gebhart/patrepeval huggingface dataset:
Molecular Beacon Lighting up on Graphene Oxide (2012)

A molecular beacon (MB) is comprised of a fluorophore and a quencher linked by a DNA hairpin. MBs have been widely used for homogeneous DNA detection. In addition to molecular quenchers, many nanomaterials such as graphene oxide (GO) also possess excellent quenching efficiency. Most reported fluorescent sensors relied on DNA probes physisorbed by GO, which may suffer from nonspecific probe displacement and false positive signal. In this work, we report the preparation and characterization of a MB using graphene oxide (GO) as quencher, where an amino and FAM (6-carboxyfluorescein) dual labeled DNA was covalently attached to GO via an amide linkage. A major challenge was to remove noncovalently attached probes due to strong DNA adsorption by GO. While DNA desorption was favored at low salt, high pH, high temperature, and by using organic solvents, the cDNA was required to achieve complete desorption of noncovalently linked DNA probes. The DNA adsorption energy was measured using isothermal titration calorimetry, revealing the heterogeneous nature of GO. The covalent probe has a detection limit of 2.2 nM using a sample volume of 0.05 mL. With a 2 mL sample, the detection limit can reach 150 pM. The covalent probe is highly resistant to nonspecific probe displacement and will find applications in serum and cellular samples where high probe stability is demanded.
Nmr Data Handbook for Biomedical Applications (1984)

The text is divided into 10 chapters, each of which covers a specific block of material and has its own references. The volume is meant to serve as a laboratory handbook and a desk reference, containing basic NMR theory, useful formulae and physical constants, and compiled data from the NMR literature. The volume attempts to cover the development of biological NMR through several decades of in vitro experiments that have laid the groundwork for and pointed to profitable areas of investigation for new in vivo techniques.
Path allocation in a three-stage broadband switch with intermediate channel grouping (2002)

A method for path allocation for use with three-stage ATM switches that feature multiple channels between the switch modules in adjacent stages is described. The method is suited to hardware implementation using parallelism to achieve a very short execution time. This allows path allocation to be performed anew in each time slot. A detailed description of the necessary hardware is presented. This hardware counts the number of cells requesting each output module, allocates a path through the intermediate stage of the switch to each cell, and generates a routing tag for each cell, indicating the path assigned to it.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Assessing Small and Medium-Sized Farmers' Willingness to Produce Alternative Biofuel Feedstocks (2015)

The study assessed the willingness of small and medium-sized farmers to produce alternative biofuel crops in Louisiana and Mississippi. Data were collected from a random sample of 304 participants. The results revealed that the majority of the respondents were males, African Americans, over 50 years, part-time farmers, and a third earned less than $1,000 per year from farming. Most of the respondents (75%) indicated an interest in alternative fuel development, and 72% do not use alternative fuels in their operations. Also, a majority of respondents (83%) indicated that they would like to learn more about opportunities for alternative fuel development; 90% were in favor of alternative fuel development, and 87% were in favor of using alternative fuel on-farm. These results will be used to develop outreach programs to increase adoption of alternative crops in Louisiana and Mississippi; thus, increasing the potential for profitability for small and medium-sized farmers.
Transforming growth factor β: a matter of life and death (1994)

A wide variety of functions, many of which represent opposing activities, have been attributed to TGF-beta, a molecule implicated in embryogenesis, development, and immune and inflammatory processes. This paradoxical behavior of promoting or inhibiting cell growth and function, while important in normal physiology and homeostasis, can contribute to or interrupt pathologic sequelae, making TGF-beta a particularly intriguing molecule for study. New transgenic mouse models displaying targeted alterations in TGF-beta 1 expression offer novel and unique opportunities to determine the essential function(s) of TGF-beta.
Hand1 regulates cardiomyocyte proliferation versus differentiation in the developing heart (2006)

