gebhart/patrepeval huggingface dataset:
DSSAT cropping system model (2003)

The decision support system for agrotechnology transfer (DSSAT) has been in use for the last 15 years by researchers worldwide. This package incorporates models of 16 different crops with software that facilitates the evaluation and application of the crop models for different purposes. Over the last few years, it has become increasingly difficult to maintain the DSSAT crop models, partly due to fact that there were different sets of computer code for different crops with little attention to software design at the level of crop models themselves. Thus, the DSSAT crop models have been re-designed and programmed to facilitate more efficient incorporation of new scientific advances, applications, documentation and maintenance. The basis for the new DSSAT cropping system model (CSM) design is a modular structure in which components separate along scientific discipline lines and are structured to allow easy replacement or addition of modules. It has one Soil module, a Crop Template module which can simulate different crops by defining species input files, an interface to add individual crop models if they have the same design and interface, a Weather module, and a module for dealing with competition for light and water among the soil, plants, and atmosphere. It is also designed for incorporation into various application packages, ranging from those that help researchers adapt and test the CSM to those that operate the DSSAT-CSM to simulate production over time and space for different purposes. In this paper, we describe this new DSSAT-CSM design as well as approaches used to model the primary scientific components (soil, crop, weather, and management). In addition, the paper describes data requirements and methods used for model evaluation. We provide an overview of the hundreds of published studies in which the DSSAT crop models have been used for various applications. The benefits of the new, re-designed DSSAT-CSM will provide considerable opportunities to its developers and others in the scientific community for greater cooperation in interdisciplinary research and in the application of knowledge to solve problems at field, farm, and higher levels.
Path design of redundant flexible robot manipulators to reduce residual vibration in the presence of obstacles (2003)

A method is presented for generating the path that significantly reduces residual vibration of the redundant, flexible robot manipulator in the presence of obstacles. The desired path is optimally designed so that the system completes the required move with minimum residual vibration, avoiding obstacles. The dynamic model and optimal path are effectively formulated and computed by using a special moving coordinate, called VLCS, to represent the link flexibility. The path to be designed is developed by a combined Fourier series and polynomial function to satisfy both the convergence and boundary condition matching problems. The concept of correlation coefficients is used to select the minimum number of design variables. A planar three-link manipulator is used to evaluate this method. Results show that residual vibration can be drastically reduced by selecting an appropriate path, in the presence of obstacles.
Evaluation of the in vivo efficacy of topical tobramycin against Pseudomonas sinonasal biofilms (2007)

Bacterial biofilms attached to the sinonasal mucosa are resistant to topical saline and tobramycin irrigation. SEM was useful in the identification of biofilms, but did not provide a quantitative evaluation for efficacy of treatment.
Writing Tools (1982)

For many people, writing is painful and editing one's own prose is difficult, tedious, and error-prone. It is often hard to see which parts of a document are difficult to read or how to transform a wordy sentence into a more concise one. It is even harder to discover that one overuses a particular linguistic construct. The system of programs described here helps writers to evaluate documents and to produce better written and more readable prose. The system consists of programs to measure surface features of text that are important to good writing style, as well as programs to do some of the tedious jobs of a copy editor. Some of the surface features measured are readability, sentence and word length, sentence type, word usage, and sentence openers. The copy editing programs find spelling errors, wordy phrases, bad diction, some punctuation errors, double words, and split infinitives.
Eventual consistency (2011)

Over the last few years, Cloud storage systems and so-called NoSQL datastores have found widespread adoption. In contrast to traditional databases, these storage systems typically sacrifice consistency in favor of latency and availability as mandated by the CAP theorem, so that they only guarantee eventual consistency. Existing approaches to benchmark these storage systems typically omit the consistency dimension or did not investigate eventuality of consistency guarantees. In this work we present a novel approach to benchmark staleness in distributed datastores and use the approach to evaluate Amazon's Simple Storage Service (S3). We report on our unexpected findings.
Thrombophilic Risk Factors in Patients with Central Retinal Vein Occlusion (2001)

