gebhart/patrepeval huggingface dataset:
Regulation of expression of the pilA gene in Myxococcus xanthus (1997)

Type IV pili are required for social gliding motility in Myxococcus xanthus. In this work, the expression of pilin (the pilA gene product) during vegetative growth and fruiting-body development was examined. A polyclonal antibody against the pilA gene product (prepilin) was prepared, along with a pilA-lacZ fusion, and was used to assay expression of pilA in M. xanthus in different mutant backgrounds. pilA expression required the response regulator pilR but was negatively regulated by the putative sensor kinase pilS. pilA expression did not require pilB, pilC, or pilT. pilA was also autoregulated; a mutation which altered an invariant glutamate five residues from the presumed prepilin processing site eliminated this autoregulation, as did a deletion of the pilA gene. Primer extension and S1 nuclease analysis identified a sigma54 promoter upstream of pilA, consistent with the homology of pilR to the NtrC family of response regulators. Expression of pilA was found to be developmentally regulated; however, the timing of this expression pattern was not entirely dependent on pilS or pilR. Finally, pilA expression was induced by high nutrient concentrations, an effect that was also not dependent on pilS or pilR.
Language Transfer Hypotheses with Linear SVM Weights (2014)

Language transfer, the characteristic second language usage patterns caused by native language interference, is investigated by Second Language Acquisition (SLA) researchers seeking to find overused and underused linguistic features. In this paper we develop and present a methodology for deriving ranked lists of such features. Using very large learner data, we show our method's ability to find relevant candidates using sophisticated linguistic features. To illustrate its applicability to SLA research, we formulate plausible language transfer hypotheses supported by current evidence. This is the first work to extend Native Language Identification to a broader linguistic interpretation of learner data and address the automatic extraction of underused features on a per-native language basis.
The effect of intracytoplasmic sperm injection and semen parameters on blastocyst development in vitro (2001)

The present study compares the development and quality of blastocysts derived from conventional oocyte insemination with those derived from intracytoplasmic sperm injection (ICSI). Oocytes were collected from patients undergoing ovarian stimulation with human menopausal gonadotrophins for IVF. Patients with normal semen were assigned to conventional oocyte insemination while those with progressive motility <20% and/or normal sperm morphology < or =4% were assigned to ICSI. Resulting embryos were cultured for up to 6 days. The mean number and percentage of embryos reaching the blastocyst stage and the mean number and percentage of blastocysts of high quality on days 5-6 were assessed for both treatment groups and compared. The influence of paternal factors (sperm concentration, motility, progressive motility, morphology) on blastocyst development and quality were assessed by regression analyses. Significantly more ICSI-derived embryos arrested at the 5- to 8-cell stage (P = 0.024) concomitant with the activation of the paternal genome than those derived from conventional oocyte insemination. Significantly fewer ICSI-derived embryos reached the blastocyst stage on days 5-6 (P<0.001) and significantly fewer ICSI-derived embryos were of high quality (P = 0.002) compared with conventional oocyte insemination. When treatment groups were combined and evaluated by regression analysis, progressive motility and sperm morphology were significantly correlated with diminished blastocyst development and quality (P < 0.05). From these data, we conclude that paternal factors and/or performing ICSI in cases of severe male factor infertility may have a detrimental effect on blastocyst development and their quality.
Absence of albumin receptor on brain capillaries in vivo or in vitro (1985)

Hormones and drugs are known to be available for transport into brain and liver in vivo from the circulating albumin-bound pool. An albumin receptor-mediated mechanism is one possible way in which the transport of ligands from the circulating albumin-bound pool into the tissue may be catalyzed. The albumin receptor model was tested for brain in the present studies using both 125I-albumin (labeled by lactoperoxidase) and [3H]albumin (labeled by reductive methylation). The interaction of the labeled albumin with brain capillaries was assessed in vivo with the carotid injection technique in rats and in vitro with isolated bovine brain capillaries. Artifactually high nonspecific binding in both the in vivo and in vitro assays was observed with 125I-albumin. Conversely, the transit time of [3H]albumin through the brain capillaries in vivo was no greater than the transit time of [14C]sucrose. The binding of [3H]albumin to isolated microvessels in vitro was low, less than [3H]inulin and was nonsaturable. In conclusion these studies do not support the albumin receptor model for the transport of albumin-bound ligands into tissues such as brain.
Object Shape and Reflectance Modeling from Color Image Sequence (1997)

