gebhart/patrepeval huggingface dataset:
FeNbBP type nanocrystalline alloy with high B s of 1.64 T optimized by sputtered thin film method (2019)

The increasing of saturation magnetic flux density (Bs) in FeNbB type nanocrystalline alloy has been widely studied. The influence of additional element to improve Amorphous Forming Ability (AFA) in precursor was investigated using substrate temperature controlled sputtering method at 523K. The AFA was improved by the addition of P, Si, V, or Mo, was decreased by the addition of Y, Cu, or Ge. Especially, the addition of 1 at% P exhibited a good effect of obtaining 85 at% of maximum Fe content with high stable amorphous precursor. The addition of P or C increased Bs. The Fe85Nb6B8P1 nanocrystalline alloy ribbon showed stable amorphous phase as quenched, exhibited a homogeneous nanocrystalline structure composed of grains with 10 to 20 nm in diameter after nanocrystallization. The ribbon exhibited high Bs of 1.64T and low coercivity of 10 A/m.
Towards an Understanding of Ligand Induced Functional Conformational Changes of MexB Efflux Transporter (2021)

&lt;p&gt;MexB, an RND-superfamily efflux pump, plays a vital role in conferring resistance to cytotoxic molecules, including antibiotics, upon Gram-negative bacteria. Although the principal mechanistic elements of switching between the access, binding and extrusion conformers of the protomers of tripartite efflux transporters have been described previously, details surrounding the further mechanism that ends in either substrate extrusion or pump inhibition are limited to observations based on the type of ligand bound to the transporter. A central but missing link in the structure/mechanism relationship is a description of how ligand-induced conformational changes in the presence of a membrane and changing transporter protonation state lead to either substrate extrusion or inhibition of the pump. Here, we report that differences in conformational changes are governed by ligand binding to the transporter. The current study describes important new information about ligand-induced structural rearrangements and conformational changes of MexB in relation to the protonation state of critical acidic residues. We used tetracycline (TET) as a model substrate of MexB and phenylalanine-arginine beta-naphthylamide (PAβN) as a model inhibitor of MexB to study the aforementioned conformational changes. This new information will contribute to the design of new, effective and selective efflux pump inhibitors that could play key roles in reversing antimicrobial resistance.&lt;/p&gt;
Nonstationary modeling of neural population dynamics (2009)

A stochastic state point-process adaptive filter was used to track the temporal evolution of several simulated nonlinear dynamical systems. The estimated Laguerre coefficients and Laguerre poles were used to reconstruct the feedforward and feedback kernels in the system. Simulations showed that the proposed method could track the actual underlying changes of nonlinear kernels using spike input and spike output information alone. The estimated models also converge quickly to the actual models after abrupt step changes in kernels. The proposed method can be used to track the functional input-output properties of neural systems as a result of learning, changes in context, aging or other factors in the natural flow of behavioral events.
Lambdoid Phages and Shiga Toxin (2014)

This chapter summarizes what is known about stx-encoding phages, it is not all-inclusive. Researchers begin with a brief discussion of Shiga toxin-producing Escherichia coli (STEC), present general information on lambdoid phages, and finally segue into a discussion of the main subject, stx-encoding phages. Shiga toxins are members of a family of bacterial toxins known as AB5 toxins, which are composed of one A subunit associated with five B subunits. In vitro studies suggest that, once it is in the lumen, Stx prevents the apoptosis of polymorphonuclear leukocytes (PMNs) and induces superoxide production by these cells, which can lead to increased endothelial damage. The excised phage genome enters the lytic cycle and is ready to be transcribed and replicated, leading to the packaging of progeny DNA into phage particles that are ultimately released by phage-directed lysis of the bacterial host. The induced fraction can be greatly increased if lysogens are treated with DNA-damaging agents that activate the expression of the SOS system. Specifically, the bacterial RecA protein activated by bound single-stranded DNA binds and facilitates autocleavage of the phage repressor, causing prophage induction. Clinically, the antibiotic treatment of STEC infections has been correlated with a significantly higher incidence of secondary sequelae such as HUS. The authors focus their discussion on the stx-encoding phages that have been best characterized biologically: H-19B and 933W.
RETRACTED: Fermented Sea Tangle (Laminaria japonica Aresch) Suppresses RANKL-Induced Osteoclastogenesis by Scavenging ROS in RAW 264.7 Cells (2019)