The precise origins of myocardial progenitors and their subsequent contribution to the developing heart has been an area of considerable activity within the field of cardiovascular biology. How these progenitors are regulated and what signals are responsible for their development are, however, much less well understood. Clearly, not only is there a need to identify factors that regulate the transition from proliferation of cardioblasts to differentiation of cardiac muscle, but it is also necessary to identify factors that maintain an adequate pool of undifferentiated myocyte precursors as a prerequisite to preventing organ hypoplasia and congenital heart disease. Here, we report how upregulation of the basic helix-loop-helix (bHLH) transcription factor Hand1, restricted exclusively to Hand1-expressing cells, brings about a significant extension of the heart tube and extraneous looping caused by the elevated proliferation of cardioblasts in the distal outflow tract. This activity is independent of the further recruitment of extracardiac cells from the secondary heart field and permissive for the continued differentiation of adjacent myocardium. Culture studies using embryonic stem (ES) cell-derived cardiomyocytes revealed that, in a Hand1-null background, there is significantly elevated cardiomyocyte differentiation, with an apparent default mesoderm pathway to a cardiomyocyte fate. However, Hand1 gain of function maintains proliferating precursors resulting in delayed and significantly reduced cardiomyocyte differentiation that is mediated by the prevention of cell-cycle exit, by G1 progression and by increased cell division. Thus, this work identifies Hand1 as a crucial cardiac regulatory protein that controls the balance between proliferation and differentiation in the developing heart, and fills a significant gap in our understanding of how the myocardium of the embryonic heart is established.
Unified framework for modern synthetic aperture imaging algorithms (1997)

Imaging using synthetic aperture techniques is a mature technique with a host of different reconstruction algorithms available. Often the same basic algorithm has a different name depending on where the particular algorithm is used, since it may have originated from the medical, nondestructive testing, geological, or remote sensing fields. All this adds to confusion for the nonspecialist. This article gives a short historical precise of active synthetic aperture imaging as it applies to airborne, spaceborne, and underwater remote sensing systems using either radar or sonar, then defines some generic imaging geometry and places all the usable synthetic aperture reconstruction algorithms in a unified framework. This is done by the introduction of mapping operators, which simplify the mapping or reformatting of data from one sampling grid to another. Using these operators, readers can see how strip-map synthetic aperture systems (both radar- and sonar-based) differ from spotlight synthetic aperture systems, how the various algorithms fit together, and how the chirp-scaling algorithm is likely to be the reconstruction algorithm of choice for most future strip-map systems, and just why that should be so. Multilook processing and methods to deal with undersampled apertures using postdetection digital spotlighting are put into the same unified framework, as both of these techniques are frequent adjuncts to synthetic aperture imaging. © 1997 John Wiley & Sons, Inc. Int J Imaging Syst Technol, 8, 343–358, 1997
Convective delivery of macromolecules into the naive and traumatized spinal cords of rats (1999)

Direct convective delivery of infusate can be used to distribute macromolecules in a predictable, homogeneous manner over significant volumes of naive and traumatized rat spinal cord. These characteristics make it a valuable tool to investigate the therapeutic potential of various compounds for the treatment of injury and spinal cord disease.
Effects of the Isoform-specific Characteristics of ATF6α and ATF6β on Endoplasmic Reticulum Stress Response Gene Expression and Cell Viability (2007)

The endoplasmic reticulum (ER)-transmembrane proteins, ATF6 alpha and ATF6 beta, are cleaved during the ER stress response (ERSR). The resulting N-terminal fragments (N-ATF6 alpha and N-ATF6 beta) have conserved DNA-binding domains and divergent transcriptional activation domains. N-ATF6 alpha and N-ATF6 beta translocate to the nucleus, bind to specific regulatory elements, and influence expression of ERSR genes, such as glucose-regulated protein 78 (GRP78), that contribute to resolving the ERSR, thus, enhancing cell viability. We previously showed that N-ATF6 alpha is a rapidly degraded, strong transcriptional activator, whereas beta is a slowly degraded, weak activator. In this study we explored the molecular basis and functional impact of these isoform-specific characteristics in HeLa cells. Mutants in the transcriptional activation domain or DNA-binding domain of N-ATF6 alpha exhibited loss of function and increased expression, the latter of which suggested decreased rates of degradation. Fusing N-ATF6 alpha to the mutant estrogen receptor generated N-ATF6 alpha-MER, which, without tamoxifen exhibited loss-of-function and high expression, but in the presence of tamoxifen N-ATF6 alpha-MER exhibited gain-of-function and low expression. N-ATF6 beta conferred loss-of-function and high expression to N-ATF6 alpha, suggesting that ATF6 beta is an endogenous inhibitor of ATF6 alpha. In vitro DNA binding experiments showed that recombinant N-ATF6 beta inhibited the binding of recombinant N-ATF6 alpha to an ERSR element from the GRP78 promoter. Moreover, siRNA-mediated knock-down of endogenous ATF6 beta increased GRP78 promoter activity and GRP78 gene expression, as well as augmenting cell viability. Thus, the relative levels of ATF6 alpha and -beta, may contribute to regulating the strength and duration of ATF6-dependent ERSR gene induction and cell viability.
Structural and functional analysis of the human Y-box binding protein (YB-1) gene promoter (1996)

