gebhart/patrepeval huggingface dataset:
Two Generalized Transducing Phages in Vibrio parahaemolyticus and Vibrio alginolyticus (1991)

Two bacteriophages named phi VP253 and phi VP143 isolated after ultraviolet induction from lysogenic strains of Vibrio parahaemolyticus have been shown to be generalized transducing phages. So far, seven different auxotrophic markers of a V. parahaemolyticus strain could be transduced at the frequencies ranging from 2.2 x 10(-7) to 7.5 x 10(-5) per infected cell at the m.o.i. of approximately 1.0. The phage phi VP143, but not phi VP253, lysed 20 of the 28 strains of V. alginolyticus and the occurrence of generalized transduction by this phage in this Vibrio species has been confirmed. Molecular size of the genomes of both phages were estimated to be approximately 48 kb as judged from electrophoretic mobilities of the DNAs digested with HindIII endonuclease. The results and similarity of the two phages in morphology and other properties suggest very close relatedness of the phages.
Affinity maturation of Fab antibody fragments by fluorescent‐activated cell sorting of yeast‐displayed libraries (2003)

We report for the first time the affinity maturation of Fab antibody fragments using fluorescent-activated cell sorting (FACS) of yeast-displayed repertoires. A single yeast display vector which enables the inducible expression of an anchored heavy chain and a soluble light chain has been constructed. The assembly and functional display on the yeast cell surface of Fab antibodies specific for different protein targets has been demonstrated by flow cytometry and immunofluorescence microscopy. We have affinity matured a Fab antibody specific for the tetravalent antigen streptavidin using FACS of yeast-displayed repertoires diversified by error-prone polymerase chain reaction. A panel of variants with up to 10.7-fold improvement in affinity was obtained after selection. Two leading clones, R2H10 (3.2 nM) and R3B1 (5.5 nM), had mutations in light chain complementarity determining region 1 LC-CDR1 (H34R) and LC-CDR3 (Y96H or Y96F) and gave a 10.7-fold and 6.3-fold affinity improvement over the starting antibody, respectively. The ability to efficiently affinity mature Fab antibodies is an important component of the antibody development pipeline and we have shown that yeast display is an efficient method for this purpose.
Therapy of chronic lymphocytic leukemia and cutaneous T-cell lymphoma with T101 monoclonal antibody. (1984)

The findings accompanying the administration of 50 intravenous courses of monoclonal antibody to human T-cell (T101) in eight patients, four with chronic lymphocytic leukemia and four with cutaneous T-cell lymphoma are reported. Infusion rates of 0.7 to 1 mg/min were associated with unacceptable toxicity in the presence of circulating target cells, but slower rates were well-tolerated. Immunofluorescence techniques confirmed that circulating cells did bind the antibody in vivo and were subsequently removed from the circulation. Modulation of the antigen on target cells in the bone marrow and skin has important implications for the schedule of administration of such antibodies, and points out the possible limitation of effector cell-mediated cytotoxicity at the tissue level. Production of anti-mouse antibodies resulted in neutralization of therapy in two patients with cutaneous T-cell lymphoma, and suggests that whether such an anti-mouse response is produced may be secondary to the underlying immune status of the patient or the amount of mouse protein to which immunocompetent cells are exposed. The relative specificity and efficacy of monoclonal antibody therapy is encouraging, but the limited clinical benefit and problems of modulation and anti-mouse antibody production underscore the need for continued research into passive therapy and suggest that cytotoxic conjugates may be of more clinical value.
Crossing the Cultural Divide: How West Michigan Companies can Confront Cultural Issues in India (2005)

India’s vast market of more than a billion people and a burgeoning middle class plays a siren song to American businesses. Many companies, including several from the West Michigan area such as Alticor and Steelcase, have been attracted by the vast potential of India and have invested in operations there. As is common to companies going to a new land, several people management issues have surfaced, pointing out the challenges of running a successful operation in India. How can West Michigan companies surmount the people problems in India? Help is available — help in the form of a major international research project that looks at cultural differences around the world.
Over‐expression of hepatocyte growth factor/scatter factor (HGF/SF) and the HGF/SF receptor (cMET) are associated with a high risk of metastasis and recurrence for children and young adults with papillary thyroid carcinoma (2000)