9224521. Views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing official policies or endorsements, either expressed or implied, of the United States Government. This thesis describes the automatic reconstruction of 3D object models from observation of real objects. As a result of the significant advancement of graphics hardware and image rendering algorithms, 3D computer graphics capability has become available even on low-end computers. However, it is often the case that 3D object models are created manually by users. That input process is normally time-consuming and can be a bottleneck for realistic image synthesis. Therefore, techniques to obtain object models automatically by observing real objects could have great significance in practical applications. For generating realistic images of a 3D object, two aspects of information are necessary: the object’s shape and its reflectance properties such as color and specularity. A number of techniques have been developed for modeling object shapes by observing real objects. However, attempts to model reflectance properties of real objects have been rather limited. In most cases, modeled reflectance properties are too simple or too complicated to
Mutations within conserved motifs in the 3'-5' exonuclease domain of herpes simplex virus DNA polymerase (1995)

We investigated mutations within the presumed 3′–5′ exonuclease domain of the DNA polymerase from herpes simplex virus type 1. The mutation sites correspond to residues in DNA polymerase I (Escherichia coli) which bind two metal ions that are required for exonuclease function. To evaluate the effect of the herpesvirus mutations on enzymatic activity, we over-expressed the wild-type DNA polymerase and one mutant enzyme using a baculovirus expression system. Both proteins exhibited DNA polymerase activity after partial purification, but the mutant protein was drastically deficient in exonuclease activity. This finding suggests that the herpesvirus exonuclease may utilize the same metal-ion-mediated mechanism employed by DNA polymerase I. We also attempted to transfer each of the mutations into the herpesvirus genome using a marker rescue protocol. Although wild-type sequences could be transferred readily, recombinant viruses carrying mutant sequences were not recovered. We discuss the possibility that the mutations are lethal and suggest mechanisms by which a deficiency in 3′–5′ exonuclease might cause loss of viability.
Online Semi-Supervised Learning on Quantized Graphs (2010)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Isolation and Bacterial Expression of a Murine Alpha Leukocyte Interferon Gene (1984)

A murine alpha interferon gene (MuIFN-alpha A) was isolated from a murine genomic DNA library in phage lambda. The gene was cloned and its sequence determined. It was expressed in Escherichia coli under the control of the trp promoter/operator which resulted in antiviral activity on mouse L-cells. MuIFN-alpha A exhibits 60% homology to HuIFN-alpha A at the amino acid level.
Development of asynchronous, intralingual electrical stimulation to treat obstructive sleep apnea (2004)

We are evaluating the feasibility of using a single intralingual BION/spl trade/ microstimulator to prevent airway obstruction in patients with obstructive sleep apnea (OSA). Neuromuscular and hypoglossal nerve stimulation of the genioglossus have been reported to expand the oropharyngeal airway and reduced the severity of sleep disordered breathing, but currently available technology is invasive and cumbersome. BIONs are chronically implanted, single channel electrical stimulators powered and commanded by inductive coupling. One such microminiature device (16 mm long /spl times/ 2 mm diameter) can be injected submentally into the genioglossus muscle to stiffen and protrude the tongue. Preliminary results suggest that intermittent opening of airway at the same rate but not synchronized to the respiratory cycle may be effective. Research is underway to complete the preclinical studies required to identify the safety, efficacy and practicality of this technology and implantation approach.
Accuracy and Precision of In Vitro Volumetric Measurements by Three-Dimensional Sonography (1996)

