gebhart/patrepeval huggingface dataset:
ViewBox: integrating local file systems with cloud storage services (2014)

Cloud-based file synchronization services have become enormously popular in recent years, both for their ability to synchronize files across multiple clients and for the automatic cloud backups they provide. However, despite the excellent reliability that the cloud back-end provides, the loose coupling of these services and the local file system makes synchronized data more vulnerable than users might believe. Local corruption may be propagated to the cloud, polluting all copies on other devices, and a crash or untimely shutdown may lead to inconsistency between a local file and its cloud copy. Even without these failures, these services cannot provide causal consistency.To address these problems, we present ViewBox, an integrated synchronization service and local file system that provides freedom from data corruption and inconsistency. ViewBox detects these problems using ext4-cksum, a modified version of ext4, and recovers from them using a user-level daemon, cloud helper, to fetch correct data from the cloud. To provide a stable basis for recovery, ViewBox employs the view manager on top of ext4-cksum. The view manager creates and exposes views, consistent in-memory snapshots of the file system, which the synchronization client then uploads. Our experiments show that ViewBox detects and recovers from both corruption and inconsistency, while incurring minimal overhead.
Large scale isolation, growth, and function of porcine neonatal islet cells. (1996)

Based upon existing methods of isolating fetal porcine islet tissue, a simple, reliable procedure was developed for the preparation of porcine neonatal islet cell aggregates with a reproducible and defined cellular composition. After 9 d of in vitro culture, tissue from one neonatal pig pancreas yielded approximately 50,000 islet cell aggregates, consisting of primarily epithelial cells (57%) and pancreatic endocrine cells (35%). During the culture period, the total beta cell mass decreased initially, but subsequently increased 1.5-fold between days 3 and 9. Transplantation of grafts consisting of 3 x 10(5) beta cells (1,000 aggregated) under the kidney capsule of alloxan-diabetic nude mice corrected hyperglycemia in 75% (10/13) of the animals, whereas, 100% (20/20) of recipients implanted with 6 x 10(5) beta cells (2,000 aggregates) achieved euglycemia within 8 wk posttransplantation. Nephrectomy of the graft bearing kidney at 14 wk posttransplantation resulted in hyperglycemia in all recipients, and examination of the grafts revealed the presence of numerous well-granulated insulin- and glucagon-containing cells. The cellular insulin content of these grafts was 20 to 30-fold higher than at the time of transplantation. These results indicate that the neonatal porcine pancrease can be used as a source of large numbers of viable islet cells, which have the potential for growth both in vitro and in vivo, and exhibit the metabolic capacity to correct diabetes in nude mice.
A robust dead-reckoning pedestrian tracking system with low cost sensors (2011)

The emergence of personal mobile device with low cost sensors, such as accelerometer and digital compass, has made dead-reckoning (DR) an attractive choice for indoor pedestrian tracking. In this paper, we propose a robust DR pedestrian tracking system on top of such commercially accessible sensor sets capable of DR. The proposed method exploits the fact that, multiple DR systems, carried by the same pedestrian, have stable relative displacements with respect to the center of motion, and therefore to each other. We first formulate the robust tracking task as a generalized maximum a posteriori sensor fusion problem, and then we narrow it to a simple computation procedure with certain assumptions. A prototype is implemented and evaluated with a benchmark system that collects ground truth efficiently and accurately. In a practical indoor testbed, the proposed scheme has exhibited robust tracking performance, with reduction in average tracking error up to 73.7%, compared to traditional DR tracking methods.
Cell studies of the DNA bis-intercalator Delta-Delta [micro-C4(cpdppz)2-(phen)4Ru2]4+: toxic effects and properties as a light emitting DNA probe in V79 Chinese hamster cells (2002)

