gebhart/patrepeval huggingface dataset:
Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile (1969)

The isolation of a new thermophilic bacterium, Thermus aquaticus gen. n. and sp. n., is described. Successful enrichment requires incubation at 70 to 75 C, and the use of nutrient media relatively dilute with respect to the organic components. Strains of T. aquaticus have been isolated from a variety of thermal springs in Yellowstone National Park and from a thermal spring in California. The organism has also been isolated from man-made thermal habitats, such as hot tap water, in geographical locations quite distant from thermal springs. Isolates of T. aquaticus are gram-negative nonsporulating nonmotile rods which frequently form long filaments at supraoptimal temperatures or in the stationary phase. All isolates form a yellow cellular pigment, probably a carotenoid. A characteristic structure formed by all isolates is a large sphere, considerably larger than a spheroplast. These large spheres, as well as lysozyme-induced spheroplasts, are resistant to osmotic lysis. Deoxyribonucleic acid base compositions of four strains were determined by CsCl density gradient ultracentrifugation and found to be between 65.4 and 67.4 moles per cent guanine plus cytosine. The growth of all isolates tested is inhibited by fairly low concentrations of cycloserine, streptomycin, penicillin, novobiocin, tetracycline, and chloramphenicol. Nutritional studies on one strain showed that it did not require vitamins or amino acids, although growth was considerably faster in enriched than in synthetic medium. Several sugars and organic acids served as carbon sources, and either NH(4) (+) or glutamate could serve as nitrogen source. The organism is an obligate aerobe and has a pH optimum of 7.5 to 7.8. The optimum temperature for growth is 70 C, the maximum 79 C, and the minimum about 40 C. The generation time at the optimum is about 50 min. The possible relationships of this new genus to the myxobacteria, flexibacteria, and flavobacteria are discussed.
Serum Immune Responses Predict Rapid Disease Progression among Children with Crohn's Disease: Immune Responses Predict Disease Progression (2006)

The presence and magnitude of immune responses to microbial antigens are significantly associated with more aggressive disease phenotypes among children with CD. This is the first study to prospectively demonstrate that the time to develop a disease complication in children is significantly faster in the presence of immune reactivity, thereby predicting disease progression to more aggressive disease phenotypes among pediatric CD patients.
Advances in Pediatric Intravenous Iron Therapy (2015)

Iron deficiency anemia (IDA) continues to be very common worldwide. Intravenous (IV) iron is an infrequently used therapeutic option in children with IDA despite numerous studies in adults and several small but notable pediatric studies showing efficacy and safety. Presently, the availability of newer IV iron products allows for replacement of the total iron deficit at a single setting. These products appear safer compared to the high molecular weight iron dextrans of the past. Herein, we review the medical literature and suggest that front line use of IV iron should be strongly considered in diseases associated with IDA in children.
Changes in Circulating VEGF Levels in Relation to Clinical Response during Chemotherapy for Metastatic Cancer (2003)

Abnormally high blood levels of vascular endothelial growth factor (VEGF) appear to be associated with a poor prognosis in advanced cancer, probably as a consequence of its angiogenic and immunosuppressive effects. The prognostic significance of changes in VEGF secretion during cancer chemotherapy is still unknown. This study aimed to investigate the relation between VEGF variations and therapeutic results during chemotherapy in advanced malignancies. The study included 90 metastatic cancer patients, 59 with non-small cell lung cancer and 31 with colorectal carcinoma. Chemotherapy consisted of cisplatin plus etoposide for NSCLC and camptothecin for colorectal cancer. Abnormally high (> 2 SD with respect to values in healthy controls) pretreatment VEGF levels were found in 38/90 (42%) patients. The percentage of non-progressive disease in response to chemotherapy was significantly higher in patients with normal levels of VEGF prior to therapy than in those with elevated pretreatment values of VEGF (10/32 vs 4/27; p < 0.05). Moreover, the percentage of VEGF level normalization during chemotherapy was significantly higher in patients with objective tumor response or stable disease than in progressing patients (10/18 vs 0/20; p < 0.001). Finally, among patients with tumor response or disease stabilization, the one-year survival rate was significantly higher in patients with chemotherapy-induced normalization of VEGF than in those with persistently high VEGF blood levels (9/10 vs 3/8; p < 0.05). These results suggest that changes in VEGF levels during chemotherapy may represent a useful biomarker to predict the effect of chemotherapy in terms of tumor response and survival in patients with metastatic solid neoplasms.
Quality of Life Is Markedly Improved in Patients With Fecal Incontinence After Sacral Nerve Stimulation (2012)