Sea tangle (<i>Laminaria japonica</i> Aresch), a brown alga, has been used for many years as a functional food ingredient in the Asia-Pacific region. In the present study, we investigated the effects of fermented sea tangle extract (FST) on receptor activator of nuclear factor-κB (NF-κB) ligand (RANKL)-stimulated osteoclast differentiation, using RAW 264.7 mouse macrophage cells. FST was found to inhibit the RANKL-stimulated activation of tartrate-resistance acid phosphatase (TRAP) and F-actin ring structure formation. FST also down-regulated the expression of osteoclast marker genes like TRAP, matrix metalloproteinase-9, cathepsin K and osteoclast-associated receptor by blocking RANKL-induced activation of NF-κB and expression of nuclear factor of activated T cells c1 (NFATc1), a master transcription factor. In addition, FST significantly abolished RANKL-induced generation of reactive oxygen species (ROS) by activation of nuclear factor-erythroid 2-related factor 2 (Nrf2) and its transcriptional targets. Hence, it seems likely that FST may have anti-osteoclastogenic potential as a result of its ability to inactivate the NF-κB-mediated NFATc1 signaling pathway and by reducing ROS production through activation of the Nrf2 pathway. Although further studies are needed to inquire its efficacy in vivo, FST appears to have potential use as an adjunctive or as a prophylactic treatment for osteoclastic bone disease.
Revealing 3D Morphological and Chemical Evolution Mechanisms of Metals in Molten Salt by Multimodal Microscopy (2020)

Growing interest in molten salts as effective high-temperature heat-transfer fluids for sustainable energy systems drives a critical need to fundamentally understand the interactions between metals and molten salts. This work utilizes the multimodal microscopy methods of synchrotron X-ray nanotomography and electron microscopy to investigate the 3D morphological and chemical evolution of two-model systems, pure nickel metal and Ni-20Cr binary alloy, in a representative molten salt (KCl-MgCl<sub>2</sub> 50-50 mol %, 800 °C). In both systems, unexpected shell-like structures formed because of the presence of more noble tungsten, suggesting a potential route of using Ni-W alloys for enhanced molten-salt corrosion resistance. The binary alloy Ni-20Cr developed a bicontinuous porous structure, reassembling functional porous metals manufactured by dealloying. This work elucidates better mechanistic understanding of corrosion in molten salts, which can contribute to the design of more reliable alloys for molten salt applications including next-generation nuclear and solar power plants and opens the possibility of using molten salts to fabricate functional porous materials.
CURRENT STATUS OF RADIO FREQUENCY/VACUUM DRYING (1996)

A significant amount of research has focused on Radio Frequency/Vacuum drying over the last few years in western Canada. Earlier work had shown (Avramidis and Zwick, 1992) that RF/V drying appeared to be independent of product thickness, and that moisture migration occurred out the ends of the pieces. This resulted in a large research project put together by the Council of Forest Industries of B.C. (COFI) which set out to build a prototype commercial-scale RF/V kiln. In addition, a small laboratory-scale RF/V kiln was built to explore the fundamental physics of RFN drying (Avramidis et al., 1994). The COFI project was completed in 1994 and a comprehensive report is now available on the project results (Zwick, 1995).
Low-profile self-sealing sample transfer flexure box (2017)

A flexural bearing mechanism has enabled the development of a self-sealing box for protecting air sensitive samples during transfer between glove boxes, micro-machining equipment, and microscopy equipment. The simplicity and self-actuating feature of this design makes it applicable to many devices that operate under vacuum conditions. The models used to design the flexural mechanism are presented in detail. The device has been tested in a Zeiss Merlin GEMINI II scanning electron microscope with Li<sub>3</sub>PS<sub>4</sub> samples, showing effective isolation from air and corrosion prevention.
Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding (2019)

