Molecular Dynamics Studies (2017)

Human African Trypanosomiasis (HAT), a disease that provokes 2184 new cases a year in Sub-Saharan Africa, is caused by <i>Trypanosoma brucei</i>. Current treatments are limited, highly toxic, and parasite strains resistant to them are emerging. Therefore, there is an urgency to find new drugs against HAT. In this context, <i>T. brucei</i> depends on glycolysis as the unique source for ATP supply; therefore, the enzyme triosephosphate isomerase (TIM) is an attractive target for drug design. In the present work, three new benzimidazole derivatives were found as TbTIM inactivators (compounds <b>1</b>, <b>2</b> and <b>3</b>) with an I<sub>50</sub> value of 84, 82 and 73 µM, respectively. Kinetic analyses indicated that the three molecules were selective when tested against human TIM (HsTIM) activity. Additionally, to study their binding mode in TbTIM, we performed a 100 ns molecular dynamics simulation of TbTIM-inactivator complexes. Simulations showed that the binding of compounds disturbs the structure of the protein, affecting the conformations of important domains such as loop 6 and loop 8. In addition, the physicochemical and drug-like parameters showed by the three compounds suggest a good oral absorption. In conclusion, these molecules will serve as a guide to design more potent inactivators that could be used to obtain new drugs against HAT.
Toward a Theory of Distributed Interdisciplinary Project-based Design Education (2005)

The efficacy of project-based learning (PBL) in design education has gained broad acceptance. Moreover, when PBL takes place in teams, it resembles design practice more closely, and offers an attractive value proposition to educational institutions for producing highly employable graduates. Therefore, most state of the art design curricula utilize PBL principles. Some innovative design curricula also recognize the significance of interdisciplinary practice, and organize student teams such that different functions associated with key disciplines of design projects are represented. However, in reality, the majority of students usually belong to a single educational discipline, and some are simply asked to wear another discipline's hat for the duration of projects. There have been few structured attempts at recruiting students with backgrounds in different educational disciplines so that a true interdisciplinary setting is achieved. This scheme is particularly meaningful when complex design tasks are tackled. The Project Oriented Learning Environment (POLE) is one such educational paradigm. This paper describes the POLE platform, discusses an assessment methodology and a toolset that have been developed over three years, and presents key findings as the outcome of that assessment. The assessment outcomes are used to substantiate a theoretical framework for distributed interdisciplinary project-based design education.
Fault Prognosis of Key Components in HVAC Air-Handling Systems at Component and System Levels (2020)

Fault prognosis of the air-handling systems, which are the key subsystems of heating, ventilation, and air conditioning systems, allows system operators to know the remaining useful life (RUL), thus preventing unexpected breakdowns and reducing the operational and maintenance costs. In this article, a new hidden semi-Markov model-based method is developed. In the method, only relevant state-transition points are selected and estimated, leading to computational efficiency. Physics-based models are used in a novel way to provide “mapping matrices” relating component capacities to fault severities, capturing impacts of multiple failure modes. Experimental results show that our method can effectively estimate the RUL of the components and the systems.
Ellipsometric measurement technique for a modified Otto configuration used for observing surface-plasmon resonance (2010)

In order to carry out precise measurements of the thickness of a dielectric layer deposited on a metal surface, we have introduced an ellipsometric measurement technique (EMT) to the modified Otto's configuration (MOC) that is used for observing surface plasmon resonance (SPR). For that purpose, we have measured the thickness of the Au layer by the EMT at four different locations on an elliptic fringe pattern obtained from the MOC basing on a four-layer structure model: prism (BK7)-air-Ausubstrate (BK7). Then, we have measured that of a TiO(2) layer deposited on the Au layer by the EMT basing on a five-layer structure model: prism (BK7)-air-TiO(2)-Au-substrate (BK7). We have found experimentally that the combination of EMT and MOC is effective for measuring the thickness of the dielectric layer on the metal.
Micro- and macro-borderless surgery using a newly developed high-resolution (4K) three-dimensional video system (2021)

MMBS using the novel system is applicable to various surgeries and valuable for both fine surgical procedures and high-level surgical education.
In vivo and in vitro characterization of the B1 and B2 zinc-binding domains from the acute promyelocytic leukemia protooncoprotein PML. (1996)