Coordination complexes of type [Ru(L)(3)](2+), where L is a nitrogen-containing aromatic bidentate ligand, can often be photolytically reduced, making them useful in studies of DNA- or protein-mediated electron transfer and in artifical photosynthesis model systems. Upon binding to DNA some Ru(L) complexes have been found to display strongly increased fluorescence compared with when free in solution, making those compounds interesting to test as DNA probes. Thus, they are becoming widely used in the chemistry community. Here, asynchronous cultures of V79 Chinese hamster cells were exposed to the DNA bis-intercalator Delta-Delta [mu-C4(cpdppz)(2)-(phen)(4)Ru(2)](4+) at 10(-10)-10(-4) M. The extraordinarily strong binding of the compound to DNA was the reason for testing its possible interference with DNA metabolism in intact mammalian cells. Exposure for 1 h to 10(-10)-10(-4) M did not significantly decrease DNA synthesis. Cells exposed to 10(-5) M for 27 h showed no staining of the nucleus, while DNA was stained in cells electroporated in the presence of the compound. However, the Ru dimer was probably taken up by pinocytosis, because numerous minute precipitates could be observed in the cytoplasm. Treatment for 24 h at concentrations of 10(-10)-10(-5) M did not inhibit growth, as indicated by cell density and mitotic activity. Neither did it affect chromosomal arrangements during mitosis. However, at 10(-4) M the density of cultures was reduced by approximately 45% and apoptotic cells were frequent, as opposed to mitoses. We also investigated the properties of the Ru dimer as a fluorescent DNA stain. The compound appears attractive as a red DNA stain when broad excitation in the visible range is desirable and extremely low background staining is essential. The low toxicity of the compound is a favourable trait in this context.
Redirecting Specificity of T-Cell Populations For CD19 Using the Sleeping Beauty System (2008)

Genetic modification of clinical-grade T cells is undertaken to augment function, including redirecting specificity for desired antigen. We and others have introduced a chimeric antigen receptor (CAR) to enable T cells to recognize lineage-specific tumor antigen, such as CD19, and early-phase human trials are currently assessing safety and feasibility. However, a significant barrier to next-generation clinical studies is developing a suitable CAR expression vector capable of genetically modifying a broad population of T cells. Transduction of T cells is relatively efficient but it requires specialized manufacture of expensive clinical grade recombinant virus. Electrotransfer of naked DNA plasmid offers a cost-effective alternative approach, but the inefficiency of transgene integration mandates ex vivo selection under cytocidal concentrations of drug to enforce expression of selection genes to achieve clinically meaningful numbers of CAR(+) T cells. We report a new approach to efficiently generating T cells with redirected specificity, introducing DNA plasmids from the Sleeping Beauty transposon/transposase system to directly express a CD19-specific CAR in memory and effector T cells without drug selection. When coupled with numerical expansion on CD19(+) artificial antigen-presenting cells, this gene transfer method results in rapid outgrowth of CD4(+) and CD8(+) T cells expressing CAR to redirect specificity for CD19(+) tumor cells.
Systematic Identification of H274Y Compensatory Mutations in Influenza A Virus Neuraminidase by High-Throughput Screening (2012)

Compensatory mutations contribute to the appearance of the oseltamivir resistance substitution H274Y in the neuraminidase (NA) gene of H1N1 influenza viruses. Here, we describe a high-throughput screening method utilizing error-prone PCR and next-generation sequencing to comprehensively screen NA genes for H274Y compensatory mutations. We found four mutations that can either fully (R194G, E214D) or partially (L250P, F239Y) compensate for the fitness deficiency of the H274Y mutant. The compensatory effect of E214D is applicable in both seasonal influenza virus strain A/New Caledonia/20/1999 and 2009 pandemic swine influenza virus strain A/California/04/2009. The technique described here has the potential to profile a gene at the single-nucleotide level to comprehend the dynamics of mutation space and fitness and thus offers prediction power for emerging mutant species.
Special regulatory T‐cell review: regulatory T cells and the intestinal tract – patrolling the frontier (2007)

Tolerance to self and harmless antigens is one of the central features of the immune system, and it is obtained through a combination of multiple mechanisms. Discriminating between pathogens and non-pathogenic antigens is especially important in the intestine, which constitutes the main contact surface between the body and the outside environment. Recently, the role of Foxp3+ regulatory T cells (Treg) in the establishment and maintenance of tolerance has been the focus of numerous studies. In this review, we briefly discuss the historical background leading to the identification of Foxp3+ Treg and give an overview of their role in controlling systemic and mucosal immune responses.
Determination of Dose Rate of Florfenicol in Feed for Control of Mortality in Channel Catfish Ictalurus punctatus (Rafinesque) Infected with Edwardsiella ictaluri, Etiological Agent of Enteric Septicemia (2004)

