gebhart/patrepeval huggingface dataset:
Phenotypic characterization of estrogen-related receptor gamma mutant mice (2006)

Nuclear hormone receptors influence transcription in reproduction, development, and adult physiology by associating with hormones and metabolic intermediates, or in the case of orphan receptors, by acting independently of endocrine or metabolic ligands. A critical role for the orphan receptor, Estrogen-Related Receptor [gamma]; (ERR[gamma]) is indicated by a lack of feeding and neonatal death (&amp;gt;72 hours after birth) of mice deficient in this transcription factor. Analysis of motor function in whole animal or in reduced preparations reveals a significant defect in ERR[gamma]-null animals. Electrophysiologic analysis of isolated lumbar spinal cords has demonstrated an increase in spontaneous activity and a defect in the central pattern generating circuits. ERR[gamma] is robustly expressed in the heart from early development (E8.5) through adulthood. Electrocardiographic analysis of ERR[gamma]-null and heterozygous animals reveals a prolongation of the QRS complex, ST and QT intervals. Isolated primary cardiomyocytes from E18.5 animals display a significant reduction in sodium current, consistent with observed ECG abnormalities. Several ion channels are dysregulated in E18.5 heart, by QPCR. Additionally, derangements of mitochondrial genes have been detected by expression and chromatin IP (ChIP) array analyses. Mitochondrial DNA is increased, per ventricular heart cell, in the ERRγ-nulls and ERR[gamma]- nulls are prone to fasting-induced lactic acidosis. These signs of mitochondrial dysfunction occur despite normal substrate utilization, electron transport chain protein levels, and electron micrographic morphology. ERR[gamma] appears to define the metabolic state of these excitable tissues--loss of which results in subtle, yet lethal alterations in the firing properties of these neurons. Ongoing studies are to define the characteristics of ERR[gamma]-positive cells in the spinal cord, and to determine the contribution of ERR[gamma] to the normal function of excitable cells in the heart and lumbar spinal cord
Inhibition of deoxyhemoglobin S polymerization by bioromatic peptides found to associate with the hemoglobin molecule at a preferred site (1985)

Association of three succinylated biaromatic peptides with deoxyhemoglobin has been measured. These peptides composed of indolyl or phenyl rings were found to have delta G values for their binding to deoxyhemoglobin between -2.9 and -3.4 kcal/mol at 23 degrees C. Binding experiments among these peptides demonstrate one preferred site, one of strongest binding of the peptide to the Hb molecule, as well as the existence of one or more weaker binding sites. Both aromatic side chains and at least one of the terminal carboxyl groups of the succinylated peptides are involved in the interactions with the hemoglobin (Hb) side chains at the preferred binding site. The latter also was found to be capable of binding monocyclic moieties of sufficient hydrophobicity, i.e., indolyl ring compounds. Increases in deoxyhemoglobin S (deoxy-HbS) solubilities in the presence of these three biaromatic peptides show a strong correlation between the values of their dissociation constants and their ability to destabilize deoxy-HbS aggregation. The symmetric site to which the peptides bind must be located at or near a contact site needed to stabilize the deoxy-HbS polymer.
Cytomegalovirus Infection Is Associated With Cardiac Allograft Rejection and Atherosclerosis (1989)

We studied the effects of cytomegalovirus (CMV) infection on 301 cardiac transplant recipients who were treated during the cyclosporine era of immunosuppression (1980 to the present). These patients received varying combinations of cyclosporine, azathioprine, prednisone, rabbit antithymocyte globulin, and OKT3 as their immunosuppressive therapy. Two hundred ten patients were free of CMV infection (non-CMV group). During the same period CMV infection developed in 91 patients, as manifested by a fourfold IgG serologic titer rise, demonstration of CMV inclusion bodies in tissue, or positive cultures for the virus (CMV group). The rate of graft rejection was significantly higher in the CMV group. Graft atherosclerosis was significantly more severe in the CMV group as judged by angiographic criteria or by pathologic study. Patient survival rates were significantly lower in the CMV group. Death caused by graft atherosclerosis was significantly more common among patients in the CMV group. Finally, the graft loss rate (from either death or retransplantation for atherosclerosis) was significantly greater in the CMV group. These data demonstrate that CMV infection in cardiac transplant recipients is associated with more frequent rejection, graft atherosclerosis, and death.
Intravenous Brain-Derived Neurotrophic Factor Reduces Infarct Size and Counterregulates Bax and Bcl-2 Expression After Temporary Focal Cerebral Ischemia (2000)

