gebhart/patrepeval huggingface dataset:
Writing Self‐Erasing Images using Metastable Nanoparticle “Inks” (2009)

Mission Impossible: Metal nanoparticles (NPs) coated with photoresponsive ligands are used as “inks” for self-erasing “paper” whereby light-induced self-assembly of the NPs is transduced into local color changes (see picture). Depending on the degree of self-assembly, multicolor images can be written using only one type of NP ink. Duration of image erasure is regulated by the surface concentration of photoactive groups and can range from seconds to days. 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.
A Plasmid Partition System of the P1-P7 <i>par</i> Family from the pMT1 Virulence Plasmid of <i>Yersinia pestis</i> (2000)

The complete sequence of the virulence plasmid pMT1 of Yersinia pestis KIM5 revealed a region homologous to the plasmid partition (par) region of the P7 plasmid prophage of Escherichia coli. The essential genes parA and parB and the downstream partition site gene, parS, are highly conserved in sequence and organization. The pMT1parS site and the parA-parB operon were separately inserted into vectors that could be maintained in E. coli. A mini-P1 vector containing pMT1parS was stably maintained when the pMT1 ParA and ParB proteins were supplied in trans, showing that the pMT1par system is fully functional for plasmid partition in E. coli. The pMT1par system exerted a plasmid silencing activity similar to, but weaker than those of P7par and P1par. In spite of the high degree of similarity, especially to P7par, it showed unique specificities with respect to the interactions of key components. Neither the P7 nor P1 Par proteins could support partition via the pMT1parS site, and the pMT1 Par proteins failed to support partition with P1parS or P7parS. Typical of other partition sites, supernumerary copies of pMT1parS exerted incompatibility toward plasmids supported by pMT1par. However, no interspecies incompatibility effect was observed between pMT1par, P7par, and P1par.
Exploiting the Link between Protein Rigidity and Thermostability for Data‐Driven Protein Engineering (2008)

Abstract Understanding and exploiting the relationship between microscopic structure and macroscopic stability is important for developing strategies to improve protein stability at high temperatures. The thermostability of proteins has been repeatedly linked to an enhanced structural rigidity of the folded native state. In the current study, the rigidity of protein structures from mesophilic and thermophilic organisms along a thermal unfolding trajectory is directly probed. In order to perform this, protein structures were modeled as constraint networks, and the rigidity in these networks was quantified using the Floppy Inclusion and Rigid Substructure Topography (FIRST) method. During the thermal unfolding, a phase transition was observed that defines the rigidity percolation threshold and corresponds to the folded‐unfolded transition in protein folding. Using concepts from percolation theory and network science, a higher phase transition temperature was observed for ca. two‐thirds of the proteins from thermophilic organisms compared to their mesophilic counterparts, when applied to a data set of 20 pairs of homologues. From both the analysis of the microstructure of the constraint networks and monitoring the macroscopic behavior during the thermal unfolding, direct evidence was found for the “corresponding states” concept, which states that mesophilic and thermophilic enzymes are in corresponding states of similar flexibility at their respective optimal temperature. Finally, the current approach facilitated the identification of structural features from which a destabilization of the structure originates upon thermal unfolding. These predictions show a good agreement with the experimental data. Therefore, the information might be exploited in data‐driven protein engineering by pointing to residues that should be varied to obtain a protein with higher thermostability.
Survey for major foliar diseases of Bt cotton in Northern Eastern Karnataka (2019)

Survey conducted in four districts of Northern Karnataka during kharif 2017-18, revealed that the disease severity of major foliar diseases viz., Alternaria leaf spot, Cercospora leaf spot and bacterial leaf blight ranged from 12 to 51, 8.50 to 30 and 3 to 13 per cent, respectively. The highest severity (51.00%) of Alternaria leaf spot was noticed at Chandrabanda village in Raichur district, maximum severity (30.00%) of Cercospora leaf spot was recorded at Indira Nagar in Raichur district. Whereas, highest severity (13.00%) of bacterial blight was noticed at Halagadda village of Kalaburgi district. The average highest Alternaria leaf spot and Cercospora leaf spot disease severity of 39.57 and 20.37 per cent, respectively was recorded in Raichur district. The average highest bacterial leaf blight severity of 9.28 per cent was recorded in Kalaburgi district.
Use of a Marked Erythropoietin Gene for Investigation of Its Cis-acting Elements (1995)