Abstract –A dose titration study was conducted to determine the appropriate dosage of florfenicol in feed to control mortality in channel catfish Ictalurus punctatus associated with enteric septicemia of catfish caused by Edwardsiella ictaluri. Six tanks (20 fish/ tank) were assigned to each of the following treatment: 1) not challenged with E. ictaluri and fed unmedicated feed; 2) challenged with E. ictaluri and fed unmedicated feed; 3) challenged and fed 5‐mg florfenicol/kg body weight (kg bw); 4) challenged and fed 10‐mg florfenicol/kg bw; or 5) challenged and fed 15‐mg florfenicol/kg bw. Treatment was initiated the day after inoculation, and feed was administered by hand at 2.5% body weight for 10 consecutive days. Feeding activity was scored for all groups and was noted to be significantly less than the challenged, unmedicated group. Cumulative mortality in the challenged untreated group was 60%. The mortality in the unchallenged untreated group was 0%, and in die 5‐, 10‐, 15‐mg florfenicol/kg bw group was 2.5%, 0.8%, and 2.5%, respectively. The mortality in each challenged, treated group and the non‐challenged control group was significantly less than the challenged, unmedicated controls (P &lt; 0.0001 for each contrast). There were no pairwise statistically significant contrasts among the florfenicol treated groups and the non‐challenged control group. All 600 fish in the study were necropsied, cultured for bacteria, and examined by gross pathology. No specific lesions that could be associated with the antibiotic were observed. The efficacy of the 10 mg/kg dosage was confirmed in a separate dose confirmation study. In this study, fish in 30 tanks (20 fish/ tank) were infected with E. icraluri by immersion. Two days post‐inoculation, fish in 15 tanks were hand‐fed unmedicated feed, and 15 tanks were hand‐fed medicated feed at a dosage of 10‐mg florfenicol/kg bw at 2.5% body weight for 10 d. Feeding activity was scored and was noted to be significantly less than the challenged, unmedicated group. Cumulative mortality in the florfenicol group (14%) was significantly less than cumulative mortality in the untreated group (87.3%) (P &lt; 0.0001). All 600 fish were submitted for bacterial culture, necropsied. and examined for gross pathology, and once again, no specific lesions that could be associated with the antibiotic were observed. The minimum inhibitory concentration of florfenicol against E. ictaluri in both studies was 0.25 ug/mL. Florfenicol was palatable, safe , and efficacious for control of mortality due to infection by E. ictaluri in catfish.
[Cytokeratins, markers of epithelial cell differentiation: expression in normal epithelia]. (1992)

Intermediate filaments, the most stable of cytoskeleton components, are extremely diverse and usually correlate with the histological subtype since in nearly all cell types a single type of intermediate filament (IF) is found. The cytokeratins, which are specific of epithelia, are the largest and most diverse class of intermediate filaments. Twenty different cytokeratin polypeptides have been identified in humans and separated on the basis of isoelectrical pH and apparent molecular weight using two-dimensional electrophoresis. These data have been used to establish a cytokeratin catalogue which currently serves as a reference [43, 48]. The number of cytokeratin polypeptides expressed ranges from 2 to 5 for each epithelial cell and from 2 to 10 for each epithelium and even of each cell layer within a given epithelium. A broad spectrum of anticytokeratin antibodies with subgroup or single polypeptide specificity is currently available. The distribution of cytokeratins in normal epithelia is reviewed herein and commercially available anti-cytokeratin antibodies are listed.
Protein Kinase D (2000)