Acute promyelocytic leukemia (APL) has been ascribed to a chromosomal translocation event which results in a fusion protein comprising the PML protein and retinoic acid receptor alpha. PML is normally a component of a nuclear multiprotein complex which is disrupted in the APL disease state. Here, two newly defined cysteine/histidine-rich protein motifs called the B-box (B1 and B2) from PML have been characterized in terms of their effect on PML nuclear body formation, their dimerization, and their biophysical properties. We have shown that both peptides bind Zn2+, which induces changes in the peptides' structures. We demonstrate that mutants in both B1 and B2 do not form PML nuclear bodies in vivo and have a phenotype that is different from that observed in the APL disease state. Interestingly, these mutations do not affect the ability of wild-type PML to dimerize with mutant proteins in vitro, suggesting that the B1 and B2 domains are involved in an additional interaction central to PML nuclear body formation. This report in conjunction with our previous work demonstrates that the PML RING-Bl/B2 motif plays a fundamental role in formation of a large multiprotein complex, a function that may be common to those unrelated proteins which contain the motif.
Molecular Modeling of Early Stage of Swelling in Na-Montmorillonite Clay (2013)

Swelling clays are found in various parts of the world. These clays cause enormous damage to infrastructure and light structures because of swelling and the exertion of swelling pressure when swelling is constrained. However, the swelling phenomenon is critical when these clays are used as barrier materials in environmental engineering applications, oil exploration, clay nanocomposites, etc. In this paper, we present the methodology and results of molecular dynamics simulations of Na-Montmorillonite clay interlayer to find the key mechanisms of swelling during early stage of hydration. Molecular models of Na-Montmorillonite clay are constructed and placed in a solvation box. Molecular dynamics simulations are conducted at room temperature and pressure. Trajectories of individual water molecules are calculated and the evolution of d-spacing and interaction energies between water molecules, cations, and clay sheets with time are computed. These simulations provide and unprecedented insight into mechanisms that lead to interlayer swelling during early stages of hydration.
Efflux pump‐deficient mutants as a platform to search for microbes that produce antibiotics (2015)

Pseudomonas putida DOT-T1E-18 is a strain deficient in the major antibiotic efflux pump (TtgABC) that exhibits an overall increased susceptibility to a wide range of drugs when compared with the wild-type strain. We used this strain as a platform to search for microbes able to produce antibiotics that inhibit growth. A collection of 2400 isolates from soil, sediments and water was generated and a drop assay developed to identify, via growth inhibition halos, strains that prevent the growth of DOT-T1E-18 on solid Luria-Bertani plates. In this study, 35 different isolates that produced known and unknown antibiotics were identified. The most potent inhibitor of DOT-T1E-18 growth was an isolate named 250J that, through multi-locus sequence analysis, was identified as a Pseudomonas sp. strain. Culture supernatants of 250J contain four different xantholysins that prevent growth of Gram-positive bacteria, Gram-negative and fungi. Two of the xantholysins were produced in higher concentrations and purified. Xantholysin A was effective against Bacillus, Lysinibacillus and Rhodococcus strains, and the effect against these microbes was enhanced when used in combination with other antibiotics such as ampicillin, gentamicin and kanamycin. Xantholysin C was also efficient against Gram-positive bacteria and showed an interesting antimicrobial effect against Pseudomonas strains, and a synergistic inhibitory effect with ampicillin, chloramphenicol and gentamicin.
Polyurethane and Epoxy Coatings for the Rehabilitation and Repair of Pipelines (2000)

Abstract The vast majority of buried pipelines have been coated with specialised protective coatings. Usually cathodic protection has been applied, leading to a combination of protective measures. However, all coatings fail to some degree and when the failure becomes critical a pipeline has to be rehabilitated. This rehabilitation is usually carried out with compatible coating materials. Polyurethane and epoxy two pack coatings are mainly used to undertake this coating rehabilitation work.
Controlled formation of high Schottky barriers on InP and related materials (2002)

The present status of the various ingenious approaches made until now to increase Schottky barrier heights (SBHs) on InP and related materials are reviewed from the viewpoints of the mechanism of SBH increase, the SBH values achieved, the controllability and reproducibility of the process, and the barrier reliability. The approaches discussed include: (1) formation of insulator interlayers, (2) formation of semiconductor interlayers, (3) sulphur and selenium surface treatments, (4) low temperature metal deposition, (5) plasma surface treatments, and (6) electrochemical deposition. Particular emphasis is placed on the in-situ electrochemical process by the author's group where Fermi level pinning seems to be removed.
DGGE-RAPD analysis as a useful tool for cultivar identification (2006)