To examine the function of conserved noncoding regions in the erythropoietin (Epo) gene, we have prepared clones and pools of Hep3B cells stably transfected with a marked 4.1-kilobase Epo gene and deletions thereof. The marked transcripts had single base substitutions at three sites in the coding portion of Exon 5, enabling them to be distinguished from endogenous Epo mRNA by ribonuclease protection and competitive polymerase chain reaction. The basal expression and hypoxic induction of the marked Epo gene that had no deletions were indistinguishable from that of the endogenous Epo gene. Likewise, deletion of conserved intervening sequence 1 had minimal effect on hypoxic induction. In contrast, a 3'-deletion that included the conserved 3'-enhancer element resulted in a substantial, but not complete, suppression of hypoxic induction while a 3'-deletion downstream of the enhancer resulted in enhancement. A 188-base pair deletion of a conserved 3'-untranslated region in Exon 5 had minimal effect on hypoxic induction. However, the truncated Epo mRNA had a markedly prolonged half-life (15 h) in comparison to the endogenous Epo mRNA (2.0 h) or the marked full-length Epo mRNA (2.1 h). Further deletions in the 3'-UTR showed that a relatively small region of approximately 50 bases is responsible for the relatively rapid turnover of Epo mRNA. These experiments provide information on cis-acting elements of the Epo gene that cannot be obtained from conventional reporter gene transfection experiments.
Overweight Children and Adolescents (2005)

A seven-year-old girl is 130 cm tall (the 90th percentile for girls of the same age) and weighs 34.6 kg (above the 95th percentile), with a body-mass index of 20.5 (above the 95th percentile). Physical examination reveals no abnormalities aside from her excess weight. She eats fast food and drinks soft drinks regularly, has limited exercise, and watches television or uses the computer for hours each day. What should you advise?
Neural networks-then and now (1991)

The emergence of neural networks as a significant subdiscipline with corresponding attempts at application to engineering problems is traced back to the 1960s, when Frank Rosenblatt, a Cornell University psychologist, showed by mathematical analysis, digital computer simulation, and experiments with special-purpose parallel analog systems that neural networks with variable-weight connections could be trained to classify spatial patterns into prespecified categories. In his attempts to provide biologically plausible explanations of the function of the central nervous system, he investigated relatively simple networks that were amenable to analysis and more complex networks whose behavior could be predicted only in terms of gross characteristics. He assembled a sizable group involving theoreticians, experimentalists, technologists, and, later, biologists. His work caught the imagination of the press and led to the wave of febrile activity that subsided at the end of that decade.
Mechanisms of antibacterial action of tachyplesins and polyphemusins, a group of antimicrobial peptides isolated from horseshoe crab hemocytes (1992)

Tachyplesins I and II and polyphemusins I and II, cationic peptides isolated from the hemocytes of horseshoe crabs, show bactericidal activities with similar efficiencies for both gram-negative and gram-positive bacteria. Tachyplesin I inhibited bacterial growth irreversibly within 40 min. A subinhibitory concentration of tachyplesin I sensitized gram-negative bacteria to the bactericidal actions of novobiocin and nalidixic acid, although polymyxin B-resistant strains which have altered lipopolysaccharides were susceptible to tachyplesin I. This implies that tachyplesin permeabilizes the outer membrane and that the likely target of its action is outer membrane constituents other than lipopolysaccharides. On the other hand, a defensin-susceptible phoP strain of Salmonella typhimurium was also susceptible to tachyplesin I. Tachyplesin I rapidly depolarized the inverted inner-membrane vesicles of Escherichia coli. These results suggest that depolarization of the cytoplasmic membrane, preceded by the permeabilization of the outer membrane for gram-negative bacteria, is associated with tachyplesin-mediated bactericidal activity. The similarity between the actions of tachyplesin and those of defensin was discussed.
Expression of a truncated FGF receptor results in defective lens development in transgenic mice (1995)

Members of the fibroblast growth factor (FGF) family are thought to initiate biological responses through the activation of cell surface receptors which must dimerize to transmit an intracellular signal. Mammalian lens epithelial cells respond to exogenous extracellular FGF, either in tissue culture or in transgenic mice, by initiating fiber cell differentiation. The role of FGF signalling in normal lens development was evaluated by lens-specific synthesis of a kinase-deficient FGF receptor type I (FGFR1) in transgenic mice. This truncated FGF receptor is thought to act as a dominant negative protein by heterodimerization with endogenous FGF receptors. The presence of transgenic mRNA in the lens was confirmed by in situ hybridization and by polymerase chain reaction amplification of reverse transcribed lens RNA (RT-PCR). The presence of transgenic protein was determined by Western blotting with antibodies to an extracellular domain of FGFR1. Three of four transgenic families expressing the truncated FGF receptor exhibited lens defects ranging from cataracts to severe microphthalmia. While the microphthalmic lenses displayed a normal pattern of differentiation-specific crystallin expression, the lens epithelial cells were reduced in number and the lens fiber cells displayed characteristics consistent with the induction of apoptosis. Our results support the view that FGF receptor signalling plays an essential role in normal lens biology.
Solvent- and Vapor-Induced Isomerization between the Luminescent Solids [CuI(4-pic)]<sub>4</sub> and [CuI(4-pic)]<sub>∞</sub> (pic = methylpyridine). The Structural Basis for the Observed Luminescence Vapochromism (2000)