Sacral nerve stimulation not only restores or improves continence in treated patients with chronic FI but also improves their quality of life and symptom severity.
On killing. II: The psychological cost of learning to kill. (2001)

Military and law enforcement studies reveal that interpersonal combat is a universal human phobia. Physiological responses include forebrain shutdown and sympathetic arousal. A resistance to killing exists in the midbrain of most healthy members of most species, becoming ascendant when the forebrain shuts down, and can prevent soldiers from performing in combat. The U.S. military has increased participation in killing activities from 20% in World War II to 95% in Vietnam by operantly conditioning responses. Conditioning is achieved through training that closely resembles battle situations and inadvertently occurs when children see violence as entertainment. The price of this conditioning is an increase in post-traumatic stress disorder which can be defrayed through debriefing, social acceptance, and prevention of atrocities. Similar techniques may be used to prevent PTSD in civilian populations involved in tragedies like school shootings.
Requirements for carotenoids in fish diets (1995)

Carotenoids are among the most widespread and important pigment classes in living organisms, and in marine animals, astaxanthin is the most commonly occurring red carotenoid. Carotenoids are vitamin A precursors and are fundamental in photosynthesis and light protection in plants. Increasing attention has been drawn to a possible light protection, cancer prevention and immune enhancement by carotenoids in mammals. Reported functions in fish range from a general enhancement of performance to specific functions in reproduction and metabolism. In this paper, we show that astaxanthin is essential for growth and survival of fish and crawfish, and discuss this fact in relation to the use of purified and semipurified diets in nutritional studies. The similarity in action of astaxanthin and canthaxanthin compared to α-tocopherol (vitamin E) and retinol (vitamin A) suggests that these two carotenoids should be listed among the fat soluble vitamins.
Recognition of mathematics using a two-dimensional trainable context-free grammar (1996)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.
Novel Taxoid-Based Tumor-Targeting Drug Conjugates. (2009)

A long standing problem of conventional cancer chemotherapy is the lack of tumor specificity. Tumor-targeting drug delivery systems have been explored to overcome this problem. These systems combine a powerful cytotoxic anticancer agent with a tumor-targeting molecule via a suitable linker to form highly efficacious drug-conjugates. These conjugates can deliver potent cytotoxic drugs specifically to tumors and cancer cells with minimal systemic toxicity. This article describes the design, development and application of novel taxoid-based tumor-targeting drug-conjugates, which possess excellent specificity and efficacy in vitro and in vivo.
Burkitt Lymphoma in the Mouse (2000)

Chromosomal translocations juxtaposing the MYC protooncogene with regulatory sequences of immunoglobulin (Ig) H chain or kappa (Ig kappa) or lambda (Ig lambda) L chain genes and effecting deregulated expression of MYC are the hallmarks of human Burkitt lymphoma (BL). Here we report that lymphomas with striking similarities to BL develop in mice bearing a mutated human MYC gene controlled by a reconstructed Ig lambda locus encompassing all the elements required for establishment of locus control in vitro. Diffusely infiltrating lymphomas with a typical starry sky appearance occurred in multiple founders and an established line, indicating independence from positional effects. Monoclonal IgM(+)CD5(-)CD23(-) tumors developed from an initially polyclonal population of B cells. These results demonstrate that the phenotype of B lineage lymphomas induced by MYC dysregulation is highly dependent on cooperativity among the regulatory elements that govern expression of the protooncogene and provide a new system for studying the pathogenesis of BL.
Hepatocyte growth factor/scatter factor induces tyrosine phosphorylation of focal adhesion kinase (p125FAK) and promotes migration and invasion by oral squamous cell carcinoma cells. (1994)