Denaturing gradient gel electrophoresis-random amplified polymorphic&#13;\nDNA (DGGE-RAPD) was used to overcome the main drawbacks of RAPD (i.e.,&#13;\nthe low levels of reproducibility and polymorphism). As a model, six&#13;\nbarley cultivars of known origin were tested for RAPD markers using&#13;\nDGGE methodology with 29 arbitrary primers. Among a total of 418 bands&#13;\nobserved, as high as 99 were polymorphic. Comparison between&#13;\nagarose-RAPD and DGGE-RAPD revealed that the latter was highly&#13;\nreproducible and gave higher level of polymorphism and consequently&#13;\nmore markers. The relationships among barley cultivars derived from&#13;\nthis study based on DGGE-RAPD are consistent with the known lineage of&#13;\nthese cultivars. In conclusion, we recommend the use of DGGE-RAPD as an&#13;\nalternative tool to the more costly DNA-based analysis in cultivar&#13;\nidentification in laboratories with limited funds.
Low-temperature annealing behavior of defects in Mg-ion-implanted GaN studied using MOS diodes and monoenergetic positron beam (2020)

Abstract Mg ions were implanted into Si-doped (5 × 10 17 cm –3 ) n-GaN at a dose of 1.5 × 10 11 or 1.5 × 10 12 cm –2 . MOS diodes were used to characterize the implanted GaN after 300 °C annealing for 3 h and after additional 500 °C annealing for 3 min. Although capacitance – voltage ( C–V ) characteristics varied with the dosage, the effects of acceptor-like defects induced by ion implantation were observed in the C–V characteristics independently of dosage and annealing temperature. A defect level at approximately 0.25 eV below the conduction band edge was detected electrically. By positron annihilation spectroscopy, its origin was identified as a divacancy consisting of Ga and N vacancies. It was found that its density compared with that of as-implanted GaN decreased with 300 °C annealing, and further increased with 500 °C annealing. This phenomenon was explained on the basis of the difference between the diffusion barriers of possible point defects.
ChemInform Abstract: Rhombohedral Prussian White as Cathode for Rechargeable Sodium‐Ion Batteries. (2015)

Abstract The novel air‐stable compound Na 1.92 Fe[Fe(CN) 6 ] with rhombohedral structure is prepared by reaction of aqueous Na 4 Fe(CN) 6 and ascorbic acid (autoclave, pH 6.5, 140 °C, 20 h).
Cathepsin B Imaging to Predict Quality of Engineered Cartilage (2015)

Cathepsin B (CB)-specific molecular imaging probe is applied to monitor the changes of CB expression in 3D cultured chondrocytes during the chondrogenesis. The probe is synthesized with a CB-cleavable peptide linked to a near infrared fluorescence (NIRF) dye and a dark quencher, which can recover the NIRF signal in the presence of CB enzyme. The CB activities in two different sets of chondrocytes are comparatively analyzed. The chondrocytes with higher CB activity show more extensive area of chondrogenesis that CB molecular imaging directly reflects the chondrogenic potency of the cells. The CB probe is expected to provide a reliable prediction for the quality of engineered cartilage by visualizing the activity of the relevant enzyme in chondrocytes.
The Coupling of Catharanthine and Vindoline to Form 3′,4′-Anhydrovinblastine by Haemoproteins and Haemin (1988)

