gebhart/patrepeval huggingface dataset:
Structure and Function of Bacillus subtilis YphP, a Prokaryotic Disulfide Isomerase with a CXC Catalytic Motif, (2009)

The DUF1094 family contains over 100 bacterial proteins, all containing a conserved CXC motif, with unknown function. We solved the crystal structure of the Bacillus subtilis representative, the product of the yphP gene. The protein shows remarkable structural similarity to thioredoxins, with a canonical alphabetaalphabetaalphabetabetaalpha topology, despite low amino acid sequence identity to thioredoxin. The CXC motif is found in the loop immediately downstream of the first beta-strand, in a location equivalent to the CXXC motif of thioredoxins, with the first Cys occupying a position equivalent to the first Cys in canonical thioredoxin. The experimentally determined reduction potential of YphP is E degrees' = -130 mV, significantly higher than that of thioredoxin and consistent with disulfide isomerase activity. Functional assays confirmed that the protein displays a level of isomerase activity that might be biologically significant. We propose a mechanism by which the members of this family catalyze isomerization using the CXC catalytic site.
Prevalence of Parasitemia and Seroreactivity to Trypanosoma Cruzi in a Rural Population of Northeast Brazil (1979)

Age-specific prevalence rates of parasitemia and seroreactivity to Trypanosoma cruzi were determined in a rural area endemic for Chagas' disease in Northeast Brazil. Parasitemia was detected by blood cultures and xenodiagnosis, and serum antibodies to the parasite were measured by the complement fixation (CF) and indirect immunofluorescence (IFA) tests. Of the 116 persons examined, 39 (33.7%) had antibodies and 23 (19.8%) had parasitemia. Ninety-six percent of parasitemic individuals were seropositive and 56% of seropositive individuals were parasitemic. The percentage of seropositive individuals with detectable parasitemia declined with age; all seropositive children in the 1- to 4-year age group and two-thirds of seropositive persons 5-19 years old had parasitemia while only one-third of seropositive adults above 19 years had parasitemia. CF and IFA tests were equally sensitive in detecting persons with parasitemia. Xenodiagnosis was more sensitive than culture for detecting parasitemia, but the two methods together were more sensitive than either method alone. Using the age-dependent relationship of parasitemia to seropositivity determined in this study, the prevalence rate of T. cruzi parasitemia was estimated in a much larger adjacent population in which seropositivity rates and the demographic structure were already known.
NV14 from serine O‐acetyltransferase of cyanobacteria influences the antioxidant enzymes in vitro cells, gene expression against H2O2 and other responses in vivo zebrafish larval model (2021)

In this study, we have identified a novel peptide NV14 with antioxidative functions from serine O-acetyltransferase (SAT) of Artrospira platensis (Ap). The full sequence of ApSAT and its derived NV14 peptide "NVRIGAGSVVLRDV" (141-154) was characterized using bioinformatics tools. To address the transcriptional activity of ApSAT in response to induce generic oxidative stress, the spirulina culture was exposed to H<sub>2</sub> O<sub>2</sub> (10 mM). The ApSAT expression was studied using RT-PCR across various time points and it was found that the expression of the ApSAT was significantly upregulated on Day 15. The in vitro cytotoxicity assay against NV14 was performed in human dermal fibroblast cells and human blood leukocytes. Results showed that NV14 treatment was non-cytotoxic to the cells. Besides, in vivo treatment of NV14 in zebrafish larvae did not exhibit the signs of developmental toxicity. Further, the in vitro antioxidant assays enhanced the activity of the antioxidant enzymes, such as SOD and CAT, due to NV14 treatment; and also significantly reduced the MDA levels, while increasing the superoxide radical and H<sub>2</sub> O<sub>2</sub> scavenging activity. The expression of antioxidant enzyme genes glutathione peroxidase, γ-glutamyl cysteine synthase, and glutathione S-transferase were found to be upregulated in the NV14 peptide pretreated zebrafish larvae when induced with generic oxidative stress, H<sub>2</sub> O<sub>2</sub> . Overall, the study showed that NV14 peptide possessed potent antioxidant properties, which were demonstrated over both in vitro and in vivo assays. NV14 enhanced the expression of antioxidant enzyme genes at the molecular level, thereby modulating and reversing the cellular antioxidant balance disrupted due to the H<sub>2</sub> O<sub>2</sub> -induced oxidative stress.
Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection (2016)