Avian coronaviruses, including infectious bronchitis virus (IBV), are important respiratory pathogens of poultry. The heavily glycosylated IBV spike protein is responsible for binding to host tissues. Glycosylation sites in the spike protein are highly conserved across viral genotypes, suggesting an important role for this modification in the virus life cycle. Here, we analyzed the <i>N</i>-glycosylation of the receptor-binding domain (RBD) of IBV strain M41 spike protein and assessed the role of this modification in host receptor binding. Ten single Asn-to-Ala substitutions at the predicted <i>N</i>-glycosylation sites of the M41-RBD were evaluated along with two control Val-to-Ala substitutions. CD analysis revealed that the secondary structure of all variants was retained compared with the unmodified M41-RBD construct. Six of the 10 glycosylation variants lost binding to chicken trachea tissue and an ELISA-presented α2,3-linked sialic acid oligosaccharide ligand. LC/MS<sup>E</sup> glycomics analysis revealed that glycosylation sites have specific proportions of <i>N</i>-glycan subtypes. Overall, the glycosylation patterns of most variant RBDs were highly similar to those of the unmodified M41-RBD construct. <i>In silico</i> docking experiments with the recently published cryo-EM structure of the M41 IBV spike protein and our glycosylation results revealed a potential ligand receptor site that is ringed by four glycosylation sites that dramatically impact ligand binding. Combined with the results of previous array studies, the glycosylation and mutational analyses presented here suggest a unique glycosylation-dependent binding modality for the M41 spike protein.
Segment Routing for Service Chaining (2017)

This document defines data plane functionality required to implement
service segments and achieve service chaining in SR-enabled MPLS and
IP networks, as described in the Segment Routing architecture.
Nonlinear optics at very low power levels (2006)

We present small modal area Surface Plasmon waveguides, with low group velocities over unusually large bandwidths. Also, we show how Electro-magnetically Induced Transparency materials, inserted into microcavities, enable optical non-linearities at single photon power levels.
Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms (2022)

Introduction. Chromophobe renal cell carcinoma (chromophobe RCC) is the third major subcategory of renal tumors after clear cell RCC and papillary RCC, accounting for approximately 5% of all RCC subtypes. Other oncocytic neoplasms seen commonly in surgical pathology practice include the eosinophilic variant of chromophobe RCC, renal oncocytoma, and low-grade oncocytic unclassified RCC. Methods. In our recent next-generation sequencing based study, we nominated a lineage-specific novel biomarker LINC01187 (long intergenic non-protein coding RNA 1187) which was found to be enriched in chromophobe RCC. Like KIT (cluster of differentiation 117; CD117), a clinically utilized chromophobe RCC related biomarker, LINC01187 is expressed in intercalated cells of the nephron. In this follow-up study, we performed KIT immunohistochemistry and LINC01187 RNA in situ hybridization (RNA-ISH) on a cohort of chromophobe RCC and other renal neoplasms, characterized the expression patterns, and quantified the expression signals of the two biomarkers in both primary and metastatic settings. Results. LINC01187, in comparison to KIT, exhibits stronger and more uniform expression within tumors while maintaining temporal and spatial consistency. LINC01187 also is devoid of intra-tumoral heterogeneous expression pattern, a phenomenon commonly noted with KIT. Conclusions. LINC01187 expression can augment the currently utilized KIT assay and help facilitate easy microscopic analyses in routine surgical pathology practice.
Carboxyl-Terminal 15-Amino Acid Sequence of NFATx1 Is Possibly Created by Tissue-Specific Splicing and Is Essential for Transactivation Activity in T Cells (1998)

