gebhart/patrepeval huggingface dataset:
Determining the impact of commercial feed additives as potential porcine epidemic diarrhea virus mitigation strategies as determined by polymerase chain reaction analysis and bioassay1 (2018)

Mitigation of porcine epidemic diarrhea virus (<b>PEDV</b>) was assessed using two feed additives (0.5% inclusion of a benzoic acid [<b>BA</b>] product and 0.02% inclusion of an essential oil [<b>EO</b>] product; DSM Nutritional Products Inc., Parsippany, NJ), and combination of both products (0.5% BA and 0.02% EO) in spray-dried porcine plasma (<b>SDPP</b>) and a swine gestation diet (FEED) as determined by real-time quantitative reverse transcriptase polymerase chain reaction (<b>qRT-PCR</b>) and bioassay. Viral RNA quantification was performed at 7 sampling days post-laboratory inoculation (d 0, 1, 3, 7, 14, 21, and 42) and infectivity was assessed via bioassay with 10-d-old pigs. There was a tendency for treatment × feed matrix × day interaction (<i>P</i> = 0.094), in which the cycle threshold (<b>Ct</b>) value increased over time in FEED when treated with both feed additives, whereas there was no increase over time observed in SDPP treated with both feed additives. There was a feed matrix × day interaction (<i>P</i> < 0.001) in which Ct increased over time in FEED, whereas very little increase over time was observed in SDPP. A tendency for a treatment × feed matrix effect (<i>P</i> = 0.085) was observed where FEED treated with the combination of EO and BA had a greater (<i>P</i> < 0.05) PEDV Ct value than other FEED treatments, and all SDPP treatments had the lower PEDV Ct values compared to FEED treatments (<i>P</i> < 0.05). Overall, the combination of both feed additives was most effective at reducing the quantity of genetic material as detected by qRT-PCR (<i>P</i> < 0.001) compared to either additive alone or no feed additive. Virus shedding was observed in the d 7 postinoculation SDPP treatment that was treated with both feed additives, as well as d 0 untreated FEED and d 0 FEED treated with both feed additives. No other treatment bioassay room had detectible RNA shed and detected in fecal swabs or cecal contents. In summary, the combination of EO and BA enhanced the degradation of PEDV RNA in feed but had little impact on RNA degradation in SDPP. Both untreated feed and feed treated with the combination of EO and BA resulted in infection at d 0 post-laboratory inoculation; however, neither set of samples was infective at d 1 postinoculation. In addition, SDPP harbored greater levels of quantifiable RNA for a longer duration of time compared to FEED, and these viral particles remained viable for a longer duration of time indicating differences in viral stability exist between different feed matrices.
Serum level of the periostin, a homologue of an insect cell adhesion molecule, as a prognostic marker in nonsmall cell lung carcinomas (2001)

The in situ RNA hybridization data from the current study suggested that expression of periostin may be involved in tumor invasionand that the serum periostin level may serve as a prognostic marker for NSCLC.
Three Systems of Insular Functional Connectivity Identified with Cluster Analysis (2010)

Despite much research on the function of the insular cortex, few studies have investigated functional subdivisions of the insula in humans. The present study used resting-state functional connectivity magnetic resonance imaging (MRI) to parcellate the human insular lobe based on clustering of functional connectivity patterns. Connectivity maps were computed for each voxel in the insula based on resting-state functional MRI (fMRI) data and segregated using cluster analysis. We identified 3 insular subregions with distinct patterns of connectivity: a posterior region, functionally connected with primary and secondary somatomotor cortices; a dorsal anterior to middle region, connected with dorsal anterior cingulate cortex, along with other regions of a previously described control network; and a ventral anterior region, primarily connected with pregenual anterior cingulate cortex. Applying these regions to a separate task data set, we found that dorsal and ventral anterior insula responded selectively to disgusting images, while posterior insula did not. These results demonstrate that clustering of connectivity patterns can be used to subdivide cerebral cortex into anatomically and functionally meaningful subregions; the insular regions identified here should be useful in future investigations on the function of the insula.
Recent developments and concepts in the cryopreservation of spermatozoa and the assessment of their post-thawing function (1995)