The molecular regulatory mechanisms of host responses to Mycobacterium avium subsp. paratuberculosis (MAP) infection during the early subclinical stage are still not clear. In this study, surgically isolated ileal segments in newborn calves (n = 5) were used to establish in vivo MAP infection adjacent to an uninfected control intestinal compartment. RNA-Seq was used to profile the whole transcriptome (mRNAs) and the microRNAome (miRNAs) of ileal tissues collected at one-month post-infection. The most related function of the differentially expressed mRNAs between infected and uninfected tissues was "proliferation of endothelial cells", indicating that MAP infection may lead to the over-proliferation of endothelial cells. In addition, 46.2% of detected mRNAs displayed alternative splicing events. The pre-mRNA of two genes related to macrophage maturation (monocyte to macrophage differentiation-associated) and lysosome function (adenosine deaminase) showed differential alternative splicing events, suggesting that specific changes in the pre-mRNA splicing sites may be a mechanism by which MAP escapes host immune responses. Moreover, 9 miRNAs were differentially expressed after MAP infection. The integrated analysis of microRNAome and transcriptome revealed that these miRNAs might regulate host responses to MAP infection, such as "proliferation of endothelial cells" (bta-miR-196 b), "bacteria recognition" (bta-miR-146 b), and "regulation of the inflammatory response" (bta-miR-146 b).
Factors affecting shoot initiation from tuber discs of potato (Solanum tuberosum) (1980)

Abstract Discs of cortical and perimedullary tissue from tubers of potato ( Solanum tuberosum L. cv. Superior) formed adventitious shoots when cultured on a medium containing Murashige and Skoog's salts, myo ‐inositol, 100 mg/l; folic acid, 0.5 mg/l; D‐biotin, 0.05 mg/l; gibberellic acid (GA 3 ), 0.5 mg/l; thiamine ˙ HCl, 0.1 mg/l; glycine, 2.0 mg/l; pyridoxine ˙ HCl, 0.5 mg/l; nicotinic acid, 0.5 mg/l; sucrose, 25 g/l; casein hydrolysate, 1 g/l; Bacto agar, 9.0 g/l; and a cytokinin [ N 6 ‐benzylaminopurine (BAP), N 6 ‐γ,γ‐dimethylallylaminopurine (2iP), or N 6 ‐furfurylaminopurine (kinetin)]. Discs of pith tissue either failed to survive or produced callus but did not undergo morphogenesis. Cytokinin was essential for explant survival, while BAP at 3.0 mg/l was most efficacious in promoting shoot initiation. Auxin was not essential for shoot initiation or development; however, a low concentration (0.03 mg/l) of α‐naphthaleneacetic acid (NAA) stimulated both explant survival and the number of shoots produced per disc. Indole‐3‐butyric acid (IBA) and indole‐3‐acetic acid (IAA) did not stimulate shoot initiation. GA 3 was essential for both shoot initiation and subsequent shoot development. The highest incidence of morphogenesis (over 100 shoots in 12 weeks) occurred from tuber discs cultured at 18°C constant and under a photon flux density of 60 μE m ‐2 s ‐1 . No difference in regenerative ability was found in explants taken from source tubers stored for 0 to 20 weeks at 4°C. A histological examination indicated that shoots developed from small clusters of meristematic cells which were initiated from within small protuberances on the surface of the tuber disc 3 weeks after transfer.
Dynamical magnetoelectric effects associated with ferroelectric domain walls (2015)

