gebhart/patrepeval huggingface dataset:
Requirement for an Aromatic Amino Acid or Histidine at the N Terminus of Sindbis Virus RNA Polymerase (1998)

The N terminal amino acid of nonstructural protein nsP4, the viral RNA polymerase, is a tyrosine in all sequenced alphaviruses; this is a destabilizing amino acid for the N-end rule pathway and results in rapid degradation of nsP4 produced in infected cells or in reticulocyte lysates. We have constructed 11 mutants of Sindbis virus bearing Phe, Ala, Thr, Cys, Leu, Met, Asn, Gln, Glu, Arg, or Pro at the N terminus of nsP4. Translation of RNAs in reticulocyte lysates showed that cleavage at the nsP3/nsP4 site occurred efficiently for all mutants except for Glu-nsP4, which was cleaved inefficiently, and Pro-nsP4, which was not detectably cleaved, and that Tyr, Cys, Leu, Arg, and Phe destabilized nsP4 but Ala, Met, Thr, Asn, Gln, and Glu stabilized nsP4 to various extents. The viability of the mutants was examined by transfection of chicken cells at 30 or 40 degrees C. The Phe-nsP4 mutant formed large plaques at both temperatures. The Met-nsP4 mutant was also viable but formed small plaques at 30 degrees C and minute plaques at 40 degrees C. The remaining mutants did not form plaques at either temperature. However, after prolonged incubation at 30 degrees C, all the mutants except Glu-nsP4 and Pro-nsP4 produced viable viruses. In the case of Cys-, Leu-, Asn-, Gln-, or Arg-nsP4, revertants that were indistinguishable in plaque phenotype from the wild-type virus arose by same-site reversion to Tyr, Trp, Phe, or His by a single nucleotide substitution in the original mutant codon. Viable viruses also arose from the Ala-, Leu-, Cys-, Thr-, Asn-, Gln-, and Arg-nsP4 mutants that retained the original mutations at the N terminus of nsP4, but these viruses formed smaller plaques than the wild-type virus and many were temperature sensitive. Our results indicate that only nsP4s bearing N-terminal Tyr, Phe, Trp, or His have wild-type or near-wild-type activity for RNA replication and that rapid degradation of nsP4 is not a prerequisite for its function. nsP4s bearing other N-terminal residues, with the exception of Met-nsP4, have only very low or negligible activity, so that no detectable infectious virus can be produced. However, suppressor mutations can arise that enable most such nsP4s to regain significant but still suboptimal activity.
High expression of gabarapl1 is associated with a better outcome for patients with lymph node-positive breast cancer (2010)

Our data show for the first time that the level of gabarapl1 mRNA expression in breast tumours is a good indicator of the risk of recurrence, specifically in pN+ patients.
ChemInform Abstract: Synthesis of Some Benzothiazole Derivatives of Expected Biological Activity. (1986)

Abstract Die Umsetzung der Grignard‐Verbindung (I) mit verschiedenen Aldehyden und Ketonen (II) wird beschrieben.
Application of thermal imaging to assess the superficial skin temperature distribution after local cryotherapy and ultrasound (2017)

Thermal imaging is a safe, noninvasive, and quite low-cost technique that allows for the rapid and noninvasive recording of thermal radiation emitted by the human body. In recent years, it is increasingly used for physiotherapy monitoring. The main goal of the study was to compare the influence of two various treatments applied in two various orders, namely local cryotherapy (CRYO) and ultrasound therapy (US). The impact of combined therapies, applied in two various orders, was studied in terms of changes of the superficial temperature distribution on the front right thigh surface. The response to the therapy depending the treated persons’ gender, along with a consensual reaction, was examined. The research material consisted of 30 healthy volunteers, 19–23-year old students, aged 19.93 (± 1.42). All treatments were performed at weekly intervals in the following order: in the first week, CRYO immediately followed by US, and in the second week, ultrasound immediately followed by local cryotherapy. All treatments were performed on the right quadriceps. The combined sequence of local cryotherapy and ultrasound therapy caused temperature decrease in the treated area regardless of their performance order. The temperature decrease considerably depends on the sequence of the applied treatments, and it was more significant after the ultrasound–cryotherapy sequence. Moreover, these changes also lasted longer. Statistically significant influence of the subjects’ gender was observed in case of consensual reaction.
Facing the Increasingly Looming Challenges from Environmental Fungal (Molds and Yeast) Contamination (2015)