We conclude that increased cMET and HGF/SF expression is associated with a high risk for metastasis and recurrence in children and young adults with papillary thyroid carcinoma.
Diagnostic techniques for the IBM S/390 600 MHz G5 microprocessor (2003)

This paper describes strategies and techniques used to diagnose failures in the IBM 600 MHz G5 (Generation 5) CMOS microprocessor and associated cache chips. Time-to-market pressure demands quick diagnostic turnaround time while the complexity, density, cycle time, and technology issues of the hardware increase the difficulty of diagnosis. Since G5 first silicon, intense diagnostics and physical failure analysis (PFA) have successfully identified the root cause of many failures, including examples of process, design, and random manufacturing defects. This success is attributed to the three techniques described in this paper. For each technique, an example is presented to demonstrate its effectiveness.
Promoter Polymorphisms in ACE (Angiotensin I–Converting Enzyme) Associated With Clinical Outcomes in Hypertension (2008)

Genetic variants of ACE are suspected risk factors in cardiovascular disease, but the alleles responsible for the variations remain unidentified. To search for regulatory polymorphisms, allelic angiotensin I-converting enzyme (ACE) mRNA expression was measured in 65 heart tissues, followed by genotype scanning of the ACE locus. Marked allelic expression imbalance (AEI) detected in five African-American subjects was associated with single-nucleotide polymorphisms (SNPs) (rs7213516, rs7214530, and rs4290) residing in conserved regions 2-3 kb upstream of ACE. Moreover, each of the SNPs affected transcription in reporter gene assays. SNPs rs4290 and rs7213516 were tested for associations with adverse cardiovascular outcomes in hypertensive patients with coronary disease (International Verapamil SR Trandolapril Study Genetic Substudy (INVEST-GENES), n = 1,032). Both SNPs were associated with adverse cardiovascular outcomes, largely attributable to nonfatal myocardial infarction in African Americans, showing an odds ratio of 6.16 (2.43-15.60) (P < 0.0001) for rs7213516. The high allele frequency in African Americans (16%) compared to Hispanics (4%) and Caucasians (<1%) suggests that these alleles contribute to variation between populations in cardiovascular risk and treatment outcomes.
Compact Hash Tables Using Bidirectional Linear Probing (1984)

An algorithm is developed which reduces the memory requirements of hash tables. This is achieved by storing only a part of each key along with a few extra bits needed to ensure that all keys are stored unambiguously. The fraction of each key stored decreases as the size of the hash table increases. Significant reductions in total memory usage can be achieved especially when the key size is not much larger than the size of a memory index and when only a small amount of data is stored with each key. The algorithm is based on bidirectional linear probing. Search and insertion times are shown by simulation to be similar to those for ordinary bidirectional linear probing.
The neuropeptide galanin modulates behavioral and neurochemical signs of opiate withdrawal (2003)

Much research has focused on pathways leading to opiate addiction. Pathways opposing addiction are more difficult to study but may be critical in developing interventions to combat drug dependence and withdrawal. Galanin decreases firing of locus coeruleus neurons, an effect hypothesized to decrease signs of opiate withdrawal. The current study addresses whether galanin affects morphine withdrawal signs by using a galanin agonist, galnon, that crosses the blood-brain barrier, and mice genetically engineered to under- or overexpress galanin peptide. Galnon significantly decreased morphine withdrawal signs in C57BL/6 mice. Further, knockout mice lacking galanin showed exacerbated morphine withdrawal signs, suggesting that endogenous galanin normally counteracts opiate withdrawal. Transgenic mice overexpressing galanin in noradrenergic neurons also showed decreased morphine withdrawal signs, suggesting a possible neuroanatomical locus for these effects of galanin. Both c-fos immunoreactivity, a marker of neuronal activity, and phosphorylation of tyrosine hydroxylase at Ser-40, a marker of cAMP levels, are decreased in the locus coeruleus by galnon treatment after morphine withdrawal, suggesting a possible molecular mechanism for the behavioral effects of galanin. These studies suggest that galanin normally acts to counteract opiate withdrawal and that small molecule galanin agonists could be effective in diminishing the physical signs of withdrawal.
Conditional Gata4 deletion in mice induces bile acid absorption in the proximal small intestine (2010)