New research on the cooling and cryopreservation of mammalian spermatozoa is reviewed in the context of the older literature. Cryoinjury to a variety of cell organelles is regarded as being due to the two major stresses of cryopreservation, i.e., the change in temperature, and the formation and dissolution of ice and its consequences. Since the cryopreservation process involves departure of the cells from and return to body temperature, both cold shock and warm shock are included as potential stresses to be considered, as well as the stages involving cooling below the freezing point of the medium. The causes of cryoinjury are reconsidered and new concepts concerning the influence of osmotic stress are presented. Heterogeneity of the sperm population is discussed in the context of the success with which spermatozoa can be cryopreserved between and within ejaculates and individuals. The functional state of frozen and thawed spermatozoa is examined on the basis of published results of structural and functional tests of sperm competence. The hypothesis is advanced that cryopreserved mammalian spermatozoa are in a state resembling capacitation, which accounts for their relatively reduced longevity and their readiness to undergo egg penetration without incubation. The importance of this to the utilization of cryopreserved spermatozoa is examined, and proposals are made for new avenues of research to overcome these problems.
Microwave dielectric heating of fluids in an integrated microfluidic device (2007)

The ability to selectively and precisely control the temperature of fluid volumes ranging from a few microliters to sub-nanoliters in microfluidic networks is vital for a wide range of applications in micro total analysis systems (μTAS). In this work, we characterize and model the performance of a thin film microwave transmission line integrated with a microfluidic channel to heat fluids with relevant buffer salt concentrations over a wide range of frequencies. A microchannel fabricated in poly(dimethylsiloxane) (PDMS) is aligned with a thin film microwave transmission line in a coplanar waveguide (CPW) configuration. The electromagnetic fields localized in the gap between the signal and ground lines of the transmission line dielectrically heat the fluid in the selected region of the microchannel. Microwave S-parameter measurements and optical fluorescence-based temperature measurements are used with a theoretical model developed based on classical microwave absorption theory to fully characterize the temperature rise of the fluid. We observe a 0.95 °C mW−1 temperature rise at 15 GHz and confirm that the temperature rise of the fluid is predominantly due to microwave dielectric heating.
Mapping of Hsp70‐binding sites on protein antigens (1994)

Hsp70-binding sites were mapped on three antigens, the 16-, 19- and 38-kDa proteins of Mycobacterium tuberculosis, using overlapping synthetic peptides in a competitive-binding assay. In each protein, two or three prominent hsp70-binding sites were identified when peptides 20-amino-acid long were used, predominantly in regions containing clusters of aliphatic amino acids. Although there was an overall concordance in the pattern of peptide binding to hsp70 from bacterial (M. tuberculosis) and mammalian sources (immunoglobulin heavy-chain-binding protein), some differences in the specificity of polypeptide binding and the effect of peptides on ATPase activity were observed.
Generation, purification, and characterization of a recombinant source of human prostate‐specific antigen (1995)

Human prostate-specific antigen (PSA), a 33- to 34-kDa serine proteinase with extensive homology to glandular kallikrein, is a single-chain glycoprotein that contains 7% carbohydrate. The presence of PSA in the serum of patients with prostatic cancer is widely employed as a marker of disease status. PSA has also been thought of as a possible target for use in active specific immunotherapy protocols. To date, the source of PSA employed has been seminal fluid from different individuals; this has raised concerns about differences among PSA batches for standardization of assays. This report is the first description of the production and the purification of a recombinant source of PSA using a baculovirus expression system. A baculovirus recombinant of the cDNA encoding the full length PSA was expressed in insect cells yielding two major immunoreactive products of 31 and 29 kDa. The latter size conforms to the molecular weight of a core preprotein deduced from the sequence of the cDNA insert. The larger protein represents the N-linked glycosylated form of the preprotein. Western blot analysis showed that both the glycosylated and aglycosylated forms of PSA reacted with a polyclonal and two different monoclonal antibodies specific for PSA. bV-PSA, like commercially available PSA, showed also low-molecular-weight immunoreactive products when culture supernatants were concentrated or taken through steps of purification. bV-PSA was purified to a final product consisting of a major 29-kDa protein and a minor 31-kDa protein.(ABSTRACT TRUNCATED AT 250 WORDS)
RAID: high-performance, reliable secondary storage (1994)