This study demonstrates a neuroprotective effect of BDNF when delivered intravenously after onset of focal cerebral ischemia. As shown here, one possible mechanism of action of neuroprotection of BDNF after focal ischemia appears to be counterregulation of Bax/Bcl-2 proteins within the ischemic penumbra.
High-power and tunable operation of erbium-ytterbium co-doped cladding-pumped fiber lasers (2003)

We describe erbium-ytterbium co-doped fiber lasers in different free-running and tunable configurations. The lasers were cladding-pumped by high-power multimode diode sources. We compare pumping at 915 and 980 nm. With a free-running laser, we obtained slope efficiencies of up to 50% with 915-nm pumping and 38% with 980-nm pumping, with respect to absorbed pump power. We reached a double-ended output power of 16.8 W from the free-running laser. Thanks to a high rare-earth concentration and a small inner cladding area (possible with the high-brightness pump sources we used), the operating pump absorption of the fiber reached 8 dB/m. With such high absorption, short fibers with high nonlinear thresholds are possible even with cladding pumping. The tunable fiber laser had a tuning range from 1533 to 1600 nm and emitted 6.7 W of output power at 1550nm in a high-brightness, single-polarization, narrow linewidth beam.
Stiffness control of a continuum manipulator in contact with a soft environment (2010)

Stiffness control of a continuum robot can prevent excessive contact forces during robot navigation inside delicate, uncertain and confined environments. Furthermore, it enables the selection of tip stiffnesses that match varying task requirements. This paper introduces a computationally-efficient approach to continuum-robot stiffness control that is based on writing the forward kinematic model as the product of two transformations. The first transformation calculates the non-contact kinematics of the robot and can be formulated based on the specific type of continuum robot under consideration. The second transformation calculates the tip deflection due to applied forces and is efficiently computed using the special Cosserat rod model. To implement a desired tip stiffness, the two transformations are used to solve for the actuator positions that deform the manipulator so as to generate the required tip force at the measured tip position. The efficacy of the proposed controller is demonstrated experimentally on a concentric-tube continuum robot.
Comparative structural studies on the light chains of human immunoglobulins. I. Protein Ka with the Inv(3) allotypic marker. (1975)

The primary structure of the variable region of the human type K Bence-Jones Protein Ka with Inv(3) genetic marker was determined by sequence analysis of 25 major tryptic peptides covering 214 residues isolated from completely reduced and aminoethylated protein. The complete sequences of 18 of these peptides were determined. These comprised the entire variable NH2-terminal half and 7 peptides from the COOH-terminal half of the protein. For the remaining peptides covering the COOH-terminus, only partial sequences or the amino acid compositions were determined. On the basis of these results all the tryptic peptides could be arranged in order. The sequence of the variable region differed from other previosly reported in 21 to 51 residues, but no variation was found in the sequence of the last 107 residues. On the basis of sequence homology the protein was classified in the kI subgroup. A brief discussion of the possible genetic mechanism of sequence variability in relation to subgroup specificity is presented.
Segmentation of pulmonary parenchyma in CT lung images based on 2D Otsu optimized by PSO (2011)