Exposure of the polymeric solid [CuI(4-pic)]∞ (pic = picoline = methyl pyridine) to liquid or vapor toluene leads to disappearance of its room-temperature blue emission (λmax 437 nm) and the appearance of a yellow emission (λmax 580 nm) characteristic of the [CuI(4-pic)]4 tetramer. The process is reversed when the latter is exposed to liquid or vapor n-pentane. Analogous transformations between the tetrameric and polymeric forms do not occur when the 3-picoline analogues [CuI(3-pic)]x are similarly treated. Single-crystal X-ray diffraction studies on the compounds [CuIL]∞ and [CuIL]4 (L = 3-, 4-pic) indicate that the 4-pic tetranuclear isomer incorporates toluene into its solid phase to give a material with the composition [CuI(4-pic)]4·2C6H5CH3, but the other three phases are solvent-free. The chains in the two polymeric phases exhibit double-zigzag configurations, also commonly observed in zeolitic tetrahedral structures. In both polymeric phases, the chains propagate along the monoclinic b axis. The 3-pic tetrameric phase can be described as a close-packed structure of [CuIL]4 units, whereas tetramers in the 4-pic phase form infinite columns along the unique tetragonal c axis segregated by four columns of toluene pairs. These structural differences explain the different behaviors during the phase transformation between tetrameric and polymeric polymorphs of the 3-pic and 4-pic compounds.
Study of Soft Switching Boost Converter using an Auxiliary Resonant Circuit (2012)

This thesis presents Soft Switching DC-DC boost Converter using an Auxiliary Resonant Circuit. The circuit consists of a general Boost Converter with an additional Auxiliary circuit which has a switch, inductor, capacitor and diode. By using an Auxiliary resonant circuit switching losses of a Boost Converter is reduced. Generally Boost Converter circuits have snubber circuit where switching losses are dissipated in external passive resistors; this is known as hard switching. In the proposed topology the generation of switching losses are avoided by forcing voltage (ZVS) or current (ZCS) to zero during switching. The efficiency is improved due to reduction in switching losses. MATLAB simulations are performed to verify the theoretical analysis.
Pulse synthesis in the single-cycle regime from independent mode-locked lasers using attosecond-precision feedback (2012)

We report the synthesis of a nearly single-cycle (3.7 fs), ultrafast optical pulse train at 78 MHz from the coherent combination of a passively mode-locked Ti:sapphire laser (6 fs pulses) and a fiber supercontinuum (1-1.4 μm, with 8 fs pulses). The coherent combination is achieved via orthogonal, attosecond-precision synchronization of both pulse envelope timing and carrier envelope phase using balanced optical cross-correlation and balanced homodyne detection, respectively. The resulting pulse envelope, which is only 1.1 optical cycles in duration, is retrieved with two-dimensional spectral shearing interferometry (2DSI). To our knowledge, this work represents the first stable synthesis of few-cycle pulses from independent laser sources.
[Growth behavior of amnion cell cultures]. (1984)

Both amniotic fluid samples and amniotic fluid cell cultures of a total of 52 patients were evaluated. At 15 to 16 weeks' gestation there are 2.2 X 10(4) cells/ml amniotic fluid increasing significantly to 3.7 X 10(4) cells/ml at 19 to 20 weeks' gestation. The percentage of viable cells is about 18. After 10 d of culture 14.4 +/- 8.2 cell colonies/culture flask are developed consisting of 61% AF-cells, 33% E-cells and 6% F-cells. After 14 d of culture 60 +/- 32 metaphases/cell culture flask were found. At the 10th day of culture 80% of cell colonies are already present indicating that reduced duration of culture appears possible. Therefore the interval to diagnosis can be shortened and a possible interruption of pregnancy can be earlier done under reduced risks.
A novel automatic tongue image segmentation algorithm: Color enhancement method based on L*a*b* color space (2015)

As the first step of tongue image analysis, tongue segmentation plays a significant role in this field. In this paper, we present a new method to segment the tongue using multiple color spaces. Based on the hue channel in HSV space, a threshold control function can be given, revealing the chromatic feature of image. Then we can extract our interested area according to the function, so that the color enhancement method can be applied in this region. In the end, we can obtain the complete outlines using the luminance features in L*a*b* color space. Compared to existing tongue segmentation algorithms, our method demonstrates satisfying performance in robustness, efficiency and accuracy.
Facts as Experts: Adaptable and Interpretable Neural Memory over Symbolic Knowledge (2020)