Disk arrays were proposed in the 1980s as a way to use parallelism between multiple disks to improve aggregate I/O performance. Today they appear in the product lines of most major computer manufacturers. This article gives a comprehensive overview of disk arrays and provides a framework in which to organize current and future work. First, the article introduces disk technology and reviews the driving forces that have popularized disk arrays: performance and reliability. It discusses the two architectural techniques used in disk arrays: striping across multiple disks to improve performance and redundancy to improve reliability. Next, the article describes seven disk array architectures, called RAID (Redundant Arrays of Inexpensive Disks) levels 0–6 and compares their performance, cost, and reliability. It goes on to discuss advanced research and implementation topics such as refining the basic RAID levels to improve performance and designing algorithms to maintain data consistency. Last, the article describes six disk array prototypes of products and discusses future opportunities for research, with an annotated bibliography disk array-related literature.
Finding the Secret of Image Saliency in the Frequency Domain (2015)

There are two sides to every story of visual saliency modeling in the frequency domain. On the one hand, image saliency can be effectively estimated by applying simple operations to the frequency spectrum. On the other hand, it is still unclear which part of the frequency spectrum contributes the most to popping-out targets and suppressing distractors. Toward this end, this paper tentatively explores the secret of image saliency in the frequency domain. From the results obtained in several qualitative and quantitative experiments, we find that the secret of visual saliency may mainly hide in the phases of intermediate frequencies. To explain this finding, we reinterpret the concept of discrete Fourier transform from the perspective of template-based contrast computation and thus develop several principles for designing the saliency detector in the frequency domain. Following these principles, we propose a novel approach to design the saliency detector under the assistance of prior knowledge obtained through both unsupervised and supervised learning processes. Experimental results on a public image benchmark show that the learned saliency detector outperforms 18 state-of-the-art approaches in predicting human fixations.
Deep Learning in Protein Structural Modeling and Design (2020)

Deep learning is catalyzing a scientific revolution fueled by big data, accessible toolkits, and powerful computational resources, impacting many fields, including protein structural modeling. Protein structural modeling, such as predicting structure from amino acid sequence and evolutionary information, designing proteins toward desirable functionality, or predicting properties or behavior of a protein, is critical to understand and engineer biological systems at the molecular level. In this review, we summarize the recent advances in applying deep learning techniques to tackle problems in protein structural modeling and design. We dissect the emerging approaches using deep learning techniques for protein structural modeling and discuss advances and challenges that must be addressed. We argue for the central importance of structure, following the "sequence <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>→</mml:mo></mml:math> structure <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>→</mml:mo></mml:math> function" paradigm. This review is directed to help both computational biologists to gain familiarity with the deep learning methods applied in protein modeling, and computer scientists to gain perspective on the biologically meaningful problems that may benefit from deep learning techniques.
Structure-Based Design of a Novel Series of Nonpeptide Ligands That Bind to the pp60src SH2 Domain (1997)