NFAT regulates transcription of a number of cytokine and other immunoregulatory genes. We have isolated NFATx, which is one of four members of the NFAT family of transcription factors and is preferentially expressed in the thymus and peripheral blood leukocytes, and an isoform of NFATx, NFATx1. Here we provide evidence showing that 15 amino acids in the carboxyl-terminal end of NFATx1 are required for its maximum transactivation activity in Jurkat T cells. A fusion between these 15 amino acids and the GAL4 DNA binding domain was capable of transactivating reporters driven by the GAL4 DNA binding site. Interestingly, this 15-amino acid transactivation sequence is well conserved in NFAT family proteins, although the sequences contiguous to the carboxyl-terminal regions of the NFAT family are much less conserved. We also report three additional isoforms of NFATx, designated NFATx2, NFATx3, and NFATx4. This transactivation sequence is altered by tissue-specific alternative splicing in newly isolated NFATx isoforms, resulting in lower transactivation activity in Jurkat T cells. NFATx1 is expressed predominantly in the thymus and peripheral blood leukocyte, while the skeletal muscle expressed primarily NFATx2. In Jurkat cells, transcription from the NFAT site of the IL-2 promoter is activated strongly by NFATx1 but only weakly by NFATx2. These data demonstrate that the 15-amino acid sequence of NFATx1 is a major transactivation sequence required for induction of genes by NFATx1 in T cells and possibly regulates NFAT activity through tissue-specific alternative splicing.
Constitutive Expression of HCA2in Human Retina and Primary Human Retinal Pigment Epithelial Cells (2013)

Based on these results, HCA2 appears to be constitutively expressed in human retina and in primary human RPE cells. Although its functional role is still unknown, HCA2 may be potentially involved in the pathogenesis of various retinopathies and may offer a new therapeutic target.
“Wet” Versus “Dry” Folding of Polyproline (2016)

When the all-cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all-trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all-cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions-indicating that some transitions observed in water (i.e., "wet" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline. Graphical Abstract ᅟ.
The Programmer’s Assistant: Conversational Interaction with a Large Language Model for Software Development (2023)

Large language models (LLMs) have recently been applied in software engineering to perform tasks such as translating code between programming languages, generating code from natural language, and autocompleting code as it is being written. When used within development tools, these systems typically treat each model invocation independently from all previous invocations, and only a specific limited functionality is exposed within the user interface. This approach to user interaction misses an opportunity for users to more deeply engage with the model by having the context of their previous interactions, as well as the context of their code, inform the model’s responses. We developed a prototype system – the Programmer’s Assistant – in order to explore the utility of conversational interactions grounded in code, as well as software engineers’ receptiveness to the idea of conversing with, rather than invoking, a code-fluent LLM. Through an evaluation with 42 participants with varied levels of programming experience, we found that our system was capable of conducting extended, multi-turn discussions, and that it enabled additional knowledge and capabilities beyond code generation to emerge from the LLM. Despite skeptical initial expectations for conversational programming assistance, participants were impressed by the breadth of the assistant’s capabilities, the quality of its responses, and its potential for improving their productivity. Our work demonstrates the unique potential of conversational interactions with LLMs for co-creative processes like software development.
Inhibition of farnesyl pyrophosphate (FPP) and/or geranylgeranyl pyrophosphate (GGPP) biosynthesis and its implication in the treatment of cancers (2019)

Dysregulation of isoprenoid biosynthesis is implicated in numerous biochemical disorders that play a role in the onset and/or progression of age-related diseases, such as hypercholesterolemia, osteoporosis, various cancers, and neurodegeneration. The mevalonate metabolic pathway is responsible for the biosynthesis of the two key isoprenoid metabolites, farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP). Post-translational prenylation of various proteins, including the small GTP-binding proteins (GTPases), with either FPP or GGPP is vital for proper localization and activation of these proteins. Prenylated GTPases play a critical role in cell signaling, proliferation, cellular plasticity, oncogenesis, and cancer metastasis. Pre-clinical and clinical studies strongly suggest that inhibition of protein prenylation can be an effective treatment for non-skeletal cancers. In this review, we summarize the most recent drug discovery efforts focusing on blocking protein farnesylation and/or geranylgeranylation and the biochemical and structural data available in guiding the current on-going studies in drug discovery. Furthermore, we provide a summary on the biochemical association between disruption of protein prenylation, endoplasmic reticulum (ER) stress, unfolded protein response (UPR) signaling, and cancer.
Metallothionein is elevated in liver and duodenum of Atp7b(−/−) mice (2018)