Molecular dynamics simulations using a first-principles-derived effective Hamiltonian are conducted on lead zirconium titanate ultrathin films possessing nanoscale ferroelectric domains and experiencing a GHz electric field. Pulses of magnetization are predicted to occur in this system when sudden changes occur in the morphology of these nanodomains. A simple equation relating the magnetization and product between the electric polarization and its time derivative is found to reproduce and explain these magnetization pulses as well as previously observed magnetoelectric effects in moving ferroelectric domain walls and phase boundaries in ferroelectrics and magnetoelectrics.
On the optimality of shape and data representation in the spectral domain (2014)

A proof of the optimality of the eigenfunctions of the Laplace-Beltrami operator (LBO) in representing smooth functions on surfaces is provided and adapted to the field of applied shape and data analysis. It is based on the Courant-Fischer min-max principle adapted to our case. % The theorem we present supports the new trend in geometry processing of treating geometric structures by using their projection onto the leading eigenfunctions of the decomposition of the LBO. Utilisation of this result can be used for constructing numerically efficient algorithms to process shapes in their spectrum. We review a couple of applications as possible practical usage cases of the proposed optimality criteria. % We refer to a scale invariant metric, which is also invariant to bending of the manifold. This novel pseudo-metric allows constructing an LBO by which a scale invariant eigenspace on the surface is defined. We demonstrate the efficiency of an intermediate metric, defined as an interpolation between the scale invariant and the regular one, in representing geometric structures while capturing both coarse and fine details. Next, we review a numerical acceleration technique for classical scaling, a member of a family of flattening methods known as multidimensional scaling (MDS). There, the optimality is exploited to efficiently approximate all geodesic distances between pairs of points on a given surface, and thereby match and compare between almost isometric surfaces. Finally, we revisit the classical principal component analysis (PCA) definition by coupling its variational form with a Dirichlet energy on the data manifold. By pairing the PCA with the LBO we can handle cases that go beyond the scope defined by the observation set that is handled by regular PCA.
Efficacious redox-responsive gene delivery in serum by ferrocenylated monomeric and dimeric cationic cholesterols (2015)

Herein, we present the design and synthesis of new redox-active monomeric and dimeric (gemini) cationic lipids based on ferrocenylated cholesterol derivatives for gene delivery. The cationic cholesterols are shown to be transfection efficient after being formulated with the neutral helper lipid DOPE in the presence of serum (FBS). The redox activity of the resulting co-liposomes and their lipoplexes could be regulated using the alkanyl ferrocene moiety attached to the ammonium head groups of the cationic cholesterols. Atomic force microscopy (AFM), dynamic light scattering (DLS) and zeta potential measurements were performed to characterize the co-liposomal aggregates and their complexes with pDNA. The transfection efficiency of lipoplexes could be tuned by changing the oxidation state of the ferrocene moiety. The gene transfection capability was assayed in terms of green fluorescence protein (GFP) expression using pEGFP-C3 plasmid DNA in three cell lines of different origins, namely Caco-2, HEK293T and HeLa, in the presence of serum. The vesicles possessing ferrocene in the reduced state induced an efficient transfection, even better than a commercial reagent Lipofectamine 2000 (Lipo 2000) as evidenced by flow cytometry and fluorescence microscopy. All the co-liposomes containing the oxidized ferrocene displayed diminished levels of gene expression. Gene transfection events from the oxidized co-liposomes were further potentiated by introducing ascorbic acid (AA) as a reducing agent during lipoplex incubation with cells, leading to the resumption of transfection activity. Assessment of transfection capability of both reduced and oxidized co-liposomes was also undertaken following cellular internalization of labelled pDNA using confocal microscopy and flow cytometry. Overall, we demonstrate here controlled gene transfection activities using redox-driven, transfection efficient cationic monomeric and dimeric cholesterol lipids. Such systems could be used in gene delivery applications where transfection needs to be performed spatially or temporally.
Correction: Weingart et al. Expanded Polycarbonate (EPC)—A New Generation of High-Temperature Engineering Bead Foams. Polymers 2020, 12, 2314 (2022)