In this paper 2D Otsu algorithm based on particle swarm optimization (PSO) is proposed to segment CT lung images. This method can extract pulmonary parenchyma from multisliced CT images, which is primary step to detect the pulmonary disease such as lung cancer, tumor, and mass cells. In the automated pulmonary disease diagnosis, image segmentation plays an important role and image analysis result are depends mainly on the effectiveness of segmentation. In CT lung image segmentation traditional 2D Otsu thresholding method plays a vital role. But its main drawback is complex computation and computation time is more. This limits the application of this algorithm in real time diagnosis of medical images. In this paper an improved 2D Otsu algorithm based on particle swarm optimization is developed to reduce the complex computation and computation time. The PSO belongs to evolutionary algorithm family it does not need gradient information. Here PSO is used to find the optimal threshold to segment and extract pulmonary parenchyma in less computation time. Experimental results show that the proposed method gives segmentation results similar to 2D Otsu algorithm. The computation time of 2D Otsu is approximately 90secs/slice and for proposed PSO method is less than 1secs/slice. Thus reducing the total time involved in automated CT lung image diagnosis. The effective performance of proposed segmentation method is evaluated and compared with traditional two dimensional Otsu algorithm.
Adoptive T cell therapy for cancer in the clinic (2007)

The transfusion of lymphocytes, referred to as adoptive T cell therapy, is being tested for the treatment of cancer and chronic infections. Adoptive T cell therapy has the potential to enhance antitumor immunity, augment vaccine efficacy, and limit graft-versus-host disease. This form of personalized medicine is now in various early- and late-stage clinical trials. These trials are currently testing strategies to infuse tumor-infiltrating lymphocytes, CTLs, Th cells, and Tregs. Improved molecular biology techniques have also increased enthusiasm and feasibility for testing genetically engineered T cells. The current status of the field and prospects for clinical translation are reviewed herein.
Amino acid sequence of the BSC-1 cell growth inhibitor (polyergin) deduced from the nucleotide sequence of the cDNA. (1988)

The complete amino acid sequence of the BSC-1 cell growth inhibitor, including its precursor polypeptide, is reported. The sequence was deduced from the nucleotide sequence of the cDNA. The N-terminal amino acid sequence of the mature bioactive BSC-1 cell growth inhibitor is identical with the N-terminal sequences of the factors that have been called type beta 2 transforming growth factor and cartilage-inducing factor B, suggesting that these are identical. The complete amino acid sequence of the mature BSC-1 cell growth inhibitor differs from that of human type beta transforming growth factor in 32 of the 112 amino acids. Polyergin is proposed as the name for the BSC-1 cell growth inhibitor.
Emulsion formulations of testosterone for nasal administration (1998)

The nasal route has received a great deal of attention due to the many advantages of nasal delivery over parenteral administration. The male sex hormone testosterone is ineffective when administered orally due to its gut wall and first-pass metabolism. Therefore, an alternative method for delivery would be the intranasal route, if the lack of aqueous solubility can be overcome. In this study a new approach to emulsion formulations of the drug has been proposed based on the hypothesis that increased absorption is possible upon solubilization of the drug and/or prolongation of the formulation residence time in the nose. Three differently charged testosterone submicron size emulsion formulations with various zeta potentials (+24.8, -23.0 and 0.06 mV) were prepared as nasal spray formulations. A dose of approximately 3.8 mg testosterone per rabbit was administered to four rabbits and the bioavailability of the emulsion formulations was assessed and compared with an i.v. formulation via solid-phase extraction, followed by an HPLC analysis method. Statistical analysis of the normalized data indicated a bioavailability of 55, 51 and 37% for positively, negatively and neutrally charged emulsions respectively. The results of this study strongly suggest that emulsion formulations have some potential to be considered for nasal delivery. Further, both the positively and negatively charged emulsion formulations provided a better bioavailability than the neutral charged emulsion, probably indicating that the charged particle interactions between emulsion globules and the mucus layer prolong the contact of drug with nasal membrane thus enhancing drug absorption.
Preliminary ATIS development at MIT (1990)

