gebhart/patrepeval huggingface dataset:
A seven‐gene operon essential for formate‐dependent nitrite reduction to ammonia by enteric bacteria (1994)

The DNA sequence of the regulatory region and the structural gene, nrfA, for cytochrome c552 of Escherichia coli K-12 have been reported. We have now established that nrfA is the first gene in a seven-gene operon, designated the nrf operon, at least five of which are essential for formate-dependent nitrite reduction to ammonia. This operon terminates just upstream of the previously sequenced gltP gene encoding a sodium-independent, glutamate and aspartate transporter. Expression of lac fused to nrfA, nrfE or nrfG is regulated by oxygen repression, FNR-dependent anaerobic induction, nitrite induction and nitrate repression during anaerobic growth, exactly as previously reported for the nrfA promoter. In contrast, expression of the gltP-lac fusion was FNR-independent. The open reading frame immediately downstream of nrfA encodes NrfB, a hydrophilic, penta-haem cytochrome c with an M(r) of 20,714. The structure of the N-terminal region is typical of a signal peptide for a periplasmic protein: cleavage at the putative signal peptide cleavage site, Ala-26, would result in a periplasmic cytochrome with a molecular mass of 18 kDa. The NrfC polypeptide, M(r) 24,567, contains 16 cysteine residues arranged in four clusters typical of the CooF super-family of non-haem iron-sulphur proteins. The NrfD sequence predicts a 318-residue hydrophobic protein with a distribution of acidic and basic amino acids which suggests that NrfD is an integral transmembrane protein with loops in both the periplasm and the cytoplasm. Proteins most similar to NrfD include the PsrC subunit of polysulphide reductase from Wolinella, but, as seven of the 10 most similar proteins are NADH-ubiquinone oxidoreductases, we propose that NrfD participates in the transfer of electrons from the quinone pool into the terminal components of the Nrf pathway. NrfE, M(r) 60,851, is predicted to be another hydrophobic, integral membrane protein homologous to the CdI1 protein of Rhodobacter capsulatus, which has been implicated in the assembly of periplasmic c-type cytochromes. The sequence of the 127 residue NrfF polypeptide, M(r) 14,522, is strikingly similar to the CcI2 protein of R. capsulatus, especially in the putative haem-binding motif, RCPQCQNQN.(ABSTRACT TRUNCATED AT 400 WORDS)
Exogenous Brain-Derived Neurotrophic Factor Rescues Synaptic Dysfunction in<i>Mecp2</i>-Null Mice (2010)

Postnatal deficits in brain-derived neurotrophic factor (BDNF) are thought to contribute to pathogenesis of Rett syndrome (RTT), a progressive neurodevelopmental disorder caused by mutations in the gene encoding methyl-CpG-binding protein 2 (MeCP2). In Mecp2-null mice, a model of RTT, BDNF deficits are most pronounced in structures important for autonomic and respiratory control, functions that are severely affected in RTT patients. However, relatively little is known about how these deficits affect neuronal function or how they may be linked to specific RTT endophenotypes. To approach these issues, we analyzed synaptic function in the brainstem nucleus tractus solitarius (nTS), the principal site for integration of primary visceral afferent inputs to central autonomic pathways and a region in which we found markedly reduced levels of BDNF in Mecp2 mutants. Our results demonstrate that the amplitude of spontaneous miniature and evoked EPSCs in nTS neurons is significantly increased in Mecp2-null mice and, accordingly, that mutant cells are more likely than wild- type cells to fire action potentials in response to primary afferent stimulation. These changes occur without any increase in intrinsic neuronal excitability and are unaffected by blockade of inhibitory GABA currents. However, this synaptopathy is associated with decreased BDNF availability in the primary afferent pathway and can be rescued by application of exogenous BDNF. On the basis of these findings, we hypothesize that altered sensory gating in nTS contributes to cardiorespiratory instability in RTT and that nTS is a site at which restoration of normal BDNF signaling could help reestablish normal homeostatic controls.
Integrins in Cancer Treatment (2006)