Few and contrasting data are available on the prevalence of hemostatic risk factors in patients with central retinal vein occlusion (CRVO). Aim of this study was to investigate the metabolic and inherited risk factors for venous thrombosis in 100 CRVO patients (age: 59 yrs; range 18-77) and in 100 controls (age: 56 yrs; range 18-84). In patients homocysteine (Hcy) levels were significantly higher than in controls and were affected by the C677T methylenetetrahydrofolate reductase (MTHFR) polymorphism (p < 0.001). The prevalences of activated protein C resistance (APCR), factor V Leiden positivity, elevated PAI-1 and Lp(a) levels were significantly higher in patients with respect to controls. At multivariate analysis, only hyperhomocysteinemia (OR 11, 95% CI 3.6-36.2; p < 0.0001) and elevated PAI-1 levels (OR 8.9, 95% CI 3.5-41.3; p < 0.01), in addition to hypertension (OR 40.5, 95% CI 8.6-188.8; p < 0.00001) and hypercholesterolemia (OR 3.1, 95% CI 1.6-20.5; p < 0.05), were independent risk factors for CRVO. These data demonstrate a potential role of hemostatic risk factors in the pathophysiology of CRVO.
IrreC/rst-mediated cell sorting during<i>Drosophila</i>pupal eye development depends on proper localisation of DE-cadherin (2005)

Remodelling of tissues depends on the coordinated regulation of multiple cellular processes, such as cell-cell communication, differential cell adhesion and programmed cell death. During pupal development, interommatidial cells (IOCs) of the Drosophila eye initially form two or three cell rows between individual ommatidia, but then rearrange into a single row of cells. The surplus cells are eliminated by programmed cell death, and the definitive hexagonal array of cells is formed, which is the basis for the regular pattern of ommatidia visible in the adult eye. Here, we show that this cell-sorting process depends on the presence of a continuous belt of the homophilic cell adhesion protein DE-cadherin at the apical end of the IOCs. Elimination of this adhesion belt by mutations in shotgun, which encodes DE-cadherin, or its disruption by overexpression of DE-cadherin, the intracellular domain of Crumbs, or by a dominant version of the monomeric GTPase Rho1 prevents localisation of the transmembrane protein IrreC-rst to the border between primary pigment cells and IOCs. As a consequence, the IOCs are not properly sorted and supernumerary cells survive. During the sorting process, Notch-mediated signalling in IOCs acts downstream of DE-cadherin to restrict IrreC-rst to this border. The data are discussed in relation to the roles of selective cell adhesion and cell signalling during tissue reorganisation.
Directed evolution of Candida antarctica lipase A using an episomaly replicating yeast plasmid† (2009)

We herein report the first directed evolution of Candida antarctica lipase A (CalA), employing a combinatorial active-site saturation test (CAST). Wild-type CalA has a modest E-value of 5.1 in kinetic resolution of 4-nitrophenyl 2-methylheptanoate. Enzyme variants were expressed in Pichia pastoris by using the episomal vector pBGP1 which allowed efficient secretory expression of the lipase. Iterative rounds of CASTing yielded variants with good selectivity toward both the (S)- and the (R)-enantiomer. The best obtained enzyme variants had E-values of 52 (S) and 27 (R).
On the Effect of Urea on Human Epidermis (1974)

The effect of urea on the horny layer of human epidermis has been studied with special regard to its osmotic and keratolytic effects. It has been shown that the water-binding capacity mainly must be of osmotic nature; the same effects could be achieved with about half the concentration (w/w) of sodium chloride. Pieces of upper epidermis kept in saturated urea solutions changed mechanically already after 1 week, and later it could be seen that the original quaternary structure of keratin is lost. No such changes could be seen in saturated sodium chloride solution. The results indicated that urea-containing creams, although certainly valuable in hyperkeratotic conditions, should be used with care as long-term cosmetical products.
Faulty use of metered dose inhalers by physicians. (1994)