We have isolated three overlapping genomic clones containing the 5'portion of the human YB-1 gene. These clones span approximately 25 kb of contiguous DNA containing 10 kb of 5' flanking sequence and 15 kb of the gene. The nucleotide sequence of the first exon and of 2000 upstream base pairs (bp) was determined. The first axon is unusually large and contains a 166 bp coding sequence and a 331 bp untranslated region. CpG sequences cover the 5'-end of the YB-1 gene including its first axon and intron as well as the upstream regions. The GC content around the first exon is approximately 70% and a CpG-free region was located in the untranslated sequence. The segment preceding the major transcription initiation site does not contain a TATA box, CCAAT box and the binding sequence for known transcription factors. A transient expression assay using the chloramphenicol acetyltransferase (CAT) gene showed that the sequence from +24 to +281 was critical for CAT expression. Fluorescence in situ hybridization demonstrated the chromosomal locus of YB-1 gene on chromosome 1p34. Polymerase chain reaction analysis on other genomic phage DNAs showed that several clones were derived from pseudogenes.
A20 controls expression of beta-cell regulatory genes and transcription factors (2021)

TNFAIP3 encodes a zinc finger protein called A20, which has potent anti-inflammatory and anti-apoptotic properties. A20 promotes beta-cell survival and protects against islet graft rejection in experimental models. The current study sought to investigate the mechanisms underlying the protective role of A20 in the pancreatic beta-cell. Two islet cell types were used for experiments: the insulin-secreting BRIN-BD11 cell line and human islet cells. A20 was silenced using siRNA against TNFAIP3, and knockdown was confirmed by qPCR and immunostaining of cells. Cell viability, cytotoxicity and apoptosis were assessed using the ApotoxGlo assay. Glucose-stimulated insulin secretion and production of inflammatory cytokines (TNFa, IL1b and IFNg) were measured by ELISA. Expression of beta-cell regulatory genes (Abcc8, Kcnj11, Kcnq1, Gck, Scl2a2) and transcription factors (Hnf1a, Pdx1, Nkx6.1, Ngn3) was determined by qPCR. A20 deficiency increased apoptosis, impaired glucose-induced insulin secretion, and reduced expression of beta-cell regulatory genes and transcription factors. Addition of recombinant A20 normalized gene expression profiles. TNFa, IL1b and IFNg were elevated in A20 deficient cells and found to independently elicit changes in gene expression. Analysis of PCR array data suggests that A20 action in the beta cell is largely, although not exclusively, driven by the P65 subunit of NF-kB. The current report demonstrates a role for A20 in controlling beta-cell integrity and survival, which likely results from the regulation of inflammatory signalling. Of particular note is the impact that A20 deficiency has on the expression of transcription factors regulating the maturation and normal function of beta cells.
Taming the bull: safety in a precise surgical robot (1991)

The authors have developed an image directed robotic system for orthopaedic bone machining applications, aimed initially at cementless total hip replacement surgery. A clinical trial in dogs needing such surgery has begun. The fact that the application requires a robot to move a tool in contact with a patient has motivated the authors to implement a number of redundant consistency checking mechanisms. The paper provides a brief system overview and outlines the requirements defined by the veterinary surgeon who uses the system. It then describes the authors' approach to implementing these requirements and concludes with a few remarks about their experience so far and possible extensions of their work.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Short-Chain Fatty Acids Stimulate Glucagon-Like Peptide-1 Secretion via the G-Protein–Coupled Receptor FFAR2 (2011)