Massive language models are the core of modern NLP modeling and have been shown to encode impressive amounts of commonsense and factual information. However, that knowledge exists only within the latent parameters of the model, inaccessible to inspection and interpretation, and even worse, factual information memorized from the training corpora is likely to become stale as the world changes. Knowledge stored as parameters will also inevitably exhibit all of the biases inherent in the source materials. To address these problems, we develop a neural language model that includes an explicit interface between symbolically interpretable factual information and subsymbolic neural knowledge. We show that this model dramatically improves performance on two knowledge-intensive question-answering tasks. More interestingly, the model can be updated without re-training by manipulating its symbolic representations. In particular this model allows us to add new facts and overwrite existing ones in ways that are not possible for earlier models.
PRESTvO: PRivacy Enabled Smartphone Based Access to Vehicle On-Board Units (2020)

Smartphones are quickly moving toward complementing or even replacing traditional car keys. We advocate a role-based access control policy mixed with attributes that facilitates access to various functionalities of vehicular on-board units from smartphones. We use a rights-based access control policy for in-vehicle functionalities similar to the case of a file allocation table of a contemporary OS, in which read, write or execute operations can be performed over various vehicle functions. Further, to assure the appropriate security, we develop a protocol suite using identity-based cryptography and we rely on group signatures which preserve the anonymity of group members thus assuring privacy and traceability. To prove the feasibility of our approach, we develop a proof-of-concept implementation with modern smartphones, aftermarket Android head-units and test computational feasibility on a real-world in-vehicle controller. Our implementation relies on state-of-the-art cryptography, including traditional building blocks and more modern pairing-friendly curves, which facilitate the adoption of group signatures and identity-based cryptography in automotive-based scenarios.
Induction of Th-1 and Th-2 Responses by Respiratory Syncytial Virus Attachment Glycoprotein Is Epitope and Major Histocompatibility Complex Independent (1999)

In BALB/c mice, sensitization to respiratory syncytial virus (RSV) attachment (G) glycoprotein leads to the development of lung eosinophilia upon challenge infection with RSV, a pathology indicative of a strong in vivo induction of a Th-2-type response. In this study, we found that a strong, RSV G-specific, Th-1-type cytokine response occurred simultaneously with a Th-2-type response in G-primed mice after RSV challenge. Both Th-1 and Th-2 effector CD4(+) T cells recognized a single immunodominant site on this protein, implying that the differentiation of memory CD4(+) T cells along the Th-1 or Th-2 effector pathway was independent of the epitope specificity of the T cells. A similar observation was made in G-primed H-2(b) haplotype mice after RSV challenge, further suggesting that this process is not dependent on the peptide epitope presented. On the other hand, genes mapping to loci outside of the major histocompatibility complex region are crucial regulators of the development of a Th-2-type response and lung eosinophilia. The implication of these findings for the immune mechanisms underlying the pathogenesis of RSV is discussed.
Optimization of Recovery Using Intelligent Completions in Intelligent Fields (2017)

Abstract Throughout the previous few years, substantial attention has been paid to the usage of smart well technologies to help improve recovery, particularly with technological improvements and an increasing expanse of opportunities in more challenging and rewarding assets. The fundamental focus has been to propose and develop workflows that integrate several surface/subsurface subprocesses and automate the entire workflow. In cases where significant investment is made to complete smart wells with remotely controlled inflow control valves (ICV), reservoir sweep becomes decisive when evaluating the efficient recovery. Application of this technology has been challenging because it is a modern concept. This study showcases the effective application of ICVs within intelligently completed fields to satisfy the objective function by augmenting reservoir sweep and oil recovery. In this study, a commercial full-physics numerical reservoir simulator has been used to evaluate a synthetic simulation model mimicking a realistic reservoir with waterflood. The wells are installed with smart well completions using ICVs that are controlled by conditional statements called procedures. The decision parameters varied to determine if the level of ICV opening within producer wells is water-cut and well-injection rates. Then, the cumulative oil recovery is used as an objective function to increase the maximum oil recovery. The ultimate goal is to reach the highest net present value (NPV) through having higher cumulative oil production values with the lower water injection and water production rates. The relatively high expenditure linked with installing intelligent completions within wells drive further the importance to apply and study the advantages of this technology on multiple, diverse cases coupled with specifically planned workflows. Recent studies have shown that a robust reservoir management plan along with an effective application of ICVs within intelligently completed fields can augment reservoir sweep and oil recovery. The results of the study demonstrated the positive impact when using ICVs on NPVs calculated compared to the base case where traditional completions have been used. It is also shown that, without a robust reservoir management plan, the use of intelligent completions might not always be successful. Augmenting the performance of the reservoirs, in addition to looking at the individual well performance, forms the crux of a sound reservoir management plan. This study, therefore, examines the big picture by following a field-wide approach rather than focusing solely on individual or near-well performance. The core of this study is to provide a framework of effective integration of data from leading performance indicators attributing to intelligent well completions, with the ultimate goal of optimizing the reservoir recovery.