DARPA has recently initiated a plan for a common spoken language task, to be developed independently by all members of the DARPA community, with the hope that it will provide a mechanism leading to appropriate formal evaluation procedures at the level of spoken language. The task that was selected for this purpose is the Air Travel Information System (ATIS) task, based on selected tables from the Official Airline Guide (OAG). It was decided that the first evaluation would be limited in scope to deal with text input only, and to cover only sentences that could be understood unambiguously out of context. Data have been recorded over the past several months at Texas Instruments, using an interface that involves a "wizard" who fully interprets the meaning of the subject's sentences, and generates database responses using a menu driven data access system.
Technologies for Single-Cell Isolation (2015)

The handling of single cells is of great importance in applications such as cell line development or single-cell analysis, e.g., for cancer research or for emerging diagnostic methods. This review provides an overview of technologies that are currently used or in development to isolate single cells for subsequent single-cell analysis. Data from a dedicated online market survey conducted to identify the most relevant technologies, presented here for the first time, shows that FACS (fluorescence activated cell sorting) respectively Flow cytometry (33% usage), laser microdissection (17%), manual cell picking (17%), random seeding/dilution (15%), and microfluidics/lab-on-a-chip devices (12%) are currently the most frequently used technologies. These most prominent technologies are described in detail and key performance factors are discussed. The survey data indicates a further increasing interest in single-cell isolation tools for the coming years. Additionally, a worldwide patent search was performed to screen for emerging technologies that might become relevant in the future. In total 179 patents were found, out of which 25 were evaluated by screening the title and abstract to be relevant to the field.
Maternal cannabinoid exposure Effects on spermatogenesis in male offspring (1986)

Maternal exposure to cannabinoids influenced spermatogenesis and fertility in their male offspring examined at 60-80 days of age. Approximately 20% less spermatozoa were found in males whose mothers had received either the non-psychoactive cannabinol (CBN) or cannabidiol (CBD) on day 1 postpartum. Males exposed to the major psychoactive component of marihuana, delta 9-tetrahydrocannabinol (THC) appeared to have spermatozoa in number comparable to controls. This finding may be consistent with the additional observation that CBN or CBD, but not THC, reduced the percentage of successful impregnations by cannabinoid-exposed males. However, males exposed to each of these cannabinoids produced significantly less live offspring compared to controls. Plasma levels of testosterone and luteinizing hormone (LH) were reduced significantly in mice exposed to THC on day 12 of gestation, while testicular weight was reduced in adult mice exposed either on day 12 of gestation to CBD or on day 1 post-partum to THC. These results indicate that perinatal exposure to psychoactive and non-psychoactive components of marihuana can produce long-term disruption of testicular function including the spermatogenic as well as the steroidogenic components.
Complete sequence of the heat shock-inducible HSP90 gene of Saccharomyces cerevisiae. (1984)

We have sequenced the yeast HSP90 gene, which encodes the (apparent) Mr = 90,000 heat shock-inducible protein of this organism. All sequences required for the heat shock-regulated expression of this gene reside on a segment of DNA containing no more than 273 nucleotides 5' to the transcription origin. Transcript mapping reveals that the mature hsp90 mRNA contains a 59-nucleotide 5' untranslated segment, a coding segment of 2130 nucleotides (sufficient to encode a protein of Mr = 81,419), and a 3' untranslated segment of 128 nucleotides. Although the sequences surrounding the coding region of the HSP90 gene are quite similar to those surrounding other sequenced yeast genes, we find as well a limited homology between sequences located 5' to this gene and the putative heat shock-regulatory sequences located 5' to the heat shock-inducible genes of Drosophila.
Whole Animal Automated Platform for Drug Discovery against Multi-Drug Resistant Staphylococcus aureus (2014)