Anchorage-independent growth, anoikis resistance, and most steps of metastasis formation are integrin-mediated or -dependent processes, which are characteristics of malignant tumor cells. Acting as oncogenes or tumor suppressor genes, integrins may be involved in the oncogenic transformation of normal cells and their growth into a primary tumor node. During tumorigenesis, a switch of integrin expression can be observed, inasmuch as growth-promoting and growth-attenuating integrins are up- and down-regulated, respectively. ECM-ligand binding to an integrin initiates signals, which eradiating from the integrins are transmitted via different yet interconnecting pathways and elicit various cell functions, such as morphological changes, adhesion, migration and gene activation. Any of these functions takes part in the metastatic cascade of tumor progression, such as epithelial-to-mesenchymal transition of carcinoma cells, tumor cell contact with the basement membrane, invasion into neighboring tissues as well as production and activation of ECM-degrading MMPs. Besides their direct involvement in tumor progression as cell surface molecules on tumor cells, integrins in normal cells surrounding a tumor, e.g. endothelial cells, can also determine various cancer characteristics, such as tumor-induced neoangiogenesis and immune resistance. Hence, integrins are relevant pharmacological targets in tumor biology. Spurred by the recent success to generate pharmaceutical mimetics of RGD-dependent integrins and by the integrin's easy accessibility on the cell surface, the hope is rising that also RGD-independent integrins, such as the collagen- and laminin-binding integrins, can be pharmacologically manipulated to fight integrin-dependent functions of cancer cells, which are necessary and at least partially specific for their proliferation and progression.
Gas permselectivity in amorphous linear and crosslinked poly(arylene ether ketones) (1990)

The present study addresses a systematic evaluation of the effect of crosslinking via terminal maleimide units on the gas transport properties through a dense polymer film of amorphous Poly(Arylene Ether Ketones) or PEK. The methodology for the preparation of crosslinked maleimide terminated PEK (or MIPEK) films from several blend ratios of different molecular weights of MIPEK is discussed in detail. The primary focus of this work has been to investigate the influence of different degrees of crosslinking on gas permeabilities and selectivities, with an objective of producing a highly selective membrane. It has been demonstrated that crosslinking markedly decreases the permeation of methane, without changing the values for molecules such as helium.
Preparation of terminal oxygenates from renewable natural oils by a one-pot metathesis–isomerisation–methoxycarbonylation–transesterification reaction sequence (2006)

Renewable natural oils can be converted into potentially high value terminal oxygenates by a single-pot, high yielding metathesis–isomerisation–methoxycarbonylation–transesterification reaction sequence.
팀제조직의 성과평가 모델에 관한 연구 - BSC 모델을 중심으로 - (2002)

Most of companies are remodeling organization into the Team System as a strategy to cope with the rapidly changing business environment and to enhance them to the competitive company by radical reform. So it is definitely required that companies prepare comprehensive and balanced view of performance evaluation method for well-settled Team System. Professional goal of this study is focused on improvement of organization by expanding the horizon on the activation of Team System and accomplishing the goal of this. We will try to review what is the Team System and how we can evaluate the performance effectively. Also we will show how we can measure the performance and what is the idea model as a method of performance evaluation to approach original purpose of this study.
Meta-analysis of consumer's willingness-to-pay premiums for certified wood products (2012)

Consumers’ willingness to pay (WTP) price premiums for environmentally certified wood products has been frequently estimated using stated preference methods. Estimates of WTP premiums for certified wood products over non-certified options reported in the literature range from 1.0% to 39.3%. This paper describes a meta-analysis used to determine the key factors associated with WTP price premium estimates by examining data from 19 different studies conducted around the world. Results of Bayesian hierarchical models show that frequently purchased wood products and wood products with lower base prices tend to capture higher percentage premiums. Survey administration method was also a statistically significant factor influencing variations in WTP estimates. Results show that conjoint analysis elicited inflated WTP estimates toward certified wood products compared with contingent valuation methods. Reported WTP estimates have increased in recent years. Recommendations to reduce the error of WTP estimates toward certified wood products and improve the validity of experimental studies are provided.
Podoplanin, novel 43-kd membrane protein of glomerular epithelial cells, is down-regulated in puromycin nephrosis. (1997)

