gebhart/patrepeval huggingface dataset:
Organic acids for performance enhancement in pig diets (1999)

Abstract Organic acids and their salts appear to be potential alternatives to prophylactic in-feed antibiotics and growth promoters in order to improve the performance of weaned piglets, fattening pigs and reproductive sows, although their growth-promoting effects are generally less than that of antibiotics. Based on an analysis of published data, the growth-promoting effect of formates, fumarates and citrates did not differ in weaned piglets. In fattening pigs, formates were the most effective followed by fumarates, whereas propionates did not improve growth performance. These acids improved the feedgain ratio of both weaned piglets and fattening pigs. In weaned piglets, the growth-promoting effects of dietary organic acids appear to depend greatly on their influence on feed intake. In sows, organic acids may have anti-agalactia properties. Successful application of organic acids in the diets for pigs requires an understanding of their modes of action. It is generally considered that dietary organic acids or their salts lower gastric pH, resulting in increased activity of proteolytic enzymes and gastric retention time, and thus improved protein digestion. Reduced gastric pH and increased retention time have been difficult to demonstrate, whereas improved apparent ileal digestibilities of protein and amino acids have been observed with growing pigs, but not in weaned piglets. Organic acids may influence mucosal morphology, as well as stimulate pancreatic secretions, and they also serve as substrates in intermediary metabolism. These may further contribute to improved digestion, absorption and retention of many dietary nutrients. Organic acid supplementation reduces dietary buffering capacity, which is expected to slow down the proliferation and|or colonization of undesirable microbes, e.g. Escherichia coli , in the gastro-ileal region. However, reduced scouring has been observed in only a few studies. As performance responses to dietary organic acids in pigs often varies, more specific studies are necessary to elucidate an explanation.
ProjectQ: an open source software framework for quantum computing (2018)

We introduce ProjectQ, an open source software effort for quantum computing. The first release features a compiler framework capable of targeting various types of hardware, a high-performance simulator with emulation capabilities, and compiler plug-ins for circuit drawing and resource estimation. We introduce our Python-embedded domain-specific language, present the features, and provide example implementations for quantum algorithms. The framework allows testing of quantum algorithms through simulation and enables running them on actual quantum hardware using a back-end connecting to the IBM Quantum Experience cloud service. Through extension mechanisms, users can provide back-ends to further quantum hardware, and scientists working on quantum compilation can provide plug-ins for additional compilation, optimization, gate synthesis, and layout strategies.
p53 is essential for chemotherapy-induced hair loss. (2000)

Anticancer drugs stimulate apoptosis in the hair follicles (HF) and cause hair loss, the most common side effect of chemotherapy. In a mouse model for chemotherapy-induced hair loss, we demonstrate that p53 is essential for this process: in contrast to wild-type mice, p53-deficient mice show neither hair loss nor apoptosis in the HF keratinocytes that maintained active proliferation after cyclophosphamide treatment. HF in p53 mutants are characterized by down-regulation of Fas and insulin-like growth factor-binding protein 3 and by increased expression of Bcl-2. These observations indicate that local pharmacological inhibition of p53 may be useful to prevent chemotherapy-associated hair loss.
Use of consomic rats for genomic insights into ventilator-associated lung injury (2007)