Staphylococcus aureus, the leading cause of hospital-acquired infections in the United States, is also pathogenic to the model nematode Caenorhabditis elegans. The C. elegans-S. aureus infection model was previously carried out on solid agar plates where the bacteriovorous C. elegans feeds on a lawn of S. aureus. However, agar-based assays are not amenable to large scale screens for antibacterial compounds. We have developed a high throughput liquid screening assay that uses robotic instrumentation to dispense a precise amount of methicillin resistant S. aureus (MRSA) and worms in 384-well assay plates, followed by automated microscopy and image analysis. In validation of the liquid assay, an MRSA cell wall defective mutant, MW2ΔtarO, which is attenuated for killing in the agar-based assay, was found to be less virulent in the liquid assay. This robust assay with a Z'-factor consistently greater than 0.5 was utilized to screen the Biomol 4 compound library consisting of 640 small molecules with well characterized bioactivities. As proof of principle, 27 of the 30 clinically used antibiotics present in the library conferred increased C. elegans survival and were identified as hits in the screen. Surprisingly, the antihelminthic drug closantel was also identified as a hit in the screen. In further studies, we confirmed the anti-staphylococcal activity of closantel against vancomycin-resistant S. aureus isolates and other Gram-positive bacteria. The liquid C. elegans-S. aureus assay described here allows screening for anti-staphylococcal compounds that are not toxic to the host.
CD73 Is Associated with Poor Prognosis in High-Grade Serous Ovarian Cancer (2015)

The cell surface nucleotidase CD73 is an immunosuppressive enzyme involved in tumor progression and metastasis. Although preclinical studies suggest that CD73 can be targeted for cancer treatment, the clinical impact of CD73 in ovarian cancer remains unclear. In this study, we investigated the prognostic value of CD73 in high-grade serous (HGS) ovarian cancer using gene and protein expression analyses. Our results demonstrate that high levels of CD73 are significantly associated with shorter disease-free survival and overall survival in patients with HGS ovarian cancer. Furthermore, high levels of CD73 expression in ovarian tumor cells abolished the good prognosis associated with intraepithelial CD8(+) cells. Notably, CD73 gene expression was highest in the C1/stromal molecular subtype of HGS ovarian cancer and positively correlated with an epithelial-to-mesenchymal transition gene signature. Moreover, in vitro studies revealed that CD73 and extracellular adenosine enhance ovarian tumor cell growth as well as expression of antiapoptotic BCL-2 family members. Finally, in vivo coinjection of ID8 mouse ovarian tumor cells with mouse embryonic fibroblasts showed that CD73 expression in fibroblasts promotes tumor immune escape and thereby tumor growth. In conclusion, our study highlights a role for CD73 as a prognostic marker of patient survival and also as a candidate therapeutic target in HGS ovarian cancers.
Good Punctured Rate k/k+s Recursive Convolutional Codes with Application to SCCCs (2004)

This paper presents the results of the search for optimum punctured recursive convolutional codes, suitable as outer codes in a serial concatenation of convolutional codes. The mother codes that are punctured are rate 1/2 recursive convolutional codes (RCC) proposed for use in parallel and/or serial concatenation schemes. Extensive tables of optimized systematic and nonsystematic puncturing patterns for various mother codes are presented along with sample simulation results
When is a serum iron really a serum iron? The status of serum iron measurements (1994)

Although serum iron determinations play an important role in the diagnostic process, the accuracy of routine methods is suspect. The poor performance of currently used methods is well documented in the quarterly College of American Pathologists survey reports. Compared with the 1990 method of the International Committee for Standardization in Haematology (ICSH), the 1978 ICSH Reference Method shows a +3.4% bias and the standard method of the National Committee for Clinical Laboratory Standards shows a -17.8% bias for iron results. All routine methods checked--DuPont aca, Abbott TDx, Kodak Ektachem (except one lot), BM/Hitachi 717, and Synermed--show a negative bias over the entire analytical range, a significant negative intercept, and extremely poor correlation with the 1990 ICSH method for iron values < 750 micrograms/L. Individual discrepancies of several hundred percent were observed. Imprecision of the methods is not the reason for these discrepancies. We question whether most routine methods measuring low iron concentrations provide results sufficiently reliable for confirmation of iron deficiency.