Puromycin aminonucleoside nephrosis (PAN), a rat model of human minimal change nephropathy, is characterized by extensive flattening of glomerular epithelial cell (podocyte) foot processes and by severe proteinuria. For comparison of expression of glomerular membrane proteins of normal and PAN rats, a membrane protein fraction of isolated rat glomeruli was prepared and monoclonal antibodies were raised against it. An IgG-secreting clone designated LF3 was selected that specifically immunolabeled podocytes of normal but not of PAN rats. The antigen of LF3 IgG was identified as a 43-kd glycoprotein. Molecular cloning of its cDNA was performed in a delta gt11 expression library prepared from mRNA of isolated rat glomeruli. The predicted amino acid sequence indicated a 166-amino-acid integral membrane protein with a single membrane-spanning domain, two potential phosphorylation sites in its short cytoplasmic tail, and six potential O-glycosylation sites in the large ectodomain. High amino acid sequence identities were found to membrane glycoproteins of rat lung and bone and mouse thymus epithelial cells as well as to a phorbol-ester-induced protein in a mouse osteoblast cell line and to a canine influenza C virus receptor. In PAN, expression of this 43-kd protein was selectively reduced to < 30%, as determined by quantitative immunogold electron microscopy, immunoblotting, and Northern blotting. These data provide evidence that transcription of the 43-kd transmembrane podocyte glycoprotein is specifically down-regulated in PAN. To indicate that this protein could be associated with transformation of arborized foot processes to flat feet (Latin, pes planus) we have called it podoplanin.
Complexes of DNA with fluorescent dyes are effective reagents for detection of autoimmune antibodies (2017)

To date, there are multiple assays developed that detect and quantify antibodies in biofluids. Nevertheless, there is still a lack of simple approaches that specifically detect autoimmune antibodies to double-stranded DNA. Herein we investigate the potential of novel nucleic acid complexes as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA. We demonstrate the detection of anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We tested the most potent non-covalent pairs of DNA and fluorescent dyes. Several complexes showed specific recognition of autoimmune antibodies in human samples of lupus patients using a simple one-step immunofluorescence method. This makes the novel assay developed herein a promising tool for research and point-of-care monitoring of anti-DNA antibodies. Using this method, we for the first time experimentally confirm that the disease-specific autoimmune antibodies are sensitive to the 3D structure of nucleic acids and not only to the nucleotide sequence, as was previously thought.
Central Nervous System Lesions Biopsied or Treated by CT-Guided Needle Placement (1979)

Computed tomography has been utilized to guide a needle into central nervous system lesions as small as one centimeter in diameter. Direct puncture has drained many abscesses effectively, provided material for immediate Gram stain and subsequent culture, and permitted irrigation with appropriate antibioties, Multilocular cerebral lesions and loculated extracerebral fluid collections have been aspirated and treated with this technique. Aspiration of known cystic tumors has reduced their mass and obviated some palliative decompressions. Unresectable gliomas and metastases have been biopsied prior to chemotherapy or radiotherapy. Hemorrhage and other rare complications of biopsy may be detected and immediately treated.
Sensitivity kernels and Fresnel volumes for transmitted waves (2008)

Two‐ and three‐dimensional sensitivity kernels corresponding to an incident plane wave (denoted by plw hereinafter) and a point source (denoted by ps hereinafter) in a homogeneous medium are derived according to the Born and Rytov approximations for traveltime and amplitude tomography. Furthermore, using the idea of constructive interference of waves, the spatial distribution ranges and properties of transmitted Fresnel volumes are summarized. These studies are important for seismic modeling and inversion based on Fresnel volume theory such as Fresnel volume tomography.
Wide‐complex Tachycardia: Continued Evaluation of Diagnostic Criteria (2000)