Increasing evidence supports the contribution of genetic influences on susceptibility/severity in acute lung injury (ALI), a devastating syndrome requiring mechanical ventilation with subsequent risk for ventilator-associated lung injury (VALI). To identify VALI candidate genes, we determined that Brown Norway (BN) and Dahl salt-sensitive (SS) rat strains were differentially sensitive to VALI (tidal volume of 20 ml/kg, 85 breaths/min, 2 h) defined by bronchoalveolar lavage (BAL) protein and leukocytes. We next exploited differential sensitivities and phenotyped both the VALI-sensitive BN and the VALI-resistant SS rat strains by expression profiling coupled to a bioinformatic-intense candidate gene approach (Significance Analysis of Microarrays, i.e., SAM). We identified 106 differentially expressed VALI genes representing gene ontologies such as "transcription" and "chemotaxis/cell motility." We mapped the chromosomal location of the differentially expressed probe sets and selected consomic SS rats with single BN introgressions of chromosomes 2, 13, and 16 (based on the highest density of probe sets) while also choosing chromosome 20 (low probe sets density). VALI exposure of consomic rats with introgressions of BN chromosomes 13 and 16 resulted in significant increases in both BAL cells and protein (compared to parental SS strain), whereas introgression of BN chromosome 2 displayed a large increase only in BAL protein. Introgression of BN chromosome 20 had a minimal effect. These results suggest that genes residing on BN chromosomes 2, 13, and 16 confer increased sensitivity to high tidal volume ventilation. We speculate that the consomic-microarray-SAM approach is a time- and resource-efficient tool for the genetic dissection of complex diseases including VALI.
The synapsis event in the homologous pairing of DNAs: RecA recognizes and pairs less than one helical repeat of DNA. (1992)

A key step in homologous recombination is the alignment and pairing of homologous DNAs. The Escherichia coli RecA protein initiates pairing by binding to single-strand DNA, forming a helical nucleoprotein filament. We demonstrate that in the presence of the nonhydrolyzable ATP analogue adenosine 5'-[gamma-thio]triphosphate and ADP, RecA can pair a homologous oligonucleotide 15 bases long with a duplex DNA to yield synaptic complexes consisting of the oligonucleotide and duplex DNA stabilized by RecA. RecA can pair as few as eight bases of homology to form such synaptic complexes. The homologous DNAs remain paired to each other upon removal of RecA provided that the length of shared homology is at least 26 base pairs. Based on our findings and the work of others, we propose that in vitro, one helical turn of a RecA nucleoprotein filament containing approximately six RecA monomers and 15 bases of single-strand DNA is the functional unit sufficient to carry out the homology search.
Photodynamic Therapy-Based Dendritic Cell Vaccination Suited to Treat Peritoneal Mesothelioma (2020)

The potential of dendritic cell (DC)-based immunotherapy to treat cancer is, nowadays, well documented. Still, the clinical success of immune checkpoint inhibitors has dampened the interest in anticancer DC vaccination. For highly life-threatening tumors that are regarded as nonimmunogenic, such as mesothelioma, however, T helper 1 immunity-biased DC-based immunotherapy could still represent an attractive strategy. In this study, we took advantage of photodynamic therapy (PDT) to induce immunogenic cell death to generate mesothelioma cell lysates for DC priming and evaluated such a vaccine to treat peritoneal mesothelioma. We found that the white light in vitro activation of the photosensitizer OR141 led to mesothelioma cell death, together with the release of bona fide danger signals that promote DC maturation. The administration of a PDT-based DC vaccine to mice bearing peritoneal mesothelioma led to highly significant survival when compared with sham or control animals treated with anti-CTLA4 antibodies. This was further supported by a strong CD8<sup>+</sup> and CD4<sup>+</sup> T cell response, characterized by an increased proliferation, cytotoxic activities and the expression of activation markers, including interferon gamma (IFN). Moreover, the PDT-based DC vaccine led to a significant increase in IFN<sup>+</sup> T cells infiltered within mesothelioma, as determined by flow cytometry and immunohistochemistry. Finally, in vivo tracking of intraperitoneally administered DCs led us to document rapid chemotaxis towards tumor-occupied lymphatics (vs. lipopolysaccharide (LPS)-treated DC). DCs pulsed with PDT-killed mesothelioma cells also exhibited a significant increase in CCR7 receptors, together with an intrinsic capacity to migrate towards the lymph nodes. Altogether, these results indicate that PDT-based DC vaccination is particularly suited to induce a potent immune response against peritoneal mesothelioma.
Issues related to the driver distraction detection algorithm AttenD (2009)