In the original publication [...].
PARP-1 inhibition prevents CNS migration of dendritic cells during EAE, suppressing the encephalitogenic response and relapse severity (2011)

Overall, data underscore the potential relevance of PARP-1 inhibitors to MS therapy and suppression of autoimmunity.
Control of specific protein biosynthesis during the adipose conversion of 3T3 cells. (1980)

Estimated by densitometry of stained gels.The 34,000, 35,000, and 37,000 proteins were measured on gels loaded with 10 pg of protein.AU other proteins were measured in gels loaded with 20 pg.The polyacrylamide content of the gels was 11%.except for the 13,000 protein (15%) and the protein of M, = 250,000 and 230,000 (8%).
Supplementary Table 3 from General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to <i>De novo</i> DNA Methylation in Cancer Cells (2023)

Supplementary Table 3 from General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to &lt;i&gt;De novo&lt;/i&gt; DNA Methylation in Cancer Cells
Review: Back-Side via Hole Etching Process for Grounding GaAs Based Monolithic Microwave Integrated Circuits (2005)

Developments in the etching process for fabrication of back-side via holes in GaAs based monolithic microwave integrated circuits are reviewed. Attention is focused on critical issues concerning via hole fabrication. The requirements of the process of via hole etching are considered. The suitability of various fabrication techniques, and the associated chemistry, has been examined. The effects of various process parameters such as power, pressure, and gas flow rate on the etch characteristics have been discussed. The influence of the masking material, via hole dimensions and the wafer size on the etch characteristics have been discussed from the point of view of increasing packing density in advanced chip fabrication. Finally, the state of the art and the issues concerning the via hole etching process are described.
Hypergraph-based overlay network model for the Internet of Things (2015)

As the Internet of Things (IoT) is gaining tremendous popularity from industries to researchers for its potential to provide business opportunities and academic contributions, several research challenges have risen to the surface. With billions of IoT objects being produced, connected and interacting, one of the challenges claim that there is an imperative need for ways to organize and manage the objects effectively. This paper, therefore, proposes a network-based multidimensional structure to model the IoT for efficient management and discovery of IoT objects. In addition, we address various research issues that must be considered in designing the proposed model. To test the feasibility of the model, we present numerous experiments performed on our smart home automation demo box, along with their justifications.
Jet Frac Porta-Skid - A New Concept in Oil Field Service Pump Equipment (1969)

This paper was prepared for the 44th Annual Fall Meeting of the of the Society of Petroleum Engineers of AIME, to be held in Denver, Colo., Sept. 28-Oct. 1, 1969. Permission to copy is restricted to an abstract of not more than 300 words. Illustrations may not be copied. The abstract should contain conspicuous acknowledgment of where and by whom the paper is presented. Publication elsewhere after publication in the JOURNAL OF PETROLEUM TECHNOLOGY or the SOCIETY OF PETROLEUM ENGINEERS JOURNAL is usually granted upon request to the Editor of the appropriate journal, provided agreement to give proper credit is made. Discussion of this paper is invited. Three copies of any discussion should be sent to the Society of Petroleum Engineers office. Such discussion may be presented at the above meeting and, with the paper, may be considered for publication in one of the two SPE magazines. Abstract Increasing demands of the free world oil industry call for pumping equipment that can be moved to any location in the world within a matter of hours. Many times these locations are remote and inaccessible to conventional equipment. Offshore drilling and production requires equipment capable of a production requires equipment capable of a high degree of portability and operation in a minimum of floor space. High performance pumping equipment is an performance pumping equipment is an example of this type service. To meet these demands containerized turbine-powered fracturing pumping units have been developed suitable for movement by air cargo plane, helicopters, boat and land vehicles. Basic features include small size, containerization, high horsepower, and high mobility. Each unit consists of three sections: A standard Halliburton HT-400 pump, a transmission and accessories section, and a gas turbine power section. Each section is interchangeable with the same section in all other units. This equipment is now available to the oil industry and is scheduled for operation in the Eastern Hemisphere after blowout pumping jobs are completed in South Louisiana. Introduction The petroleum industry is supported by numerous, highly-specialized, service companies. Creating, providing, and operating equipment capable of pumping fluids beyond the capacities of pumping fluids beyond the capacities of normal drilling rig components is one such service. Generally, operating time at the well site for this service is brief and long periods may elapse before service is again necessary on any given location Normally, this pumping equipment is made available where ground transportation is feasible with equipment mounted on trucks or trailers. (A truck-mounted unit may be viewed in Fig. 1). Marine installations commonly are equipped with service company skid units permanently installed on the rig. (A permanently installed on the rig. (A typical offshore skid is shown in Fig. 2).
Modeling physiology of crop development, growth and yield (2012)