Neither the emergency physicians nor the cardiologists were able to achieve a sensitivity or specificity as high as that reported by the original investigators when using the Brugada algorithm to determine the presence of VT.
Mobilization and Mechanism of Transcription of Integrated Self-Inactivating Lentiviral Vectors (2005)

Permanent genetic modification of replicating primitive hematopoietic cells by an integrated vector has many potential therapeutic applications. Both oncoretroviral and lentiviral vectors have a predilection for integration into transcriptionally active genes, creating the potential for promoter activation or gene disruption. The use of self-inactivating (SIN) vectors in which a deletion of the enhancer and promoter sequences from the 3' long terminal repeat (LTR) is copied over into the 5' LTR during vector integration is designed to improve safety by reducing the risk of mobilization of the vector genome and the influence of the LTR on nearby cellular promoters. Our results indicate that SIN vectors are mobilized in cells expressing lentiviral proteins, with the frequency of mobilization influenced by features of the vector design. The mechanism of transcription of integrated vector genomes was evaluated using a promoter trap design with a vector encoding tat but lacking an upstream promoter in a cell line in which drug resistance depended on tat expression. In six clones studied, all transcripts originated from cryptic promoters either upstream or within the vector genome. We estimate that approximately 1 in 3,000 integrated vector genomes is transcribed, leading to the inference that activation of cryptic promoters must depend on local features of chromatin structure and the constellation of nearby regulatory elements as well as the nature of the regulatory elements within the vector.
Data and knowledge bases as integral parts of a distributed object infrastructure (2002)

Atlas is a prototype of an object infrastructure. It is designed to support hundreds of millions of objects, distributed in a heterogeneous wide area network of thousands or millions of computers. Atlas is implemented mainly as a vehicle for experimenting with distributed office and information systems. Atlas supported much finer-granularity objects than traditional client/server networking models. Atlas provides location-transparent method invocation and dynamic creation, deletion, and migration of persistent and non-persistent objects. Iris is an object-oriented database management system, supporting OSQL as its main implementation language. KBMS1 is a knowledge-base management system supporting kbProlog as its implementation language. Both these databases have been integrated with Atlas. The purpose of the integration is to demonstrate that object-oriented technology is appropriate for integration of heterogeneous sources of information and information processing facilities. Atlas objects can be implemented in OSQL and reside in Iris or implemented in kbProlog and reside in KBMS1. Atlas objects can also be implemented in traditional programming language such as C. Objects implemented in any of the two databases or in traditional programming languages can communicate uniformly with each other.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Relational queries over program traces (2005)

Instrumenting programs with code to monitor runtime behavior is a common technique for profiling and debugging. In practice, instrumentation is either inserted manually by programmers, or automatically by specialized tools that monitor particular properties. We propose Program Trace Query Language (PTQL), a language based on relational queries over program traces, in which programmers can write expressive, declarative queries about program behavior. We also describe our compiler, Partiqle . Given a PTQL query and a Java program, Partiqle instruments the program to execute the query on-line. We apply several PTQL queries to a set of benchmark programs, including the Apache Tomcat Web server. Our queries reveal significant performance bugs in the jack SpecJVM98 benchmark, in Tomcat, and in the IBM Java class library, as well as some correct though uncomfortably subtle code in the Xerces XML parser. We present performance measurements demonstrating that our prototype system has usable performance.
Meters to Models: Using Smart Meter Data to Predict Home Energy Use (2014)

Access to smart meter data in the United States presents an opportunity to better understand residential energy consumption and energy-related behaviors. Air-conditioning (A/C) use, in particular, is a highly variable and significant contributor to residential energy demand. Most current building simulation software tools require intricate detail and training to accurately model A/C use within an actual house. However, integrating existing modeling software and empirical data has the potential to create highly portable and accurate models. Reduced-order models (ROM) are low-dimensional approximations of more complex models that use only the most impactful variables. In this paper, we report on the development of ROMs for 41 physical houses in Austin, Texas, using smart meter data. These models require outdoor dry bulb temperature, thermostat set points and A/C energy use data to regress model coefficients. A nonintrusive load monitoring technique is used to disaggregate A/C electricity consumption from whole-house electricity data reported by smart meters. Thermostat set points are provided by smart thermostats. Once trained, the models can use thermostat set points and dry bulb temperatures to predict A/C loads. The ROMs are used to evaluate the potential of automated thermostat control to reduce the aggregate peak demand. A centralized model predictive controller reduces the aggregate peak load by adjusting the thermostat set points to pre-cool houses and staggers the time A/C units turn on.
Differential Work-Function Enabled Bifunctional Switching in Strontium Titanate Flexible Resistive Memories (2020)