Driver distraction is a contributing factor to many crashes and a real-time distraction warning system has the potential to mitigate or circumvent many of these crashes. The objective of this paper is to thoroughly describe the distraction detection algorithm AttenD and explain the theory underlying different design choices. Future aspects and distraction warning strategies will be discussed as well. In summary, AttenD is an eye-tracker based distraction detection algorithm which identifies visual distraction in real-time based on single long glances as well as repetitive glances. The core idea of the algorithm is a 2-second time buffer which is decremented when the driver looks away from the road and incremented when the driver looks back at the road. If the buffer runs empty, the driver’s state is classified as distracted.
Potentiation of radiation effects in plateau phase human glioma cells by combination of metabolic inhibitors. (1993)

Effects of glycolytic inhibitor 2-deoxy-D-glucose (2-DG) on radiation damage were studied in a human glioma cell line (BMG-1), grown to confluence in monolayer. After irradiation (60Co-gamma-rays, 2 Gy) and incubation with low concentrations of 2-DG (0.5, 1.25 mM; 2-DG/glucose = 0.1, 0.25; 2 hr), in the absence or presence of respiratory inhibitor KCN (0.5-2 mM), cells were trypsinized and plated to assay radiation induced cytogenetic damage (micronuclei formation). The observations made were: (1) 2-DG and/or KCN treatments did not induce damage in unirradiated cells. (2) Either of these treatments did not increase radiation induced micronuclei formation. (3) Presence of 2-DG along with KCN (1,2 mM) significantly enhanced the radiation induced micronuclei formation. (4) Preliminary experiments by macrocolony assay showed that radiation induced cell death was also significantly increased by the combined treatment. These observations suggest that presence of clinically feasible, low concentrations of 2-DG (2-DG/glucose < 0.5) for short intervals of time after radiation could increase radiation damage in non-cycling, hypoxic tumour cells with impaired oxidative and increased glycolytic energy metabolism.
<title>Combined ultrasound image guidance and therapy using a therapeutic phased array</title> (1998)

Ultrasonic imaging has been suggested for guidance of high intensity focused ultrasound therapy. This is typically implemented using two different ultrasonic transducer systems. However the need for two transducers may pose practical difficulties such as alignment and different coordinate systems. In this paper we investigate the possibility of using the same physical transducer array for performing both therapy and imaging. A spherically shaped 1D 64-element high intensity focused ultrasound transducer capable of operating in therapeutic and imaging modes was designed and fabricated. In vitro experiments were conducted to show that this transducer is capable of creating well defined lesions 30-50 mm deep into bovine muscle samples. Furthermore, an experimental pulse-echo system was designed to collect full synthetic aperture data using this transducer. Images of multiple-wire and speckle-generating phantoms are shown to illustrate the imaging capability of this transducer. Although the image quality achieved with this array is inferior to that obtained by conventional diagnostic imaging transducers, it is sufficiently high to produce image features suitable for guidance.
Feasibility of drug targeting to the retinal pigment epithelium with biodegradable microspheres (1994)

There are several systems of delivering drugs to cells with phagocytic activity. We studied the possibility of targeting drugs to retinal pigment epithelial (RPE) cells with the use of surface-modified microspheres. A fluorescent dye, 1,4-bis[2-(5-phenyloxazolyl)]-benzene (POPOP), was incorporated into microspheres of poly(lactic acid) for use as a marker to evaluate drug delivery. Phagocytosis of the microspheres, with or without gelatin precoating, was carried out at 37 degrees C and 4 degrees C. The cell-incorporated fluorescence of POPOP was measured, and scanning electron microscopy was used to confirm phagocytosis. At 4 degrees C, no uptake of POPOP was noted; however at 37 degrees C, cell-associated fluorescence was observed to increase for up to 24 hr. In comparison with bare microspheres, gelatin precoating significantly enhanced phagocytosis (P < 0.001) at the same incubation times. These results suggested that drug delivery to RPE cells may be feasible by means of surface-modified polymer microspheres.
Measuring c-erbB-2 oncogene amplification in fresh and paraffin-embedded tumors by competitive polymerase chain reaction (1994)