Fibroblasts or their conditioned medium stimulated invasion by squamous cell carcinoma cells. The fibroblast-derived activity responsible for increased invasion is the hepatocyte growth factor/scatter factor (HGF/SF), a ligand for the c-Met receptor. HGF/SF stimulated migration of the cells on various extracellular matrix substrates but did not alter their adhesion efficiency nor integrin expression. HGF/SF stimulated motility in a two step process: initially cells spread rapidly and formed focal adhesions, and then they disassembled these condensations, which was followed by increased cell locomotion. The focal adhesions contained vinculin, p125FAK, beta 1 integrin, and phosphotyrosine. Within minutes after exposure of cells to HGF/SF, proteins of 125 and 145 kDa showed elevated tyrosine phosphorylation and were identified as p125FAK and c-Met, respectively. Gradual loss of tyrosine phosphorylation coincided with disruption of focal adhesions and conversion to a motile phenotype. HGF/SF-mediated tyrosine phosphorylation of p125FAK was inhibited by the tyrosine kinase inhibitor, herbimycin A, which also blocked spreading and the migratory response. These results indicate that fibroblast-derived HGF/SF triggers migration through the initial recruiting of integrins, cytoskeletal proteins, and p125FAK into focal adhesions that is dependent on tyrosine kinase activity.
Solar conversion efficiency of photovoltaic and photoelectrolysis cells with carrier multiplication absorbers (2006)

We calculate the maximum power conversion efficiency for conversion of solar radiation to electrical power or to a flux of chemical free energy for the case of hydrogen production from water photoelectrolysis. We consider several types of ideal absorbers where absorption of one photon can produce more than one electron-hole pair that are based on semiconductor quantum dots with efficient multiple exciton generation (MEG) or molecules that undergo efficient singlet fission (SF). Using a detailed balance model with 1 sun AM1.5G illumination, we find that for single gap photovoltaic (PV) devices the maximum efficiency increases from 33.7% for cells with no carrier multiplication to 44.4% for cells with carrier multiplication. We also find that the maximum efficiency of an ideal two gap tandem PV device increases from 45.7% to 47.7% when carrier multiplication absorbers are used in the top and bottom cells. For an ideal water electrolysis two gap tandem device, the maximum conversion efficiency is 46.0% using a SF top cell and a MEG bottom cell versus 40.0% for top and bottom cell absorbers with no carrier multiplication. We also consider absorbers with less than ideal MEG quantum yields as are observed experimentally.
VLSI design of large-scale soft-output MIMO detection using conjugate gradients (2015)

We propose an FPGA design for soft-output data detection in orthogonal frequency-division multiplexing (OFDM)-based large-scale (multi-user) MIMO systems. To reduce the high computational complexity of data detection, our design uses a modified version of the conjugate gradient least square (CGLS) algorithm. In contrast to existing linear detection algorithms for massive MIMO systems, our method avoids two of the most complex tasks, namely Gram-matrix computation and matrix inversion, while still being able to compute soft-outputs. Our architecture uses an array of reconfigurable processing elements to compute the CGLS algorithm in a hardware-efficient manner. Implementation results on Xilinx Virtex-7 FPGA for a 128 antenna, 8 user large-scale MIMO system show that our design only uses 70% of the area-delay product of the competitive method, while exhibiting superior error-rate performance.
Pancreatic beta-cell replication and amelioration of surgical diabetes by Reg protein. (1994)