Protein kinase Cs (PKCs) are activated by antigen receptors in lymphocytes, but little is known about proximal targets for PKCs in antigen receptor-mediated responses. In this report, we define a role for diacylglycerol-regulated PKC isoforms in controlling the activity of the serine/threonine kinase protein kinase D (PKD; also known as PKC mu) in T cells, B cells, and mast cells. Antigen receptor activation of PKD is a rapid and sustained response that can be seen in T cells activated via the T cell antigen receptor, B cells activated via the B cell antigen receptor, and in mast cells triggered via the high-affinity receptor for IgE (FcepsilonR1). Herein, we show that antigen receptor activation of PKD requires the activity of classical/novel PKCs. Moreover, PKC activity is sufficient to bypass the requirement for antigen receptor signals in the induction of PKD activity. These biochemical and genetic studies establish a role for antigen receptor-regulated PKC enzymes in the control of PKD activity. Regulation of PKD activity through upstream PKCs reveals a signaling network that exists between different members of the PKC superfamily of kinases that can operate to amplify and disseminate antigen receptor signals generated at the plasma membrane.
Expression and Function of the C5a Receptor in Rat Alveolar Epithelial Cells (2002)

Although alveolar epithelial cells (AEC) form an important barrier for host defenses in the lung, there is limited information about ways in which AEC can directly participate in the lung inflammatory response. In the current studies, primary cultures of rat AEC (RAEC) have been shown to specifically bind recombinant rat C5a at high affinity and in a saturable manner. This binding was enhanced in a time-dependent manner by pre-exposure of RAEC to LPS, IL-6, or TNF-alpha, the increased binding of C5a being associated with increased levels of mRNA for the C5a receptor (C5aR). Exposure of RAEC to C5a also caused increased expression of mRNA for C5aR. As compared with exposure of RAEC to LPS or to C5a alone, exposure to the combination caused enhanced production of TNF-alpha, macrophage inflammatory protein-2, and cytokine-induced neutrophil chemoattractant-1, as well as increased intracellular levels of IL-1beta. These data indicate that RAEC, when activated, have enhanced binding of C5a in association with increased mRNA for C5aR. The functional outcome is enhanced release of proinflammatory mediators. These data underscore the phlogistic potential of RAEC and the ability of C5a to enhance the phlogistic responses of RAEC.
Reducing the peak-to-average power ratio of OFDM (2002)

The distribution of the peak-to-average power (PAP) ratio of an OFDM signal is derived, showing that large PAP ratios only occur very infrequently. Because of this, PAP reducing techniques which distort the signal can be quite effective, since only a small fraction of the OFDM signal has to be distorted. One example of such a technique is peak windowing. It is shown that peak windowing can achieve PAP ratios around 4 dB for an arbitrary number of subcarriers, at the cost of a slight increase in the BER and out-of-band radiation. Simulations with realistic power amplifier models show that a backoff of about 5 dB is required to get an out-of-band radiation level of 30 dB below the in-band spectral density.
Response Properties of Mechanoreceptors and Nociceptors in Mouse Glabrous Skin: An In Vivo Study (2001)

The increasing use of transgenic mice for the study of pain mechanisms necessitates comprehensive understanding of the murine somatosensory system. Using an in vivo mouse preparation, we studied response properties of tibial nerve afferent fibers innervating glabrous skin. Recordings were obtained from 225 fibers identified by mechanical stimulation of the skin. Of these, 106 were classed as A beta mechanoreceptors, 51 as A delta fibers, and 68 as C fibers. A beta mechanoreceptors had a mean conduction velocity of 22.2 +/- 0.7 (SE) m/s (13.8--40.0 m/s) and a median mechanical threshold of 2.1 mN (0.4--56.6 mN) and were subclassed as rapidly adapting (RA, n = 75) or slowly adapting (SA, n = 31) based on responses to constant force mechanical stimuli. Conduction velocities ranged from 1.4 to 13.6 m/s (mean 7.1 +/- 0.6 m/s) for A delta fibers and 0.21 to 1.3 m/s (0.7 +/- 0.1 m/s) for C fibers. Median mechanical thresholds were 10.4 and 24.4 mN for A delta and C fibers, respectively. Responses of A delta and C fibers evoked by heat (35--51 degrees C) and by cold (28 to -12 degrees C) stimuli were determined. Mean response thresholds of A delta fibers were 42.0 +/- 3.1 degrees C for heat and 7.6 +/- 3.8 degrees C for cold, whereas mean response thresholds of C fibers were 40.3 +/- 0.4 degrees C for heat and 10.1 +/- 1.9 degrees C for cold. Responses evoked by heat and cold stimuli increased monotonically with stimulus intensity. Although only 12% of tested A delta fibers were heat sensitive, 50% responded to cold. Only one A delta nociceptor responded to both heat and cold stimuli. In addition, 40% of A delta fibers were only mechanosensitive since they responded neither to heat nor to cold stimuli. Thermal stimuli evoked responses from the majority of C fibers: 82% were heat sensitive, while 77% of C fibers were excited by cold, and 68% were excited by both heat and cold stimuli. Only 11% of C fibers were insensitive to heat and/or cold. This in vivo study provides an analysis of mouse primary afferent fibers innervating glabrous skin including new information on encoding of noxious thermal stimuli within the peripheral somatosensory system of the mouse. These results will be useful for future comparative studies with transgenic mice.
Widespread histologic distribution of the alpha 2 beta 1 integrin cell-surface collagen receptor. (1990)