The accuracy and precision of volume estimates via three-dimensional ultrasound is at least as good as those obtained via conventional ultrasound.
NFV: state of the art, challenges, and implementation in next generation mobile networks (vEPC) (2014)

As mobile network users look forward to the connectivity speeds of 5G networks, service providers are facing challenges in complying with connectivity demands without substantial financial investments. Network function virtualization (NFV) is introduced as a new methodology that offers a way out of this bottleneck. NFV is poised to change the core structure of telecommunications infrastructure to be more cost-efficient. In this article, we introduce an NFV framework, and discuss the challenges and requirements of its use in mobile networks. In particular, an NFV framework in the virtual environment is proposed. Moreover, in order to reduce signaling traffic and achieve better performance, this article proposes a criterion to bundle multiple functions of a virtualized evolved packet core in a single physical device or a group of adjacent devices. The analysis shows that the proposed grouping can reduce the network control traffic by 70 percent.
Local Crack Closure Measurements: Development of a Measurement System Using Computer Vision and a Far-Field Microscope (1999)

An accurate and relatively simple methodology for estimating crack closure loads has been developed. Using this method, measurements may be taken at a user-specified position behind the crack tip during the entire fatigue crack growth process. The methodology has three distinct components: (a) an imaging system having adequate magnification with minimal distortion, (b) a simple, Windows-based procedure for image acquisition and image analysis, and (c) techniques for applying a random, high contrast pattern on the specimen's surface. To meet the imaging requirements, a far-field microscope objective capable of high magnifications was employed to image small regions on the order of 0.5 mm by 0.5 mm. The regions were near the crack tip. To meet the requirements of a user-friendly system, a Windows-based data-acquisition interface was developed to run the system on a common PC. Using the interface, images are acquired automatically during a loading/unloading cycle and stored digitally. Image analysis is performed on the saved images to rapidly obtain the crack opening displacement as a function of load; these data are used to estimate the crack closure load. Finally, two methodologies for applying a random, high-contrast pattern with average sizes of 4 to 20 μm were developed. The first method uses 11 μm filter paper and a low-pressure compressed air supply to apply small particles of photocopier toner powder to the surface of the specimen. The second method uses contact lithography to achieve a random pattern with smaller feature sizes, on the order of 2 to 8 μm. Baseline tests of the overall system have demonstrated that it is both easy to use and accurate. Specifically, (a) the PC interface has demonstrated that images can be acquired automatically while the loading frame is cycling at 0.01 Hz, and (b) the crack tip opening displacement data have been shown to have errors on the order of 0.05 pixels for the toner powder patterns, corresponding to 27 nm for the magnification used.
Gene expression profiling identifies a subset of adult T-cell acute lymphoblastic leukemia with myeloid-like gene features and over-expression of miR-223 (2010)

Using gene profiling we identified a subset of adult T-cell acute lymphoblastic leukemia, accounting for 10% of the cases analyzed, which displays myeloid features. These cases were not recognized by standard approaches, underlining the importance of gene profiling in identifying novel acute leukemia subsets. The recognition of this subgroup may have clinical, prognostic and therapeutic implications.
Infections caused by Mycobacterium avium complex in immunocompromised patients: diagnosis by blood culture and fecal examination, antimicrobial susceptibility tests, and morphological and seroagglutination characteristics (1985)