We previously isolated from a rat regenerating islet cDNA library a gene named Reg, which is expressed in regenerating islets but is not expressed in normal islets. Here we examined the effect of rat Reg protein on pancreatic beta-cell replication using both 90% depancreatized rats and isolated islets. The depancreatized rats that received i.p. administration of recombinant rat Reg protein (1 mg/kg per day) for 2 months showed amelioration of the surgical diabetes, as evidenced by a significant decrease in blood glucose with an increased beta-cell mass in the residual pancreas. In isolated rat islets, Reg protein (18-180 nM: 0.3-3 micrograms/ml) significantly increased [3H]thymidine incorporation into the nuclei of beta cells. These results indicate that Reg protein is a growth factor for pancreatic beta cells and also suggest that the administration of Reg protein could be used as another therapeutic approach for diabetes mellitus.
Chronic Daily Headache in A Tertiary Care Population: Correlation Between the International Headache Society Diagnostic Criteria and Proposed Revisions of Criteria for Chronic Daily Headache (2002)

The International Headache Society (IHS) has been criticized for its approach to classification of chronic daily headache (CDH); Silberstein and Lipton criteria provide an alternative to this approach. The aim of this study is to apply the alternative diagnostic approaches to a sample of CDH patients consulting in specialty care. Our sample consisted of 638 patients with CDH. Patients were classified according to both classification systems. Patients were predominantly female (65.0%), with ages ranging from 11 to 88 years. According to the Silberstein and Lipton classification, we found eight different diagnoses. The most common diagnosis was chronic migraine (87.4%), followed by new daily persistent headache (10.8%). Just six patients had chronic tension-type headache (CTTH). Applying the IHS criteria we found 14 different diagnoses. Migraine was found in 576 (90.2%) patients. CTTH occurred in 621 (97.3%), with only 10 (1.57%) having this as the sole diagnosis. We conclude that both systems allow for the classification of most patients with CDH when daily headache diaries are available. The main difference is that the IHS classification is cumbersome and requires multiple diagnoses. The Silberstein and Lipton system is easier to apply, and more parsimonious. These findings support revision of the IHS classification system to include chronic migraine.
GPU accelerated parallel FFT processing for Fourier transform hyperspectral imaging (2015)

Sequentially processing massive 1D fast Fourier transformations (FFT) on raw interferograms using a CPU has limited the speed of conventional Fourier transform imaging spectrometers (FTIS). This paper reports the implementation of highly paralleled FFT computation using a low-end graphics processing unit (GPU) device for acceleration of this process. Comparison experiment results have demonstrated &#x223C;10&#x2013;30 times acceleration improvement using GPU-based parallel processing over conventional CPU-based serial processing upon the input data with same sizes: GPU processing time of only 630 and 173&#xA0;ms of datacubes with 512&#xD7;512&#xD7;1024 and 64&#xD7;64&#xD7;16&#x2009;&#x2009;k pixels, respectively, has presented its potential for online and even real-time FTIS raw data processing. The addition of a cheap GPU device into any FTIS system involves no optical modifications, so it is a highly cost-effective technique for temporal resolution enhancement of FTIS-based hyperspectral imaging applications.
Quantum Control of Population Transfer in Green Fluorescent Protein by Using Chirped Femtosecond Pulses (1998)

We demonstrate that the methods of quantum control can be applied successfully to very large molecules in room temperature liquid solution. Chirped femtosecond pulses are used to excite a green fluorescent protein mutant in both buffered aqueous solution and solid acrylamide gel. At high energy densities, the fluorescence shows a strong chirp dependence, with positively chirped pulses transferring almost 50% more population to the excited state than negatively chirped pulses. By measuring the photobleaching rate in the gel as a function of pulse chirp, we find that the data are consistent with the bleaching of the protein being due to a thermal mechanism rather than to an excited-state photoreaction.
Glucagon-like peptide (GLP)-2 reduces chemotherapy-associated mortality and enhances cell survival in cells expressing a transfected GLP-2 receptor. (2001)