The alpha 2 beta 1 integrin (platelet membrane glycoprotein Ia-IIa, VLA-2, ECMR-II) functions as a cell surface receptor for collagen. The authors have determined the histologic distribution of the alpha 2 beta 1 receptor in normal tissues by immunohistochemical technique. The studies revealed that the alpha 2 beta 1 receptor was expressed on fibroblasts, endothelial cells, and epithelial cells from multiple sites including skin, tonsil, breast, sweat gland, gastrointestinal tract, lung, bladder, cervix, and prostate. Follicular dendritic cells of the lymph node, tonsil, and spleen and dendritic cells of the thymus also expressed the alpha 2 beta 1 receptor. The receptor also was present on Schwann cells of ganglia and on neuroglia. Greatly enhanced expression of the receptor in regions of proliferating epithelium suggests that enhanced expression of alpha 2 beta 1 is associated with orderly, regulated cell proliferation. The circumferential staining pattern of the alpha 2 beta 1 integrin within many epithelia is virtually identical to that observed for other adhesive receptors, such as the cadherins, which have been implicated in cell-cell adhesion.
Comparative Protein Structure Modeling Using Modeller (2006)

Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
Mechanisms of Carcinogenesis Focus on Oxidative Stress and Electron Transfer (2001)

For more than half a century, numerous proposals have been advanced for the mode of action of carcinogens. This review presents a wide array of evidence that implicates oxidative stress (OS) in many aspects of oncology, including: formation of reactive oxygen species (ROS) by the major classes of carcinogens (as well as minor ones), cancer stages, oncogene activation, aging, genetic and infectious illnesses, nutrition, and the role of antioxidants (AOs). Although diverse origins pertain, including both endogenous and exogenous agents, ROS are frequently generated by redox cycling via electron transfer (ET) groups, e.g., quinones (or phenolic precursors), metal complexes (or complexors), aromatic nitro compounds (or reduced products), and conjugated imines (or iminium species). We believe it is not coincidental that these functionalities are often found in carcinogens or their metabolites. The pervasive aspects of DNA binding by ultimate carcinogens, and mutations caused by ROS are treated. Often, ROS are implicated in more conventional rationales, such as oncogenes. A multi-faceted approach to mechanisms appears to be the most logical. The OS unifying theme represents an approach which is able to rationalize the diverse data associated with carcinogenesis. Because this theoretical framework aids in the understanding of cancer initiation, it can serve as a useful tool in combating cancer, particularly in relation to prevention. Significantly, the electron transfer--oxidative stress (ET-OS) scenario can also be applied to many drug categories, toxins, enzymes, and hormones.
Single phase power factor correction: a survey (2003)

New recommendations and future standards have increased the interest in power factor correction circuits. There are multiple solutions in which line current is sinusoidal. In addition, a great number of circuits have been proposed with nonsinusoidal line current. In this paper, a review of the most interesting solutions for single phase and low power applications is carried out. They are classified attending to the line current waveform, energy processing, number of switches, control loops, etc. The major advantages and disadvantages are highlighted and the field of application is found.