The Mycobacterium avium complex, only rarely described as an invasive pathogen in humans, has recently been reported to frequently cause disseminated disease in patients with the acquired immune deficiency syndrome. Between February 1981 and February 1984 at Memorial Sloan-Kettering Cancer Center, 30 patients with acquired immune deficiency syndrome, 3 patients with leukemia, and 2 patients with congenital severe combined immunodeficiency syndrome developed disseminated M. avium complex infection. Mycobacteria were often found in multiple sites both antemortem and postmortem. Blood cultures were a reliable method for detecting disseminated infection, and the new lysis blood culture systems provided an efficient technique for determining the number of organisms per milliliter of blood. Acid-fast stains and cultures of fecal specimens were also helpful in diagnosing infection. Most of the mycobacteria were serovar 4 (77%), and most (86%) produced a deep yellow pigment. All isolates were susceptible to standard concentrations of clofazimine, cycloserine, and ansamycin, but tended to be resistant to isoniazid, streptomycin, ethambutol, ethionamide, and rifampin.
Differential Regulation of Thrombospondin-1 and Thrombospondin-2 After Focal Cerebral Ischemia/Reperfusion (2003)

Robust expression of TSP-1 and TSP-2, 2 major angiostatic factors, was noted in the ischemic brain with different temporal expression profiles from different cellular origins. The expression of these angiostatic factors, especially TSP-2, likely contributes to the spontaneous resolution of postischemic angiogenesis. Further studies are needed to explore the molecular mechanisms that regulate the balance of angiogenic and angiostatic factors in the ischemic brain.
Acute lung injury and acute respiratory distress syndrome (2010)

Every year, more information accumulates about the possibility of treating patients with acute lung injury or acute respiratory distress syndrome with specially designed mechanical ventilation strategies. Ventilator modes, positive end-expiratory pressure settings, and recruitment maneuvers play a major role in these strategies. However, what can we take from these experimental and clinical data to the clinical practice? In this article, we discuss substantial options of mechanical ventilation together with some adjunctive therapeutic measures, such as prone positioning and inhalation of nitric oxide.
Rabies virus glycoprotein. II. Biological and serological characterization (1977)

Purified rabies virus glycoprotein (G) was shown by complement fixation and immunodiffusion tests to be a second distinct antigen of the virus. It it the only structural protein of the virus that induces the formation of virus-neutralizing antibodies and which confers immunity to animals. When the G protein is taken as antigen, the complement fixation test can be used for the assay of virus-neutralizing antibodies. The total protective activity of the virus was recovered in the purified G protein preparation. The protective activity of G protein increased with purification: 9 ng of G protein was required to protect 50% of the mice as compared to 1.63 micrograms of the virus. Selective immunofluorescent membrane staining and immunocytolysis of rabies virus-infected cells were shown to be G protein specific. Due to its purity and potency, the G protein preparation can be considered the ideal human antirabies vaccine.
Characterization of the mouse analogues of CD59 using novel monoclonal antibodies: tissue distribution and functional comparison (2003)

CD59, the sole membrane regulator of the membrane attack complex of complement, is broadly and abundantly expressed in man and other mammals. In mouse, CD59 is encoded by two homologous genes. The expression patterns and functional roles of the proteins encoded by these genes, mCD59a and mCD59b, have not been well characterized. Here we describe the generation of monoclonal and polyclonal antibodies detecting specifically mCD59a and mCD59b. These reagents have been used to study function and to ascertain the cell and tissue distributions of mCD59a and mCD59b. mCD59a was broadly distributed on endothelia, erythrocytes, platelets, and on numerous other cell types in organs, a distribution pattern resembling that of CD59 in other species. In marked contrast, expression of mCD59b was restricted to germ cell elements in the testis and mature spermatozoa. Both mCD59a and CD59b inhibited human and rodent complement with similar efficiency. These findings demonstrate that the broadly distributed mCD59a is the key regulator of the terminal complement pathway in mice whereas CD59b, expressed only in testis and on sperm, probably plays other roles in vivo.
Asymmetric [4 + 3] Cycloadditions between Benzofuranyldiazoacetates and Dienes:  Formal Synthesis of (+)-Frondosin B (2008)