In an unprecedented and extraordinary case of a deadly multi-state meningitis outbreak in the fall of 2012, 64 people died and 751 cases were treated across 20 states within the USA, according to the Centers for Disease Control and Prevention (CDC)[1]. Exserohilum rostratum , a fungus commonly found in the environment, was identified as the predominant organism in the patients with meningitis and was associated with the growth in the meninges [2]. One of the early patients from the outbreak was infected with Aspergillus fumigatus
Platelet P-selectin is required for pulmonary eosinophil and lymphocyte recruitment in a murine model of allergic inflammation (2004)

Platelets are necessary for lung leukocyte recruitment in a murine model of allergic inflammation, and platelet-leukocyte aggregates are formed in circulating blood of patients with asthma after allergen exposure. However, it is unknown how platelets induce pulmonary leukocyte recruitment in asthma. Here, we have investigated the importance of platelet adhesion molecule expression on pulmonary eosinophil and lymphocyte recruitment and on leukocyte CD11b and very late antigen (VLA)-4 expression in mice. Pulmonary leukocyte recruitment in platelet-depleted mice (sensitized and exposed to ovalbumin) transfused with fixed, unstimulated platelets (FUSPs) was abolished, whereas transfusion with platelets stimulated and fixed (FSPs), expressing P-selectin and P-selectin glycoprotein ligand-1 (PSGL-1), restored eosinophil and lymphocyte recruitment. Transfusion with platelets from P-selectin-deficient mice, or with FSPs stimulated in the presence of a blocking anti-P-selectin antibody, were unable to restore pulmonary leukocyte recruitment. Flow cytometric analysis revealed increased expression of CD11b and VLA-4 on leukocytes attached to platelets after allergen exposure, and CD11b expression on leukocytes was suppressed in thrombocytopenic mice but was restored with the transfusion of FSPs, but not FUSPs, a phenomenon concurrent with the formation of platelet-leukocyte complexes. P-selectin expression on the surfaces of platelets is a major requirement for pulmonary eosinophil and lymphocyte recruitment, allowing circulating platelets to bind to and stimulate leukocytes for endothelial attachment.
Traffic flow estimation with data from a video surveillance camera (2019)

This study addresses the problem of traffic flow estimation based on the data from a video surveillance camera. Target problem here is formulated as counting and classifying vehicles by their driving direction. This subject area is in early development, and the focus of this work is only one of the busiest crossroads in city Chelyabinsk, Russia. To solve the posed problem, we employed the state-of-the-art Faster R-CNN two-stage detector together with SORT tracker. A simple regions-based heuristic algorithm was used to classify vehicles movement direction. The baseline performance of the Faster R-CNN was enhanced by several modifications: focal loss, adaptive feature pooling, additional mask branch, and anchors optimization. To train and evaluate detector, we gathered 982 video frames with more than 60,000 objects presented in various conditions. The experimental results show that the proposed system can count vehicles and classify their driving direction during weekday rush hours with mean absolute percentage error that is less than 10%. The dataset presented here might be further used by other researches as a challenging test or additional training data.
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework (2019)

ABSTRACT Background The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria (PS3/BS3) for functional assays that specified a “strong” level of evidence. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes is a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation. Methods The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development. Results The SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are: 1. Define the disease mechanism; 2. Evaluate applicability of general classes of assays used in the field; 3. Evaluate validity of specific instances of assays; 4. Apply evidence to individual variant interpretation. We found that a minimum of eleven total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis. Conclusions The recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.
A Comparative Analysis of Traditional and Modern Data Compression Schemes for Large Multi-Dimensional Extendible Array (2019)

Data analysis and mining in scientific domains involve storage of large-scale multi-dimensional datasets for scientific, statistical & engineering applications in multidimensional online analytical processing (MOLAP) databases. Because of the size of the datasets is increasing and the degree of data-sparsity is being high, it is important to find the suitable and efficient compression scheme for storing data at a minimal scheme. This paper represents a comparative analysis of Traditional and Modern Data Compression Schemes for Multi-Dimensional data ranging from dimension 1 to 3. The main idea is to compare the space savings of four different & significant compressions schemes i.e. Bit Map, Header Compression, Compressed Row Storage (CRS) & Extendible Array Based Compression Scheme (EaCRS). The results from experiments show that EaCRS scheme is better than the other schemes in case of space complexity especially for higher data density.
Impact of lifestyle diseases on income and household consumption: evidence from an emerging economy (2021)

With increase in lifestyle diseases such as diabetes, hypertension and heart disease in emerging economies, it is important to understand the impact of acquiring these health issues on household income and consumption. Using a panel data of Indian households, we show that acquiring diabetes, hypertension or heart disease results in increased medical and non-medical expenses for high-income households. However, affected low-income households, to meet their increased medical expenses, had to divert resources from non-medical expenses. Our findings add to the extant marketing literature on impact of crises on consumption behaviour and the marketing implications of such changes in consumption behaviour.
Amino acid sequence of Streptomyces griseus trypsin. Cyanogen bromide fragments and complete sequence (1975)