Reduction of intestinal GATA4 activity induces bile acid absorption in proximal small intestine without inducing major changes in bile acid homeostasis. This induction is sufficient to correct bile acid malabsorption caused by ICR in mice.
Modular, open-source software transceiver for PHY/MAC research (2013)

The USRPTM (Universal Software Radio Peripheral) is a software-defined radio platform that has been widely adopted for wireless research in cognitive radio, cellular networks, and other application areas. USRP devices are often used with GNU Radio, a free and open-source DSP framework that allows designers to prototype with a combination of C++, Python, and graphical tools. This paper will investigate various methods that can be used to build complete communications stacks within GNU Radio. These methods will leverage advanced features of UHDTM (USRP Hardware Driver) and GNU radio to implement TDMA, CSMA and FHSS transceivers that can be modified in GNU Radio Companion - a graphical development environment. The implementation will also show how to interact with upper network and application layers, all within GNU Radio. The implementation presented in this paper will be open-source. It can serve as an educational resource, or as a basis for additional research.
The Immunoglobulin Heavy Chain Locus Control Region Increases Histone Acetylation along Linked c-myc Genes (1998)

In chromosome translocations characteristic of Burkitt lymphomas (BL) and murine plasmacytomas, c-myc genes become juxtaposed to immunoglobulin heavy-chain (IgH) sequences, resulting in aberrant c-myc transcription. Translocated c-myc alleles that retain the first exon exhibit increased transcription from the normally minor c-mycpromoter, P1, and increased transcriptional elongation through inherent pause sites proximal to the major c-myc promoter, P2. We recently demonstrated that a cassette derived from four DNase I-hypersensitive sites (HS1234) in the 3′Cα region of the IgH locus functions as an enhancer-locus control region (LCR) and directs a similar pattern of deregulated expression of linked c-mycgenes in BL and plasmacytoma cell lines. Here, we report that the HS1234 enhancer-LCR mediates a widespread increase in histone acetylation along linked c-myc genes in Raji BL cells. Significantly, the increase in acetylation was not restricted to nucleosomes within the promoter region but also was apparent upstream and downstream of the transcription start sites as well as along vector sequences. Histone hyperacetylation of control c-myc genes, which was induced by the deacetylase inhibitor trichostatin A, mimics the effect of the HS1234 enhancer on expression from the c-myc P2 promoter, but not that from the P1 promoter. These results suggest that the HS1234 enhancer stimulates transcription of c-myc by a combination of mechanisms. Whereas HS1234 activates expression from the P2 promoter through a mechanism that includes increased histone acetylation, a general increase in histone acetylation is not sufficient to explain the HS1234-mediated activation of transcription from P1.
Current issues in nutritional management of very low birth weight infants. (2004)

Infants less than 1,500 g birth weight (very low birth weight, VLBW) are at risk for significant nutritional deficiencies. Enhancing nutritional care of these infants during their first months of life may have important short and long-term benefits. In this article we will consider several areas of recent research in the nutritional management of VLBW infants. In particular we will focus on issues related to the introduction and use of enteral nutrition. These issues include avoiding mineral deficiencies, early (minimal) enteral nutrition, human milk fortification, and postdischarge nutrition. Transitioning VLBW infants successfully to enteral nutrition is a key to their achieving adequate growth and development without the long-term risks related to parenteral nutrition. Human milk is a key component of any strategy for enteral nutrition of all infants. Its introduction in the first days of life leads to improved growth and better health outcomes for infants. However, although some nutrients are initially increased in the milk of mothers delivering prematurely, there are inadequate amounts of calcium, phosphorus, zinc and other nutrients to meet the needs of the VLBW infant during growth. Therefore, safe and effective means of fortifying human milk are essential to the care of VLBW infants. The optimal approaches for this fortification and the potential risks related to human milk fortification remain controversial. Limited data are available for the optimal content, initiation and methods for mixing fortifier with human milk.
Multiplexed Immunobead-Based Cytokine Profiling for Early Detection of Ovarian Cancer (2005)