The reaction of benzofuranyldiazoacetates with 1,3-dienes catalyzed by the dirhodium tetracarboxylate Rh2(R-DOSP)4, generates formal [4+3] cycloadducts with >94% de and 91-98% ee. The reaction proceeds by a tandem cyclopropanation/Cope rearrangement followed by a stereoselective tautomerization. This methodology was extended to a formal synthesis of (+)-frondosin B.
Biosynthesis of the Type I and Type II TGF-β Receptors (1997)

The TGF-beta type I and type II receptors (TbetaRI and TbetaRII) are signaling receptors that form heteromeric cell surface complexes with the TGF-betas as one of the earliest events in the cellular response to these multifunctional growth factors. Using TGF-beta-responsive mink lung epithelial cells (Mv1Lu), we have determined the half-lives of the endoplasmic reticulum (ER) and mature forms of these receptors. In metabolically labeled cells, approximately 90% of newly synthesized type II receptor undergoes modification of N-linked sugars in the Golgi, with a half-life of 30-35 min; the Golgi-processed form of the receptor has a relatively short metabolic half-life of 2.5 h. In contrast, only 50% of pulse-labeled type I receptor is converted to the Golgi-processed and therefore endoglycosidase H-resistant form, and the endoglycosidase H-sensitive ER form has a half-life of 2.8-3 h. Addition of 100 pM TGF-beta1 causes the Golgi-processed type II receptor to become less stable, with a half-life of 1.7 h, and also destabilizes the Golgi-processed type I receptor. TGF-beta1 binding and cross-linking experiments on cells treated with tunicamycin for various times confirm different ER to cell surface processing times for TbetaRI and TbetaRII. Our results, which suggest that stable complexes between type I and II TGF-beta receptors do not form until the proteins reach a post-ER compartment (presumably the cell surface), have important implications for our understanding of complex formation and receptor regulation.
Gene Dosage Determines the Negative Effects of Polymorphic Alleles of the P2X7Receptor on Adenosine Triphosphate–Mediated Killing of Mycobacteria by Human Macrophages (2005)

Various polymorphisms in P2X7 abrogate IFN- gamma /ATP-induced killing of mycobacteria by human macrophages and, thus, may contribute to variability in susceptibility to mycobacterial infections.
N-annulated perylene diimide dimers: the effect of thiophene bridges on physical, electronic, optical, and photovoltaic properties (2017)

In this work, we report on the synthesis, characterization, and photovoltaic properties of two new N-annulated PDI derivatives connected with one (<bold>M1</bold>) or two (<bold>M2</bold>) thiophene bridging units and directly compare to a twisted PDI dimer with no thiophene units (<bold>tPDI-Hex</bold>).
Fatty acid transport: difficult or easy? (1998)

Transport of unesterified fatty acids (FA) into cells has been viewed either as a simple diffusion process regulated mainly by lipid physical chemistry or as a more complex process involving protein catalysis. In this review FA transport in cell membranes is broken down into three essential steps: adsorption, transmembrane movement, and desorption. The physical properties of FA in aqueous, membrane, and protein environments relevant to transport mechanisms are discussed, with emphasis on recent information derived from NMR and fluorescence studies. Because of their low solubility in water and high hydrophobicity, FA bind rapidly and avidly to model membranes (phospholipid bilayers); if albumin is a donor, FA desorb rapidly to reach their equilibrium distribution between the membrane and albumin. The ionization properties of FA in a phospholipid bilayer result in a high population of the un-ionized form (approximately 50%) at pH 7.4, which diffuses across the lipid bilayer (flip-flops) rapidly (t(1/2) < 1 sec). Desorption of FA from a phospholipid surface is slower than transmembrane movement and dependent on the FA chain length and unsaturation, but is rapid for typical dietary FA. These physical properties of FA in model systems predict that proteins are not essential for transport of FA through membranes. The only putative FA transport protein to be purified and reconstituted into phospholipid bilayers, the mitochondrial uncoupling protein (UCP1), was shown to transport the FA anion in response to FA flip-flop. New experiments with cells have found that FA movement into cells acidifies the cytosol, as predicted by the flip-flop model.