The SH2 domain of pp60c-src (Src), a nonreceptor tyrosine kinase, facilitates signal transduction in a number of cell types through binding to cognate phosphorylated protein sequences. Phosphotyrosine-containing peptides have been shown to bind to the Src SH2 domain with micromolar affinity. Guided by the X-ray crystal structure of a phosphorylated peptide bound to the Src SH2 domain, we have designed a de novo series of small molecule ligands that bind with affinity comparable to the parent phosphopeptide. An X-ray crystal structure of the Src SH2 domain bound with a nonpeptide analog from this series verifies interactions targeted in the molecular design. However, a unique mode of binding has been revealed for the P-site phenyl phosphate group of the nonpeptide that differs from that observed for the phosphotyrosine side chain in peptide ligands bound to the Src SH2 domain. This novel binding mode is being used in guiding future design efforts.
Calcium and Colorectal Epithelial Cell Proliferation in Sporadic Adenoma Patients: a Randomized, Double- Blinded, Placebo-Controlled Clinical Trial (1995)

These results support further study of whether alterations in colon cell proliferative kinetics represent true intermediate steps in colon carcinogenesis that can be used to investigate the etiology and prevention of, and whether a higher calcium consumption can reduce the risk of, colon cancer.
Cloning of a Thermomonospora fusca xylanase gene and its expression in Escherichia coli and Streptomyces lividans (1989)

Thermomonospora fusca chromosomal DNA was partially digested with EcoRI to obtain 4- to 14-kilobase fragments, which were used to construct a library of recombinant phage by ligation with EcoRI arms of lambda gtWES. lambda B. A recombinant phage coding for xylanase activity which contained a 14-kilobase insert was identified. The xylanase gene was localized to a 2.1-kilobase SalI fragment of the EcoRI insert by subcloning onto pBR322 and derivatives of pBR322 that can also replicate in Streptomyces lividans. The xylanase activity produced by S. lividans transformants was 10- to 20-fold higher than that produced by Escherichia coli transformants but only one-fourth the level produced by induced T. fusca. A 30-kilodalton peptide with activity against both Remazol brilliant blue xylan and xylan was produced in S. lividans transformants that carried the 2.1-kilobase SalI fragment of T. fusca DNA and was not produced by control transformants. T. fusca cultures were found to contain a xylanase of a similar size that was induced by growth on xylan or Solka Floc. Antiserum directed against supernatant proteins isolated from a Solka Floc-grown T. fusca culture inhibited the xylanase activity of S. lividans transformants. The cloned T. fusca xylanase gene was expressed at about the same level in S. lividans grown in minimal medium containing either glucose, cellobiose, or xylan. The xylanase bound to and hydrolyzed insoluble xylan. The cloned xylanase appeared to be the same as the major protein in xylan-induced T. fusca culture supernatants, which also contained at least three additional minor proteins with xylanase activity and having apparent molecular masses of 43, 23, and 20 kilodaltons.
Mechanisms associated with corpus luteum development (1994)

The transition of a preovulatory follicle into a corpus luteum is a complex process involving mechanisms similar to wound healing and tumor formation. The objective of this review is to focus on mechanisms associated with corpus luteum development with specific attention to the follicular lineage of luteal cells, mechanisms associated with luteinization, and neovascular changes during luteal development. Corpora lutea are a continuation of follicular maturation and form from granulosal and theca interna cells. There is morphological and immunological evidence in ruminant species for the differentiation of granulosal and theca interna cells into large and small steroidogenic luteal cells, respectively. Different morphological, physiological, and biochemical characteristics of large and small luteal cells may reflect different follicular lineages with separate embryological origins. Following the preovulatory gonadotropin surge, follicular cells begin morphological, endocrinological, and biochemical changes associated with luteinization. Luteinization involves the transition of a preovulatory follicle into a highly vascular corpus luteum capable of secreting large quantities of progesterone. In addition, various cell types undergo hyperplasia, hypertrophy, and(or) migration during corpus luteum formation. An essential component of corpus luteum development is the recruitment of a blood supply. The development of a new microcirculatory bed involves breakdown of the follicular basement membrane, endothelial cell migration, endothelial cell proliferation, and development of capillary lumina. This process is regulated by the interaction of angiogenic and antiangiogenic substances. Further clarification of the preceding mechanisms may result in the development of improved methodologies for controlling the time of ovulation and(or) increasing pregnancy rates.
Efficient, Low Operating Voltage Polymer Light-Emitting Diodes with Aluminum as the Cathode Material (1998)