Early detection of ovarian cancer might improve clinical outcome. Some studies have shown the role of cytokines as a new group of tumor markers for ovarian cancer. We hypothesized that a panel comprised of multiple cytokines, which individually may not show strong correlation with the disease, might provide higher diagnostic power. To evaluate the diagnostic utility of cytokine panel, we used a novel multianalyte LabMAP profiling technology that allows simultaneous measurement of multiple markers. Concentrations of 24 cytokines (cytokines/chemokines, growth, and angiogenic factors) in combination with cancer antigen-125 (CA-125), were measured in sera of 44 patients with early-stage ovarian cancer, 45 healthy women, and 37 patients with benign pelvic tumors. Six markers, i.e., interleukin (IL)-6, IL-8, epidermal growth factor (EGF), vascular endothelial growth factor (VEGF), monocyte chemoattractant protein-1 (MCP-1), and CA-125, showed significant differences in serum concentrations between ovarian cancer and control groups. Out of this group, IL-6, IL-8, VEGF, EGF, and CA-125, were used in a classification tree analysis that resulted in 84% sensitivity at 95% specificity. The receiver operator characteristic curve created using the combination of markers produced sensitivities between 90% and 100% in the area of 80% to 90% specificity, whereas the receiver operator characteristic curve for CA-125 alone resulted in sensitivities of 70% to 80%. The classification tree analysis for discrimination of benign condition from ovarian cancer used CA-125, granulocyte colony-stimulating factor (G-CSF), IL-6, EGF, and VEGF resulting in 86.5% sensitivity and 93.0% specificity. The presented data show that simultaneous testing of a panel of serum cytokines and CA-125 using LabMAP technology may present a promising approach for ovarian cancer detection.
Electrowetting-based on-chip sample processing for integrated microfluidics (2004)

In this work, results and data are reported on key aspects of sample processing protocols performed on-chip in a digital microfluidic lab-on-a-chip. We report the results of experiments on aspects of sample processing, including on-chip preconcentration and dilution, on-chip sample injection or dispensing, and sample mixing. It is shown that high speed transport and mixing of analytes and reagents can be performed using biological solutions without system contamination.
Synthesis of silicone graft polymers and a study of their surface active properties (1984)

Abstract Silicone macromers 5 , having a methacryloyl group at one end, and controiled molecular weights, were prepared by anionic polymerization of hexamethylcyclotrisiloxane ( 2 ) and subsequent termination with chlorosilane compounds containing a polymerizable vinyl groups. Graft polymers with siloxane grafts were prepared by copolymerization of these macromers with methyl methacrylate (MMA) or styrene. The surface active properties of MMA‐based graft polymers were investigated by studying the extent of surface modification of films of graft polymer‐poly(methyl methacrylate) blends.
Comprehensive Studies of Drug Resistance Mediated by Overexpression of Response Regulators of Two-Component Signal Transduction Systems in Escherichia coli (2003)

In Escherichia coli, there are 32 open reading frames (ORFs) that are assumed to be response regulator genes of two-component signal transduction systems on the basis of sequence similarities. We cloned all of these 32 ORFs into a multicopy expression vector and investigated whether or not they confer drug resistance via control of drug resistance determinants. Fifteen of these ORFs, i.e., baeR, citB, cpxR, evgA, fimZ, kdpE, narL, narP, ompR, rcsB, rstA, torR, yedW, yehT, and dcuR, conferred increased single- or multidrug resistance. Two-thirds of them conferred deoxycholate resistance. Five of them, i.e., evgA, baeR, ompR, cpxR, and rcsB, modulated the expression of several drug exporter genes. The drug resistance mediated by evgA, baeR, and cpxR could be assigned to drug exporters by using drug exporter gene knockout strains.
Single Photon Emission Computed Tomography and the Source of Lumbar Pain in Advanced Ankylosing Spondylitis (1995)