The enzymic coupling of catharanthine and vindoline can be performed with plant peroxidases in a reaction which yields 3',4'-anhydrovinblastine (AVLB) as the major product. This has led to an investigation of other sources of peroxidase activity and haem. High levels of AVLB were obtained using microperoxidase (haem-undecapeptide) and haemin, and lower yields were also detected with lactoperoxidase, cytochrome C, and haemoglobin. The activity with haemin and microperoxidase has been optimized and it is concluded that, in comparison with horseradish peroxidase, these systems provide an improved means of coupling.
Catalytic asymmetric hydrogenation of imines. Use of rhodium(I)/phosphine complexes and characterization of rhodium(I)/imine complexes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic asymmetric hydrogenation of imines. Use of rhodium(I)/phosphine complexes and characterization of rhodium(I)/imine complexesAdam G. Becalski, William R. Cullen, Michael D. Fryzuk, Brian R. James, Guo J. Kang, and Steven J. RettigCite this: Inorg. Chem. 1991, 30, 26, 5002–5008Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/ic00026a027https://doi.org/10.1021/ic00026a027research-articleACS PublicationsRequest reuse permissionsArticle Views722Altmetric-Citations114LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
ANNULAR PERIPHERAL RETINAL DETACHMENT ASSOCIATED WITH VITREOUS CONDENSATION (1961)

VERY occasionally, in the course of deep anterior scleral inflammation, an irregular peripheral ring of retinal detachment can be seen, presumably exudative in origin, which subsides spontaneously after giving rise to apprehension and a prolonged search for a non-existent retinal hole. Stallard (1954) has reported six patients with annular peripheral retinal detachment, in three of whom the condition was bilateral. A definite aetiology could not be ascribed to any of the cases. Three recovered after surgical treatment and one spontaneously.
Guidance for pediatric use in prescription information for novel medicinal products in the EU and the US (2022)

Pediatric legislations in the European Union (EU) and the United States (US) have increased medicines approved for use in the pediatric population. Despite many similarities between these frameworks, the EU Paediatric Regulation more often provides regulators with a mandate to require pediatric drug development for novel medicinal products compared to US regulators. If used, this could give rise to differences in the guidance for pediatric use provided for clinicians in the two regions. However, the level of discordance in the guidance for pediatric use between the two regions is unknown. This cross-sectional study compares guidance for pediatric use in the EU Summary of Product Characteristics (SmPC) and the US Prescription Information (USPI) on the level of indications granted for novel medicinal products approved after the pediatric legislations came in to force in both regions. For all indications granted as of March 2020 for novel medicinal products approved in both regions between 2010 and 2018, we compared the guidance for pediatric use in the EU SmPC and the USPI. The guidance for pediatric use differed for 18% (61/348) of the listed indications covering 21% (45/217) of the products, but without the guidance being contradictory. Where guidance differed, an equal share was observed for indications with a higher level of information for pediatric use in one region over the other (49% (30/61) in the US; 51% (31/61) in the EU). The discrepancies in pediatric information could be explained by differences in regulations for 21% (13/61) of the indications. Only a few conditions and diseases (EU n = 4; US n = 1) were observed to cover potential pediatric use outside the approved adult indication. Although the EU Paediatric Regulation more often provides regulators a mandate for requiring pediatric drug development as compared to the US PREA, this was not reflected in the prescription information approved by the two regulatory authorities.
Real Differences between OT and CRDT in Building Co-Editing Systems and Real World Applications (2019)

OT (Operational Transformation) was invented for supporting real-time co-editors in the late 1980s and has evolved to become a core technique used in today's working co-editors and adopted in major industrial products. CRDT (Commutative Replicated Data Type) for co-editors was first proposed around 2006, under the name of WOOT (WithOut Operational Transformation). Follow-up CRDT variations are commonly labeled as "post-OT" techniques and have made broad claims of superiority over OT solutions, in terms of correctness, time and space complexity, simplicity, etc. Over one decade later, however, OT remains the choice for building the vast majority of co-editors, whereas CRDT is rarely found in working co-editors. Why? To seek truth from facts, we set out to conduct a comprehensive and critical review of representative OT and CRDT solutions and working co-editors based on them. From this work, we have made important discoveries about OT and CRDT, and revealed facts and evidences that refute CRDT claims over OT on all accounts. We present our discoveries in three related and complementary articles. In prior two articles, we have revealed the similarities of OT and CRDT in following the same general transformation approach in co-editors, and their real differences in correctness and complexity. In this article, we examine the role of building working co-editors in shaping OT and CRDT research and solutions, and consequential differences in the choice between OT and CRDT in real world co-editors and industry products. In particular, we review the evolution of co-editors from research vehicles to real world applications, and discuss representative OT-based co-editors and alternative approaches in industry products and open source projects. Moreover, we evaluate CRDT-based co-editors in relation to published CRDT solutions, and clarify some myths surrounding "peer-to-peer" co-editing.