A questionnaire regarding use of metered dose inhalers (MDI) was administered to 38 physicians, 9 faculty members and 29 residents. Fifty-five percent of faculty members answered at least three or more of the seven steps of inhalation technique correctly as compared with 86% of residents, this was statistically significant (p value < 0.01). All the participants used to prescribe MDI to their patients. 80% of them responded that they followed package insert instructions to educate their patients. It was concluded that doctors involved with MDI use, should learn and become familiar with proper recommendation for its optimal aerosol delivery.
High-temperature superconductor Josephson junctions for voltage standards (2016)

This paper presents the results of investigations of the high-frequency properties of multi-junction Josephson circuits based on high-temperature superconductors and the specific features of their use in voltage standards.
Peroxiredoxin 2: a potential biomarker for early diagnosis of Hepatitis B Virus related liver fibrosis identified by proteomic analysis of the plasma (2010)

This study showed that 2-D DIGE-based proteomic analysis of the plasma was helpful in screening for new plasma biomarkers for liver disease. The significant up-expression of Prx II could be used in the early diagnosis of HBV related liver fibrosis.
In Search of Effective Honeypot and Honeynet Systems for Real-Time Intrusion Detection and Prevention (2016)

A honeypot is a deception tool for enticing attackers to make efforts to compromise the electronic information systems of an organization. A honeypot can serve as an advanced security surveillance tool for use in minimizing the risks of attacks on information technology systems and networks. Honeypots are useful for providing valuable insights into potential system security loopholes. The current research investigated the effectiveness of the use of centralized system management technologies called Puppet and Virtual Machines in the implementation automated honeypots for intrusion detection, correction and prevention. A centralized logging system was used to collect information of the source address, country and timestamp of intrusions by attackers. The unique contributions of this research include: a demonstration how open source technologies is used to dynamically add or modify hacking incidences in a high-interaction honeynet system; a presentation of strategies for making honeypots more attractive for hackers to spend more time to provide hacking evidences; and an exhibition of algorithms for system and network intrusion prevention.
The effects of sodium butyrate on lymphokine production. (1985)

The effect of sodium butyrate on lymphokine production in WEHI-3, LBRM-33, and JURKAT cells, as well as an IL-2-dependent T cell line (I) was studied. Constitutive production of IL-3 by WEHI-3 cells was enhanced by sodium butyrate and was accompanied by the growth arrest of WEHI-3 cells in the G1 phase of the cell cycle. Treatment of I cells with ConA and sodium butyrate led to an increase in IL-3 production and the initiation of IL-2 production. In contrast, the synthesis of IL-2 and IL-3 by the ConA-activated T lymphoma line LBRM-33 was coordinately inhibited by sodium butyrate. Similarly, the synthesis of IL-2 by the human T cell lymphoma JURKAT was inhibited by sodium butyrate. No cell cycle-specific effects of sodium butyrate were observed in LBRM-33 or JURKAT cells.
Leaching and Recovery of Rare-Earth Elements from Neodymium Magnet Waste Using Organic Acids (2018)