Information compiled by automatic Edman degradation of Streptomyces griseus trypsin coupled with previous data has permitted the assignment of the first 36 residues at the NH2 terminus of the protein. Cyanogen bromide cleavage at the three methionine residues followed or preceded by reduction and aminoethylation resulted in the production of four fragments, Cnl to Cn4, which were separated by gel filtration on Sephadex G-50 or G-75. Fragments CN4 (15 RESIDUES) AND Cn3 (5 residues) were shown to be derived from the NH2 terminus of the protein while Cn2 (47 residues and devoid of homoserine) was from the COOH terminus. The arrangement of the fragments was thus Cn4-Cn3-Cn1-Cn2. Automatic Edman degradation in the sequenator coupled with peptides derived from alpha-lytic protease and chymotryptic digestion and from the peptic and tryptic peptides previously elucidated have permitted the sequence determination of fragments Cn1 and Cn2 and therefore of the whole protein. These studies show that extensive regions of identity or similarity exist between Streptomyces griseus trypsin and bovine trypsin. These include the NH2-terminal four residues, the sequences near histidine-57 (chymotrypsinogen A numbering system), aspartic acid-102, aspartic acid-189, and serine-195, the regions of the three disulfide bridges, and the COOH-terminal end (residues 225-229) of the proteins. When aligned to maximize homology the identity of residues is 34%. This identity is increased to 54% when only those residues classified as internal by Stroud et al. (Stroud, R. M., Kay, L. M., and Dickerson, R. E. (1971) Cold Spring Harbor Symp. Quant. Biol. 36, 125) are considered. These results indicate that the folding of the polypeptide chains of the two enzymes is very similar and are in agreement with the very similar enzymic, chemical, and physical properties of the two enzymes.
Mortality in congenital hemophilia A – a systematic literature review (2020)

Against a background of a rapidly evolving treatment landscape, a contemporary, evidence-based consolidated understanding of mortality in people with congenital hemophilia A (PwcHA) is lacking. This systematic literature review examines the available data on mortality and causes of death in PwcHA to enable a better understanding of fatalities in PwcHA and evaluate the impact of new treatment paradigms on mortality. A systematic literature review of observational studies was conducted by searching Medline, Embase, and clinical trials registries for articles published from January 2010 to March 2020, using the search terms: hemophilia A (HA), mortality, cause of death. Interventional studies, studies not reporting fatalities, and those reporting only on hemophilia B, acquired HA, or mixed other coagulopathies were excluded. Overall, 7818 unique records were identified and 17 were analyzed. Of these, six reported mortality rates and five reported mortality ratios. Mortality generally decreased over time, despite a spike associated with human immunodeficiency virus (HIV)/hepatitis C virus (HCV) infection in the 1980s and 1990s. Mortality was strongly correlated with age and hemophilia severity. People with hemophilia had a raised mortality risk compared with the general population, particularly in severe hemophilia, and when infected with HIV or HCV. Causes of death varied across populations, countries, and time in 15 identified studies; however, incomplete and heterogeneous reporting limits evidence. Hemorrhage, HIV, HCV, and hepatic disease were the leading causes of death. A unified approach to reporting mortality and cause of death is needed to understand mortality in PwcHA as treatments continue to advance.
Simulation and measurement of corona for electrostatic pulse powered precipitators (1985)

The use of pulse powering for electrostatic precipitators has shown several advantages but the underlying physics has been insufficiently understood to allow any optimization. A numerical model has been assembled which allows the controlling corona process to be simulated in both time and space to permit estimation of the ion densities and field distributions to be expected for a wide range of transient electrical parameters and gas properties. Supporting laboratory measurements have been undertaken under dc and pulse conditions both to verify the simulation and to provide corona spot density data not readily obtainable by other means.
Can Architecture Design Help Eliminate Some Common Vulnerabilities? (2017)

As technology improves in size and the number of smart devices increases, security in personal devices undoubtedly becomes an important aspect of today's life. However, the complexity in hardware and software systems expose vulnerabilities in security. Vulnerabilities may exist in many layers of systems and would require a specific inputs or events to trigger it. Discovery of vulnerabilities require significant time and also system specific knowledge, and even then some are difficult to patch.In this paper, we study open source tools for finding potential vulnerabilities and represent the advantages and disadvantages in their use. We present HardVul, a vulnerability checking tool which can be run on any architecture and reports which vulnerabilities were found from our testbed.
A hierarchical choice modelling approach for incorporating customer preferences in vehicle package design (2009)