<title>Abstract</title> This book presents quantitative hypotheses for key processes in crop development, growth and yield. The emphasis is on functions that offer comparatively simple hypotheses, yet are appropriate over a range of conditions. The book is organized into four parts. The first part (chapters 1-5) presents fundamental perspectives required in developing crop models. This section also presents examples of how the crop models can be applied to explore important issues in crop improvement and production. The second part (chapters 6-12) develops expressions for crop development (i.e. phenology), growth and partitioning into plant components, including grains. The functions developed in this section are used to assess the potential growth and yield of a crop when it is not limited by the availability of water or nutrients, and there is no limitation as a result of insects, diseases and weeds. The third part (chapters 13-16) accounts for water limitation of specific processes in crop growth. The last part (chapters 17-19) accounts for nitrogen limitation of plant growth processes. Each chapter ends with exercises for the reader to better understand how the functions operate and the implications of adjustments in the parameters of the functions. This book is intended for those who have an interest in the quantitative understanding of crop development, growth and yield, whether or not his primary interest is in constructing a model.
Extracting heartrate from optical signal of functional near-infrared spectroscopy based on mathematical morphology (2017)

Functional near-infrared spectroscopy (fNIRS), as a new optical functional neuroimaging method, has been widely used in neuroscience research. In some research fields with NIRS, heartrate (HR) (or heartbeat) is needed as useful information to evaluate its influence, or to know the state of subject, or to remove its artifact. If HR (or heartbeat) can be detected with high accuracy from the optical intensity, this will undoubtedly benefit a lot to many NIRS studies. Previous studies have used the moving time window method or mathematical morphology method (MMM) to detect heartbeats in the optical intensity. However, there are some disadvantages in these methods. In this study, we proposed a method combining the periodic information of heartbeats and the operator of mathematical morphology to automatically detect heartbeats in the optical intensity. First the optical intensity is smoothed using a moving average filter. Then, the opening operator of mathematical morphology extracts peaks in the smoothed optical intensity. Finally, one peak is identified as a heartbeat peak if this peak is the maximum in a predefined point range. Through validation on experimental data, our method can overcome the disadvantages of previous methods, and detect heartbeats in the optical signal of fNIRS with nearly 100% accuracy.
Breast pathologies: Kaleidoscope of conventional mammography, sonography, magnetic resonance mammography, and histopathology features (2014)

Breast can be the seat of a number of benign and malignant pathologies. Even though digital mammography - with or without correlative ultrasonography - is still largely the mainstay of breast imaging, the newer technique of magnetic resonance mammography has come of age. Capable of capturing wide and varied morphology of diverse breast lesions, it can contribute in a major way to the diagnosis and management of some patients. Characteristic magnetic resonance mammography features can help obviate the need of a biopsy in lesions like hamartomas, and benign virginal hyperplasia, whereas in conditions like invasive lobular carcinoma and Paget's disease, it can make a significant difference to the surgical plan. This pictorial kaleidoscope presents the imaging and histopathology characteristics of many usual and unusual breast lesions.