Over the last decade, rare-earth elements (REEs) have become critical in the European Union (EU) in terms of supply risk, and they remain critical to this day. End-of-life electronic scrap (e-scrap) recycling can provide a partial solution to the supply of REEs in the EU. One such product is end-of-life neodymium (NdFeB) magnets, which can be a feasible source of Nd, Dy, and Pr. REEs are normally leached out of NdFeB magnet waste using strong mineral acids, which can have an adverse impact on the environment in case of accidental release. Organic acids can be a solution to this problem due to easier handling, degradability, and less poisonous gas evolution during leaching. However, the literature on leaching NdFeB magnets waste with organic acids is very scarce and poorly investigated. This paper investigates the recovery of Nd, Pr, and Dy from NdFeB magnets waste powder using leaching and solvent extraction. The goal was to determine potential selectivity between the recovery of REEs and other impurities in the material. Citric acid and acetic acid were used as leaching agents, while di-(2-ethylhexyl) phosphoric acid (D2EHPA) was used for preliminary solvent extraction tests. The highest leaching efficiencies were achieved with 1 mol/L citric acid (where almost 100% of the REEs were leached after 24 h) and 1 mol/L acetic acid (where >95% of the REEs were leached). Fe and Co—two major impurities—were co-leached into the solution, and no leaching selectivity was achieved between the impurities and the REEs. The solvent extraction experiments with D2EHPA in Solvent 70 on 1 mol/L leachates of both acetic acid and citric acid showed much higher affinity for Nd than Fe, with better extraction properties observed in acetic acid leachate. The results showed that acetic acid and citric acid are feasible for the recovery of REEs out of NdFeB waste under certain conditions.
<i>Rhizobium japonicum</i> Serogroup and Hydrogenase Phenotype Distribution in 12 States (1984)

A survey was conducted in 1980 on 972 isolates of Rhizobium japonicum obtained from 65 soybean field locations in 12 states. Isolates were examined for the hydrogenase (Hup) phenotype and somatic serogroup identity. Only 20% of the isolates were Hup, with a majority of Hup isolates occurring in 10 of the 12 states. The most predominant serogroup was 31 (21.5%), followed by 123 (13.6%). Although most serogroups contained a majority of Hup isolates, marked differences occurred. None of the isolates in serogroup 135 were Hup, but 93% of the isolates in serogroup 122 were Hup. The serogroups with relatively high frequencies of Hup isolates (122 and 110) constitute only a small part (<5% each) of the R. japonicum field population in the 12 states.
A low complexity LDPC-BCH concatenated decoder for NAND flash memory (2018)

Low-density parity-check (LDPC) codes are widely used in NAND flash memory as an advanced error correction method due to their excellent correcting capability. The major challenge is the error floor problem. Dispersed array LDPC (DA-LDPC) code is highly structured and provides implementation convenience due to its regularity. In this paper, it is shown that the constructed (18289, 16384) DA-LDPC code suffers the error floor at BER of 10−9, which is far from the demand of flash memory error control. Carefully observing the error patterns in the error floor region, we propose a concatenation of BCH code to alleviate this issue. The error floor has been successfully brought down to BER of 10−14 by concatenating a BCH code with correcting capability of 14 bits. Compared to the standalone LDPC decoder, the concatenated decoder only consumes 7% extra hardware and the code rate penalty is less than 1%. Meanwhile, hardware implementation has shown that the throughput can achieve 3.52 Gbps with 6 iterations under a clock frequency of 200 MHz.
Chlorine-Substituted Bent-Core LC-Based Sono-Gel Hybrid Materials: Synthesis and Optical Properties (2008)

We implemented the catalyst-free sonogel method to disperse and encapsulate a chlorine substituted thermotropic bent shaped liquid crystalline compound. By this means, advanced organic-inorganic hybrid materials with high optical and mechanical quality, suitable for different kind of optical applications, were obtained. Bent-core molecules have shown interesting optical properties, which have not yet been investigated in the solid-state. Therefore, we implemented the sonogel route to fabricate highly pure SiO2 porous glassy networks which allowed the inclusion of this kind of mesogens in the colloidal sol-state. In this work, we present the preparation and optical performance of these amorphous “banana”-based hybrids via absorption and fluorescence spectroscopies, electro-optical and cubic third-harmonic generation nonlinear optical measurements.
The target landscape of N4-hydroxycytidine based on its chemical neighborhood (2020)