Multifunctional electronic memories capable of demonstrating both analog and digital switching on-demand are extremely attractive for miniaturization of electronics without significant drain on energy consumption. Simultaneously translating functionality onto mechanically conformable platforms will further enhance their suitability. Here, we demonstrate the ability to engineer multifunctionality in strontium titanate (STO)-based resistive random-access memories (ReRAM) on a flexible polyimide platform. By utilizing different bottom electrodes of various work functions while the top electrode is fixed, differential work functions are induced in STO, to induce bipolar or complementary switching behaviors whenever required. This work-function difference-induced bifunctional switching on the flexible platform reveals a streamlined route for achieving flexible artificial neural networks, high density integration, and logic operation using a single ReRAM.
The Ratio of Splicing Variants of MGC-24/CD164, a Sialomucin, Correlates with the Metastatic Potential of Colorectal Carcinomas (2000)

MGC-24/CD164 is a sialomucin expressed in many normal and cancerous tissues. In humans, soluble and transmembrane forms of MGC-24 are produced by alternative splicing. The total MGC-24 RNA level was found to be lower in human colorectal carcinomas as compared with the adjacent normal mucosal tissues. Lower MGC-24 mRNA levels in colon carcinomas and in the adjacent normal mucosa epithelium correlate with lymphatic vessel invasion by the carcinoma. The ratio of the soluble form to the transmembrane form of the mRNA in colorectal carcinomas was determined by ribonuclease protection assay. Higher ratios were correlated with less venous invasion and less remote metastasis, which became evident during postoperative observation.
Modification of local structures in multicrystals revealed by spatially resolved x-ray rocking curve analysis (2007)

We show that spatially resolved x-ray rocking curve analysis can be a useful technique to investigate local structures in bulk multicrystals and their modification during crystal growth when combined with appropriate samples. For this purpose, a model crystal growth experiment was carried out using a Si seed crystal with artificially controlled ⟨110⟩ tilted grain boundaries. The growth orientation was chosen as the scan axis for rocking curve measurements in different crystal grains. Thanks to the superior angle resolution, the gradual structural changes can be monitored by the changes in the rocking curve profile such as the peak shift and the peak splitting. The amount as well as the sign of the peak shift was found to be strongly dependent on the initial grain boundary structure. Furthermore, the technique was applied to investigate local structures of Si multicrystals with controlled grain orientation grown without any seeds.
Preparation of SiO2-PVA nanocomposite and monolithic transparent silica glass by sintering (2011)

We present a procedure for fabricating transparent silica glass that involves the sintering of green bodies prepared from an inorganic–organic nanocomposite. The nanocomposite was prepared from fumed silica and poly(vinyl alcohol) (PVA). We investigated the SiO2–PVA nanocomposite by Fourier transform infrared spectrometry (FT-IR) measurement, transmission electron microscopy and electron energy-loss spectroscopy, and the results revealed homogeneously dispersed SiO2 nanoparticles and PVA. We examined the relationship between the pH and ζ potential of the SiO2 suspension and the formability of the SiO2–PVA nanocomposite. Formability of the SiO2–PVA nanocomposite was dependent on the pH of the SiO2 suspension, and a monolithic SiO2–PVA nanocomposite without cracks was obtained using a SiO2 suspension at around the isoelectric point (pI). By sintering the SiO2–PVA nanocomposite in air at 1100°C, monolithic transparent silica glass was obtained with no cracks. The glass is highly transparent from the ultraviolet to the visible region.