Chemotherapeutic agents produce cytotoxicity via induction of apoptosis and cell cycle arrest. Rapidly proliferating cells in the bone marrow and intestinal crypts are highly susceptible to chemotherapy, and damage to these cellular compartments may preclude maximally effective chemotherapy administration. Glucagon-like peptide (GLP)-2 is an enteroendocrine-derived regulatory peptide that inhibits crypt cell apoptosis after administration of agents that damage the intestinal epithelium. We report here that a human degradation-resistant GLP-2 analogue, h[Gly2]-GLP-2 significantly improves survival, reduces bacteremia, attenuates epithelial injury, and inhibits crypt apoptosis in the murine gastrointestinal tract after administration of topoisomerase I inhibitor irinotecan hydrochloride or the antimetabolite 5-fluorouracil. h[Gly2]-GLP-2 significantly improved survival and reduced weight loss but did not impair chemotherapy effectiveness in tumor-bearing mice treated with cyclical irinotecan. Furthermore, h[Gly2]-GLP-2 reduced chemotherapy-induced apoptosis, decreased activation of caspase-8 and -3, and inhibited poly(ADP-ribose) polymerase cleavage in heterologous cells transfected with the GLP-2 receptor. These observations demonstrate that the antiapoptotic effects of GLP-2 on intestinal crypt cells may be useful for the attenuation of chemotherapy-induced intestinal mucositis.
Phase II AIDS Malignancy Consortium Trial of Topical Halofuginone in AIDS-Related Kaposi Sarcoma (2010)

Using a novel blinded intrapatient vehicle control design, we conducted a phase II study of topically administered halofuginone, an angiogenesis inhibitor that inhibits collagen type-I and matrix metalloproteinases (MMPs), in patients with AIDS-related Kaposi sarcoma. Serial Kaposi sarcoma biopsies assessed treatment effects on angiogenic factors and Kaposi sarcoma herpesvirus-latency associated nuclear antigen-1 (KSHV-LANA). We observed marked heterogeneity of KSHV-LANA expression. Although the small number of subjects whose response could be evaluated precluded definitive assessment of halofuginone's efficacy, we observed a significant decrease in type-I collagen only in halofuginone-treated lesions, but no effect on MMP-2. The trial design is applicable to future studies of topical agents.
Bim Protein Degradation Contributes to Cisplatin Resistance (2011)

Cisplatin is the first-line chemotherapy for the treatment of several cancers. However, the development of cisplatin resistance represents a major clinical problem, and the mechanisms of acquired resistance are not fully understood. Here we show that degradation of the Bcl-2 homology 3-only proapoptotic protein Bim plays an important role in cisplatin resistance in ovarian cancer. Specifically, we show that treatment of ovarian cancer cells with cisplatin caused Bim phosphorylation and subsequent degradation and that its degradation is associated with cisplatin resistance. We also show that cisplatin treatment caused the activation of ERK, which correlated with Bim phosphorylation and degradation. By inhibiting ERK phosphorylation with the MEK inhibitor and knocking down ERK expression with siRNA, we show that Bim phosphorylation and degradation were blocked, which suggests that Bim is phosphorylated by ERK and that such phosphorylation is responsible for cisplatin-induced Bim degradation. We show that ERK was activated in cisplatin-resistant OV433 cells as compared with their counterpart parental OV433 cells. We also show that Bim was phosphorylated and degraded in cisplatin-resistant OV433 cells but not in the parental OV433 cells. Importantly, we show that inhibition of Bim degradation by the proteasome inhibitor MG132 sensitized resistant OV433 cells to cisplatin-induced death. Taken together, our data indicate that degradation of Bim via ERK-mediated phosphorylation can lead to cisplatin resistance. Therefore, these findings suggest that cisplatin resistance can be overcome by the combination of cisplatin and the proteasome inhibitors in ovarian cancer cells.