Different mutations in the copper transporter gene Atp7b are identified as the primary cause of Wilson's disease. These changes result in high copper concentrations especially in the liver and brain, and consequently lead to a dysfunction of these organs. The Atp7<sup>(-/-)</sup> mouse is an established animal model for Wilson's disease and characterized by an abnormal copper accumulation, a low serum oxidase activity and an increased copper excretion in urine. Metallothionein (MT) proteins are low molecular weight metal-binding proteins and essential for the zinc homeostasis but also play a role for the regulation of other metals, e.g. copper. However the molecular mechanisms of MT in regard to Atp7b remain still elusive. In this study we investigate the expression of MT in the liver and duodenum of Atp7b<sup>(-/-)</sup> mice and wildtype mice. Hepatic and duodenal expression of MT was measured by real-time reverse transcription-polymerase chain reaction and post-translational expression was analyzed by immunoblot and immunofluorescence. Expression of MT in liver und duodenum was significantly higher in Atp7b<sup>(-/-)</sup> mice than in controls. Hepatic and duodenal copper, iron and zinc content were also studied. Compared to control hepatic copper and iron content was significantly higher while hepatic zinc content was significantly lower in Atp7b<sup>(-/-)</sup> mice. In the duodenum copper and zinc content of Atp7b<sup>(-/-)</sup> mice was significantly lower than in controls. Duodenal iron content was also lower in Atp7b<sup>(-/-)</sup> mice, but did not reach statistical significance. The results of our study suggest that metallothionein is elevated in the liver and duodenum of Atp7b<sup>(-/-)</sup> mice.
EtNBS and EtNBS-COOH PDT efficacy in ovarian cancer cells (2011)

The effective treatment of metastatic cancer continues to be a challenge due to the highly invasive nature of metastatic lesions and their propensity to develop therapeutic resistance. Optimal therapeutic regimens for peritoneal metastases should have both rapid uptake and penetrate throughout cancerous lesions. Using in vitro models of ovarian cancer, we have found that the cores of tumor nodules are both hypoxic and acidic, rendering most chemotherapeutic agents ineffective, and considerably reducing the therapeutic efficacy of the majority of photodynamic therapy (PDT) and radiation therapy regimens. PDT using EtNBS, a cationic photosensitizer, is a promising approach for treating these hypoxic and acidic nodule cores as it rapidly accumulates into the hypoxic cores of tumor nodules, and is effective even in completely anoxic environments. To improve the uptake rate of EtNBS into cells, we utilized a carboxylic acid terminated derivative of EtNBS that is zwitterionic at biological pH levels. In this study, we investigated the effect of this structural change on PDT efficacy in ovarian cancer cells.
cAMP Stimulates Transepithelial Short-Circuit Current and Fluid Transport Across Porcine Ciliary Epithelium (2016)

Our results suggest that cAMP triggers a sustained stimulation of Cl- and fluid transport across porcine ciliary epithelium; Cl- channels in the NPE cells are potentially a cellular site for this PKA-sensitive cAMP-mediated response.
Computational method hybridizing 2D periodic green’s functions and DCIM for the strips in layered media (2007)

This paper suggests the hybridized calculation method of 2D periodic Green’s functions(VM2DPG) and the Discrete Complex Image Method(DCIM to take the profits of the VM2DPG for a periodic structure and DCIM for a layered media problem. With the Method of Moment(MoM), this hybrid method efficiently solves an integral equation, saving the overall computation time by over 50%. Scattering problems of PEC and resistive strips are dealt with for its validation.
Ischemic acute renal failure (1998)

Renal Epithelial Biology Experimental Laboratories, Indiana University Department of Medicine; and the Roudebush Veterans' Affairs Medical Center, Indianapolis, Indiana, USA