The use of customer preference models to evaluate the economic impact of design changes and new product introductions has become prevalent in the literature. However, existing approaches do not sufficiently address the needs of complex design artefacts, which typically consist of many subsystems and components designed and manufactured with significant autonomy. Characteristics of complex systems, such as heterogeneity of consumer preferences throughout the system hierarchy, multiple sources of information and qualitative consumer-desired attributes, have not been adequately addressed. In this work, we propose a hierarchical choice modelling approach for complex systems to model customer preferences for attributes throughout the system hierarchy, and to subsequently predict consumer choice behaviours. A system of hierarchical models is used to link the design attributes used for engineering design to the attributes used by consumers to choose among competing products. The model framework utilises Discrete Choice Analysis at the top level to model customer choices and Ordered Logit regression at the lower levels to model ordinal survey responses as a function of product attributes. An approach for combining choice data from multiple sources based on the Nested Logit methodology is developed. The framework is demonstrated on the vehicle occupant package case study.
Down‐regulation of protein and mRNA expression for transforming growth factor‐β (TGF‐β1) type I and type II receptors in human prostate cancer (1997)

Transforming growth factor-β (TGF-β1) is a potent negative regulator of cell growth that transduces signals through interactions with type I and II receptors. Abnormal expression and mutational alterations of these receptors have been observed in several human malignancies. In this study, we investigated the expression of the two types of TGF-βI receptors, R-I and R-II, in a normal human prostate, primary prostate adenocarcinoma and lymph nodes with metastatic deposits. Expression of receptor proteins was examined by immunohistochemical analysis in paraffin-embedded prostatic tissue sections, and mRNA expression was determined by Northern blot and RT-PCR analysis. Uniformly strong immunoreactivity for both TGF-β receptor proteins, R-I and R-II, was exclusively localized to the prostatic glandular epithelium of normal prostates. In contrast, tumor epithelial cells in primary and metastatic prostatic cancer specimens exhibited a weak heterogeneous immunoreactivity for both R-I and R-II receptors; 25% of primary prostatic tumors and 45% of the lymph nodes with metastases were totally negative for R-I and R-II expression, while the rest exhibited a significantly reduced immunoreactivity for both types of receptors compared to the normal prostate (p < 0.05). Moreover, there was a significant decrease in the expression of R-I and R-II mRNA, in all 20 primary prostatic tumors and 4 lymph nodes positive for metastases, indicating that the decreased protein expression was due to down-regulation of gene expression for the two receptors. Our findings imply that decreased expression of TGF-βI type I and type II receptors might be involved in prostate tumorigenesis. Int. J. Cancer 71:573-579, 1997. © 1997 Wiley-Liss, Inc.
An Insight into the Reactivity of the Electrogenerated Radical Cation of Caffeine (2020)

Controlled potential electrolyses of caffeine (CAF) were carried out at a Pt electrode in undried acetonitrile (ACN) and ACN-H2O and the products of the anodic oxidation were analyzed by HPLC-PDA-ESI-MS/MS. A higher current efficiency occurred in ACN-H2O, but an analogous chromatographic outline was found in both media, evidencing a reactive pathway of the electrogenerated radical cation CAF•+ with water, added or in trace, as nucleophile. No dimeric forms were evidenced, excluding any coupling reactions. Neither was 1,3,7-trimethyluric acid found, reported in the literature as the main oxidative route for CAF in water. Four main chromatographic peaks were evidenced, assigned to four proposed structures on the base of chromatographic and spectral data: a 4,5-diol derivative and an oxazolidin-2-one derivative were assigned as principal oxidation products, supporting a mechanism proposed in a previous work for the primary anodic oxidation of the methylxanthines olefinic C4 = C5 bond. Two highly polar degradation products were also tentatively assigned, that seemed generating along two different pathways, one opening the imidazolic moiety and another one opening the purinic one.
Visible Light-Induced Immobilization of Gold Nanoparticles on Silicon Substrates (2013)

Ordered and high-density AuNP structures were successfully immobilized on Si(111) substrates via a photochemical reaction, using the immersion method and the LB method, respectively. Because of partial oxidation of the substrate, island-like structures were formed using the immersion method. While that in the LB method, because AuNPs were immobilized in nitrogen atmosphere and not in liquid solution, oxidation was minimized thus a more compact structure was obtained. Furthermore, the plasmonic properties of the AuNP structure were found to be tunable by controlling the particle density and the interparticle distance.