Interest in how the gut microbiome can influence the metabolic state of the host has recently heightened. One postulated link is bacterial fermentation of "indigestible" prebiotics to short-chain fatty acids (SCFAs), which in turn modulate the release of gut hormones controlling insulin release and appetite. We show here that SCFAs trigger secretion of the incretin hormone glucagon-like peptide (GLP)-1 from mixed colonic cultures in vitro. Quantitative PCR revealed enriched expression of the SCFA receptors ffar2 (grp43) and ffar3 (gpr41) in GLP-1-secreting L cells, and consistent with the reported coupling of GPR43 to Gq signaling pathways, SCFAs raised cytosolic Ca2+ in L cells in primary culture. Mice lacking ffar2 or ffar3 exhibited reduced SCFA-triggered GLP-1 secretion in vitro and in vivo and a parallel impairment of glucose tolerance. These results highlight SCFAs and their receptors as potential targets for the treatment of diabetes.
Evidence for an associative mechanism in the phosphoryl transfer step catalyzed by rabbit muscle creatine kinase. (1980)

Creatine kinase does not catalyze the scrambling of 18O in adenosine 5'-[alpha beta-18O, beta-18O2]triphosphate in the absence of creatine, in the presence of L-arginine or taurocyamine (competitive inhibitors of creatine), or in the presence of poor substrates where single turnover experiments were performed. In order to support this prima facie evidence for an associative mechanism of phosphoryl transfer, an investigation was undertaken of 1-carboxymethyl-2-aminoimidazole, a new substrate analogue of creatine. This analogue has a binding constant for rabbit muscle creatine kinase similar to creatine and 1-carboxymethyl-2-iminoimidazolidine, but the initial rate of phoshorylation by MgATP in the presence of creatine kinase is almost 5 orders of magnitude slower. The phosphorylation product, assigned the structure 1-carboxymethyl-2-imino-3-phospho-4-imidazoline is also a poor substrate for the phosphorylation of MgADP by creatine kinase. These observations can be accounted for by an associative SN2(P) mechanism of phosphoryl transfer and by a microenvironment of the enzyme-bound creatine (or creatine analogue) which lowers the pKa of the guanidino group by several pH units compared with that in aqueous solution.
Emergency Department Use of Galectin-3 (2014)

Emergency medicine represents a unique practice environment where diagnostic accuracy, treatment, and critical disposition decisions must occur in a time-sensitive environment intolerant of both errors and inefficiency. These pressures can make an accurate heart failure diagnosis challenging, as it must be predominately based on clinical findings. Although accuracy is improved by natriuretic peptide testing, at some point in the clinical course a disposition is required regardless of diagnostic certainty. Disposition options range widely from expensive and highly specialized intensive care unit admissions to low-tech/low-cost observation management or even discharge directly to home. In this vein, success is predicated on matching patient needs to available resources while minimizing the untimely discharge that results in a return visit to the emergency room. Thus, the role of the emergency physician is to predict the future based on limited objective data. Biomarkers may aid in this task, and the newly available galectin-3 assay may be of particular utility. Elevated galectin-3, reflective of myocardial fibrosis and inflammation, is associated with increased risk of short-term death and the necessity for 30-day rehospitalization. The availability of accurate risk stratification tools for predicting the probability of rehospitalization or death could guide in the matching of resource-intensive heart failure disease management efforts to the higher risk cohort, while simultaneously identifying lower risk candidates for successful observation unit or outpatient management. This article reviews the potential utility of galectin-3 measurement for use in emergency department decision making.
Iron-Clad Fibers: A Metal-Based Biological Strategy for Hard Flexible Coatings (2010)

The extensible byssal threads of marine mussels are shielded from abrasion in wave-swept habitats by an outer cuticle that is largely proteinaceous and approximately fivefold harder than the thread core. Threads from several species exhibit granular cuticles containing a protein that is rich in the catecholic amino acid 3,4-dihydroxyphenylalanine (dopa) as well as inorganic ions, notably Fe3+. Granular cuticles exhibit a remarkable combination of high hardness and high extensibility. We explored byssus cuticle chemistry by means of in situ resonance Raman spectroscopy and demonstrated that the cuticle is a polymeric scaffold stabilized by catecholato-iron chelate complexes having an unusual clustered distribution. Consistent with byssal cuticle chemistry and mechanics, we present a model in which dense cross-linking in the granules provides hardness, whereas the less cross-linked matrix provides extensibility.
Results of nine international pressure ulcer prevalence surveys: 1989 to 2005. (2008)