The architecture of polymer light-emitting diodes (LEDs) consists of a thin film of luminescent conjugated polymer sandwiched between two contacts. The difficulty of working with low-workfunction, electron-injecting metals such as calcium, which are generally considered necessary for high luminescence efficiency, has led to relatively high-workfunction metals such as aluminum being examined for their potential as cathode materials. The performance enhancement produced by blending the electroluminescent polymer with a specific class of surfactant molecules is reported.
Regulation of Ethylene-Induced Transcription of Defense Genes (2000)

Ethylene-induced gene expression has been studied in systems in which the biosynthesis of ethylene is stimulated during developmental process such as ripening of fruit, senescence of flower petals, or during pathogen infection. Functional analysis of the promoters of these genes revealed that the ethylene-responsive cis-elements of fruit ripening genes and senescence genes differed from that of defense genes whose expression is induced by ethylene in response to pathogen infection. The ethylene-responsive element identified as the GCC box (AGCCGCC) is commonly found in the promoter region of the ethylene-inducible defense genes. The ethylene responsive element binding factors that interact with the GCC box were demonstrated to be the transcription factors, which respond to extracellular signals to modulate GCC box-mediated gene expression positively or negatively.
Heterogeneous Nucleation of Crystals from Vapor (1954)

A rate equation is derived for heterogeneous nucleation of crystals from the vapor on the basis of an adsorption, surface diffusion, and statistical fluctuation mechanism. It should be emphasized that the term surface diffusion as used in this development does not imply the existence of a gradient. Rather it refers to random movement of absorbed atoms on the subtrate surface. It is shown that this mechanism results in a rate at least 102 to 103 times greater than that calculated on the basis of direct addition of atoms to the critical nucleus from the vapor phase. The equation describes the temperature dependence of existing critical supersaturation data for heterogeneous nucleation. Analysis of the existing data by this treatment permits an evaluation of the standard free energy of adsorption. Particular attention is given to heterogeneous nucleation from atomic beams.
Phase I Study of Adoptive T-Cell Therapy Using Antigen-Specific CD8+ T Cells for the Treatment of Patients With Metastatic Melanoma (2006)

Our data indicate that the adoptive transfer of antigen-specific T cells in melanoma patients can induce clinical tumor-specific immune responses without major adverse effects.
Determination of Single-Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing (2000)

The characterization of naturally occurring variations in the human genome has evoked an immense interest during recent years. Variations known as biallelic Single-Nucleotide Polymorphisms (SNPs) have become increasingly popular markers in molecular genetics because of their wide application both in evolutionary relationship studies and in the identification of susceptibility to common diseases. We have addressed the issue of SNP genotype determination by investigating variations within the Renin-Angiotensin-Aldosterone System (RAAS) using pyrosequencing, a real-time pyrophosphate detection technology. The method is based on indirect luminometric quantification of the pyrophosphate that is released as a result of nucleotide incorporation onto an amplified template. The technical platform employed comprises a highly automated sequencing instrument that allows the analysis of 96 samples within 10 to 20 minutes. In addition to each studied polymorphic position, 5-10 downstream bases were sequenced for acquisition of reference signals. Evaluation of pyrogram data was accomplished by comparison of peak heights, which are proportional to the number of incorporated nucleotides. Analysis of the pyrograms that resulted from alternate allelic configurations for each addressed SNP revealed a highly discriminating pattern. Homozygous samples produced clear-cut single base peaks in the expected position, whereas heterozygous counterparts were characterized by distinct half-height peaks representing both allelic positions. Whenever any of the allelic bases of an SNP formed a homopolymer with adjacent bases, the nonallelic signal was added to those of the SNP. This feature did not, however, influence SNP readability. Furthermore, the multibase reading capacity of the described system provides extensive flexibility in regard to the positioning of sequencing primers and allows the determination of several closely located SNPs in a single run.