We present an original application of competitive polymerase chain reaction (PCR) for measuring oncogene amplification in DNA from human tumors by simultaneous PCR amplification of genomic DNA with fixed amounts of an internal standard (competitor DNA). Competitors share the same sequence as the target genes but contain an additional 15- to 20-base-pair insert, which allows resolution of the amplified products after polyacrylamide gel electrophoresis and ethidium bromide staining. The gene copy number is derived from the ratio between the intensities of the bands corresponding to the amplified products. Using this procedure, we measured c-erbB-2 amplification in breast and bladder carcinomas in both fresh tumor tissues and paraffin-embedded tissue samples and assessed the precision, sensitivity, and accuracy of the assay. Competitive PCR is a simple, reliable, and accurate method for the evaluation of c-erbB-2 amplification and is potentially suitable for use in the clinical laboratory.
Unanticipated Heterogeneity in Growth Rate and Virulence among Candida albicans AAF1 Null Mutants (1999)

The disruption of a specific gene in Candida albicans is commonly used to determine the function of the gene product. We disrupted AAF1, a gene of C. albicans that causes Saccharomyces cerevisiae to flocculate and adhere to endothelial cells. We then characterized multiple heterozygous and homozygous mutants. These null mutants adhered to endothelial cells to the same extent as did the parent organism. However, mutants with presumably the same genotype revealed significant heterogeneity in their growth rates in vitro. This heterogeneity was not the result of the transformation procedure per se, nor was it caused by differences in the expression or function of URA3, a marker used in the process of gene disruption. The growth rate among the different heterozygous and homozygous null mutants was positively correlated with in vivo virulence in mice. It is possible that the variable phenotypes of C. albicans were due to mutations outside of the AAF1 coding region that were introduced during the gene disruption process. These results indicate that careful phenotypic characterization of mutants of C. albicans generated through targeted gene disruption should be performed to exclude the introduction of unexpected mutations that may influence pathogenicity in mice.
Optimized Message Passing Schedules for LDPC Decoding (2006)

The major drawback of the LDPC codes versus the turbo-codes is their comparative low convergence speed: 25-30 iterations vs. 8-10 iterations for turbo-codes. Recently, Hocevar showed by simulations that the convergence rate of the LDPC decoder can be accelerated by exploiting a `turbo-scheduling' applied on the bit-node messages (rows of the parity check matrix). In this paper, we show analytically that the convergence rate for this type of scheduling is about two times increased for most of the regular LDPC codes. Second we prove that `turbo-scheduling' applied on the rows of the parity check matrix is identical belief propagation algorithm as standard message passing algorithm. Furthermore, we propose two new message passing schedules: 1) a turbo-scheduling is applied on the check-node messages (columns of the parity check matrix); and 2) a hybrid version of both previous schedules where the turbo-effect is applied on both check-nodes and bit-nodes. Frame error rate simulations validate the effectiveness of the proposed schedules
Activity of SU11248, a Multitargeted Inhibitor of Vascular Endothelial Growth Factor Receptor and Platelet-Derived Growth Factor Receptor, in Patients With Metastatic Renal Cell Carcinoma (2005)

SU11248, a multitargeted receptor tyrosine kinase inhibitor of VEGF and PDGF receptors, demonstrates antitumor activity in metastatic RCC as second-line therapy, a setting where no effective systemic therapy is presently recognized. The genetics of RCC and these promising clinical results support the hypothesis that VEGF and PDGF receptor-mediated signaling is an effective therapeutic target in RCC.
Response of malignant glioma cell lines to epidermal growth factor and platelet-derived growth factor in a serum-free medium (1990)