Pressure ulcers continue to be a significant problem for patients and healthcare facilities. Since 1989, results from the International Pressure Ulcer Prevalence surveys--observational, cross-sectional cohort studies--conducted by Hill-Rom, Batesville, Ind, have been used to document aggregate prevalence rates and provide acute care, long-term acute care, and long-term care facilities with internal and external benchmarks of process improvement. During each of the nine surveys conducted between 1989 and 2005, clinical teams in participating facilities predominantly in the US (some facilities in Canada, Saudi Arabia, and Australia participated after 2003) assessed admitted patients on assigned study dates. For this study, trends using all records (n = 447,930; average, 49,770 per year) were reviewed. The majority of facilities in each survey year were in the US (99% overall). Overall and nosocomial pressure ulcer prevalence rates ranged from 9.2% and 5.6% in 1989 to 15.5% and 10% in 2003 and 2004, respectively. The highest prevalence was documented in long-term acute care (27.3% overall, 8.5% nosocomial). Most commonly, ulcers were located at the sacrum (28%), heels (23.6%), and buttocks (17.2%). Ulcers were more commonly assessed as Stage I and Stage II (>70%). However, in patients with dark skin tone (2004 and 2005 data, n = 162,296), 13% of identified ulcers were Stage I compared to 32% in patients with medium and 38% in patients with light skin tone. Using the most complete data sets (2003, 2004, and 2005), more severe pressure ulcer prevalence (Stage III+) was not found to be age-related. Approximately 48% of all patients who had pressure ulcers and 48% of patients with nosocomial pressure ulcers were assessed at mild or no risk (Braden scale score >14). Prevalence within the Braden Score risk categories aligned with risk for developing pressure ulcers. Despite increased attention to the pressure ulcer problem, prevalence rates from the last five survey years are relatively unchanged.
Laser modulation of angiogenic factor production by T‐lymphocytes (2000)

Background and Objective In previous investigations, small variations in the energy densities of low level light therapy (LLLT) were found to produce significant differences in the proliferation of resting T-lymphocytes in vitro. Pulsing these cells with mitogen in addition to laser therapy produced inhibitory effects regardless of the amplitude of the energy density used. In the current study, the effect of LLLT on the production of angiogenic factor(s) by T-lymphocytes was investigated in vitro. Study Design/Materials and Methods Human T-cells isolated from peripheral blood were prepared in suspension either with or without addition of mitogen. Cell suspensions were irradiated with laser by using the following energy densities: 1.2, 3.6, 6.0, and 8.4 J/cm2. Wavelength, pulsing frequency, and power output were kept constant at 820 nm, 5,000 Hz, and 50 mW, respectively. After either 3 or 5 days of incubation, lymphocyte supernatants were collected and added as conditioned media to cultured endothelial cells (ECs). The effect on the proliferation of these ECs was assessed over a 72-hour period by using a methylene blue assay. Results Endothelial cell proliferation increased significantly when incubated with conditioned media collected from resting T-cells exposed to 1.2 and 3.6 J/cm2. Day 5 conditioned media produced similar patterns of EC proliferation to that of day 3 but at lower magnitude. Pulsing of T-lymphocytes with mitogen in addition to laser irradiation significantly lessened their angiogenic capability. Conditioned media from 3.6 J/cm2 laser-treated T-cells induced the maximal EC proliferation in all groups studied. Conclusion It would seem that laser therapy stimulates lymphocytes to produce factor(s) that can modulate EC proliferation in vitro; this effect on the lymphocytes is influenced by (1) the amplitude of energy density used for T-cell irradiation, (2) exposing T-cells to both mitogen and laser, and (3) the duration of T-cell incubation in culture. Lasers Surg. Med. 26:357–363, 2000 © 2000 Wiley-Liss, Inc.