Abstract N4-hydroxycytidine (NHC) has been recently reported to have promising antiviral activity against SARS-CoV-2. To join worldwide efforts in identifying potential drug targets against this pandemic, the target landscape of NHC was defined by extracting all known targets of its chemical neighborhood, including drugs, analogues, and metabolites, and by performing target predictions from two independent platforms, following the recent Public Health Assessment via Structural Evaluation (PHASE) protocol. The analysis provides a list of over 30 protein targets that could be useful in future design activities of new COVID-19 antivirals. The relevance for existing drugs within the same chemical space, such as remdesivir, is also discussed.
Controlling Intracellular Macrocyclization for the Imaging of Protease Activity (2011)

Reporter an der Basis: Durch ein spezifisches Enzym und die Reduktion durch Glutathion (GSH) wird eine hoch effiziente intramolekulare Makrocyclisierung in lebenden Zellen gesteuert (siehe Bild). Die in den Zellen erzeugten Makrocyclen (als blaue Ringe dargestellt) ordnen sich zu Nanopartikeln an, die in der Nähe des Enzyms bleiben und so Informationen über die lokale Proteolyseaktivität in lebenden Zellen liefern. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Predicting the Presence of Oral Squamous Cell Carcinoma Using Commonly Dysregulated MicroRNA in Oral Swirls (2018)

Oral swirls are a noninvasive, rapidly collected source of salivary microRNA (miRNA) potentially useful in the early detection of disease states, particularly oral squamous cell carcinoma (OSCC). The aim of this study was to predict the presence of OSCC using a panel of OSCC-related dysregulated miRNA found in oral swirls, identified jointly in data from formalin-fixed paraffin-embedded (FFPE) and fresh-frozen specimens. Next-generation sequencing (NGS) was used to determine miRNA fold changes in FFPE OSCC specimens relative to histologically normal epithelium. These data were placed with NGS of fresh-frozen tissue data of The Cancer Genome Atlas database to select a panel of commonly dysregulated miRNA. This panel was then analyzed by RT-qPCR in RNA extracted from oral swirls collected from 30 patients with OSCC and 30 controls. Upregulation of miR-31 and miR-21 and downregulation of miR-99a, let-7c, miR-125b, and miR-100 were found between OSCC and controls in both FFPE and fresh-frozen samples. These miRNAs were studied in a training set of 15 OSCC versus 15 control oral swirls to develop a dysregulation score [AUC, 0.95; 95% confidence interval (CI), 0.88-1.03] and classification tree. A test cohort of 15 OSCC versus 15 control oral swirls yielded a dysregulation score AUC of 0.86 (95% CI, 0.79-1.00) with the classification tree identifying 100% (15/15) of OSCC and 67% (10/15) of controls. This study debuts the use of OSCC-associated miRNA, commonly dysregulated in both FFPE and frozen specimens, in oral swirls to indicate the presence of OSCC with high accuracy. <i>Cancer Prev Res; 11(8); 491-502. ©2018 AACR</i>.
Electrical Monitoring of sp<sup>3</sup> Defect Formation in Individual Carbon Nanotubes (2016)

Many carbon nanotube (CNT) applications require precisely controlled chemical functionalization that is minimally disruptive to electrical performance. A promising approach is the generation of sp3 hybridized carbon atoms in the sp2-bonded lattice. We have investigated the possibility of using a carboxylic acid-functionalized diazonium reagent to introduce a defined number of sp3 defects into electrically contacted CNTs. Having performed real-time measurements on individually contacted CNTs, we show that the formation of an individual defect is accompanied by an upward jump in resistance of approximately 6 kΩ. Additionally, we observe downward jumps in resistance of the same size, indicating that some defects are unstable. Our results are explained by a two-step reaction mechanism. Isolated aryl groups, formed in the first step, are unstable and dissociate on the minute time scale. Stable defect generation requires a second step: the coupling of a second aryl group adjacent to the first. Additional mechanistic understanding is provided by a systematic investigation of the gate voltage dependence of the reaction, showing that defect formation can be turned on and off. In summary, we demonstrate an unprecedented level of control over sp3 defect formation in electrically contacted CNTs, and prove that sp3 defects are minimally disruptive to the electrical performance of CNTs.