The use of a serum-free culture system for assessing the growth factor responsiveness of malignant glial cells is described. The mitogenic properties of epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) were examined in three human malignant glioma cell lines (T98G, U87, and U138). Each of the three had high-affinity EGF receptors and all responded in a dose-dependent fashion to physiological concentrations of EGF. These cell lines also showed a pronounced mitogenic response to PDGF which equaled or exceeded that achieved with EGF. Simultaneous stimulation with both factors produced an additive response, which approximated that obtained in medium supplemented with 10% fetal calf serum. The authors conclude that functional EGF and PDGF receptors were present in the human malignant glial tumors studied. The response of the human glioma lines to these growth factors in many respects parallels the response seen in fetal astrocytes tested under similar conditions. In contrast, the behavior of two chemically induced rat gliomas (9L and C6) differed significantly from that seen in the human lines, suggesting that the rat lines may not be entirely acceptable as models for studying the growth characteristics of human malignant glial tumors.
Down-regulation of TET2 in CD3⁺ and CD34⁺ cells of myelodysplastic syndromes and enhances CD34⁺ cells proliferation. (2015)

The TET2 expression of in CD3(+) and CD34(+) cells of MDS patients was decreased. Suppression of TET2 expression renders the CD34(+) cells harboring more aggressive phenotype. This preliminary finding suggests that CD34(+) cells lowering expression of TET2 may play an oncogenic role on myeloid tumor and CD3(+) T cells of MDS patients may be derived from the malignant clone.
Intraprostatic Androgens and Androgen-Regulated Gene Expression Persist after Testosterone Suppression: Therapeutic Implications for Castration-Resistant Prostate Cancer (2007)

Androgen deprivation therapy (ADT) remains the primary treatment for advanced prostate cancer. The efficacy of ADT has not been rigorously evaluated by demonstrating suppression of prostatic androgen activity at the target tissue and molecular level. We determined the efficacy and consistency of medical castration in suppressing prostatic androgen levels and androgen-regulated gene expression. Androgen levels and androgen-regulated gene expression (by microarray profiling, quantitative reverse transcription-PCR, and immunohistochemistry) were measured in prostate samples from a clinical trial of short-term castration (1 month) using the gonadotropin-releasing hormone antagonist, Acyline, versus placebo in healthy men. To assess the effects of long-term ADT, gene expression measurements were evaluated at baseline and after 3, 6, and 9 months of neoadjuvant ADT in prostatectomy samples from men with localized prostate cancer. Medical castration reduced tissue androgens by 75% and reduced the expression of several androgen-regulated genes (NDRG1, FKBP5, and TMPRSS2). However, many androgen-responsive genes, including the androgen receptor (AR) and prostate-specific antigen (PSA), were not suppressed after short-term castration or after 9 months of neoadjuvant ADT. Significant heterogeneity in PSA and AR protein expression was observed in prostate cancer samples at each time point of ADT. Medical castration based on serum testosterone levels cannot be equated with androgen ablation in the prostate microenvironment. Standard androgen deprivation does not consistently suppress androgen-dependent gene expression. Suboptimal suppression of tumoral androgen activity may lead to adaptive cellular changes allowing prostate cancer cell survival in a low androgen environment. Optimal clinical efficacy will require testing of novel approaches targeting complete suppression of systemic and intracrine contributions to the prostatic androgen microenvironment.
Detection of Giardia cysts by using the polymerase chain reaction and distinguishing live from dead cysts (1991)

A method was developed for the detection of Giardia cysts by using the polymerase chain reaction (PCR) and the giardin gene as the target. DNA amplification by PCR, using giardin DNA as the target, resulted in detection of both live and dead cysts. When giardin mRNA was used as the target, the ability to amplify cDNA by PCR depended on the mode of killing. Cysts killed by freezing were not detected by PCR when giardin mRNA was the target. Cysts killed by heating or exposure to monochloramine, however, gave positive detection signals for both DNA and giardin mRNA targets. The amount of giardin mRNA and total RNA was significantly increased in live cysts following the induction of excystation. Cysts killed by freezing, heating, or exposure to monochloramine did not show a change in RNA content. The detection of the giardin gene by PCR permits a sensitive and specific diagnosis for Giardia spp. Discrimination between live and dead cysts can be made by measuring the amounts of RNA or PCR-amplified product from the giardin mRNA target before and after the induction of excystation.