Spinal pain is a characteristic of ankylosing spondylitis (AS) that can persist indefinitely, even when laboratory indices of inflammation are normal. We used single photon emission computed tomography to study 28 symptomatic patients with established disease, half of whom had complete ankylosis of sacroiliac and one-third of whom had complete ankylosis of intervertebral joints. Pain in the lumbar region was associated with increased uptake of isotope in the facetal joints. There was no relationship of pain with impaired lumbar flexion, erythrocyte sedimentation rate, serum immunoglobulin A nor with radiologic change in the sacroiliac, intervertebral and facetal joints. We suggest that persistent lumbar pain with AS might be associated with facetal joint inflammation and that treatment directed at these sites may be rewarding.
Regiospecific Metalation of Oligobromobenzenes (2003)

The metalation of selected oligobromobenzenes with lithium diisopropylamide (LDA) was investigated. 1,3-Dibromo-substituted benzenes were metalated without special precautions since the resultant 2,6-dibromophenyllithium intermediates are relatively stable under reaction conditions: corresponding benzaldehydes were obtained in good or moderate yields after subsequent quench with N,N-dimethylformamide (DMF). Aryllithium compounds derived from 1,4- and 1,2-dibromobenzene are much less stable, but they could be trapped by the in situ use of chlorotrimethylsilane. The one-pot metalation/disilylation of 1,4-dibromo- and 1,2-dibromobenzene afforded 1,4-dibromo-2,5-bis(trimethylsilyl)benzene and 2,3-dibromo-1,4-bis(trimethylsilyl)benzene, respectively.
Short term benefit of battery depletion in vagus nerve stimulation for epilepsy (2004)

Interest in neurostimulation to treat epilepsy has rekindled over the past decade, with vagus nerve stimulation (VNS) now an accepted part of the algorithm for care of patients with medically refractory epilepsy.1 More than 15 000 VNS devices have been surgically implanted in patients around the world. The reported improvements in seizure control are modest and the mechanism by which VNS may exert its effects is unclear, however, the benefits are presumed to be directly related somehow to the electrical stimulation applied to the nerve. A small number of relevant experimental studies have shown antiepileptic effects related to VNS, although the effects may be non-specific, for example, in rats heating of the tail is equally effective as stimulation of the vagus nerve in …
Hydraulic Fracture Complexity: Diagnosis, Remediation, and Exploitation (2008)

Abstract Recent advances in hydraulic fracture mapping technologies have provided a wealth of information on fracture propagation in numerous geologic settings. Prior to such detailed measurements of actual fracture growth, fracture propagation was either assumed to be simple (single planar fracture) or the complexity was inferred based solely on fracturing pressure data. The nature or detail of this inferred fracture complexity and how it related to actual fracture growth (real fracture geometry) could not be determined. This resulted in significant uncertainty in fracture modeling, treatment designs, and many times, suboptimum field development. This paper illustrates the application of the various methods and techniques available to diagnose fracture complexity, including simple pressure diagnostics such as G-function pressure decline analysis and sophisticated microseismic and tiltmeter fracture mapping technologies. After identifying complexity in hydraulic fracture growth, this information must be integrated with fracture, reservoir, and geologic models to properly evaluate stimulation, completion, and develop options; however, without properly identifying the nature and detail of the fracture complexity, the solution can many times be wrong – resulting in economic loss. This paper documents field observations of different mechanisms that result in fracture complexity and the corresponding physics that govern fracture growth in these reservoirs. These field observations of fracture complexity are supplemented by and related to results from mine-back and core-through experiments to better understand the relationship between fracture complexity, rock properties, and geology. Distinguishing between the various types of fracture complexity and properly modeling these complexities (in both reservoir and fracture models) can lead to significantly different treatment designs and field development strategies. The paper includes field case histories that document how the remediation of fracture complexity can lead to stimulation success, while in other cases it is the exploitation of fracture complexity that is the key to success.