gebhart/patrepeval huggingface dataset:
Antibody-secreting B cells in HIV infection (2009)

It is likely that the defects found in total B cells in HIV-infected patients also play a role in the poorly effective HIV-specific antibody response. A subset of HIV-infected patients produced broadly neutralizing antibodies. Understanding this antibody response, and the B cells that underlie it, may be critical in efforts to elicit neutralizing antibodies against HIV.
Smart Toy Car Localization and Navigation Using Projected Light (2015)

In this paper, we present the design and implementation of toy car localization and navigation system, which enables toy cars and "passengers" to learn and exchange their fine-grained locations in an indoor environment with the help of the projected light based localization technique. The projected light consists of a sequence of gray code images which assigns each pixel in the projection area a unique gray code to distinguish their coordination. The light sensors installed on a toy cars and a potential "passenger" receive the light streams from the projected light, based on which their locations are inferred. The toy car then utilizes A* algorithm to plan a route based on its location, its orientation, the target's location and the map of "roads". The fast speed of projected light based localization technique enables the toy car to adjust its own orientation while "driving" and keep itself on "roads". The toy car system demonstrates that the localization technique and the client-server architecture can benefit similar applications that require fine-grained location information of multiple objects simultaneously.
Perspective on a Superconducting 30 T/1.3 GHz NMR Spectrometer Magnet (2006)

The COHMAG report of the National Academy of Sciences provides an assessment of high field magnet science and technology in the United States, and identifies possible new initiatives for future high field magnets. Regarding NMR, the report identifies high resolution NMR spectrometers in the range of 30 T/1.3 GHz as having great scientific interest. This paper discusses technology issues associated with 30 T superconducting magnets. The enabling technology is HTS conductors and coil technology. Significant issues remain for application of HTS conductors to large coils, including long length quality, heat treatment, anisotropy and strain dependence. The outer LTS coil sections are large, with high stress and stored energy. Structural issues, including high strength conductor and reinforcement, and quench protection issues are significant. The status of technology required for a 30 T NMR magnet is examined. A preliminary conceptual design of the 30 T magnet is presented
Undifferentiated Small Round Cell Sarcoma With t(4;19)(q35;q13.1) CIC-DUX4 Fusion (2013)

A subset of small round cell sarcomas remains difficult to classify. Among these, a rare tumor harboring a t(4;19)(q35;q13.1) with CIC-DUX4 fusion has been described. The aim of this study is to better understand its clinicopathologic features. Four cases of CIC-DUX4 sarcoma, all arising in adults (3 women, 1 man, aged 20 to 43 y), were identified using conventional cytogenetic, reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) methods. All 4 tumors demonstrated CIC-DUX4 fusion transcript by both RT-PCR and FISH and CIC rearrangement by FISH. Cytogenetic results from 2 tumors showed t(4;19)(q35;q13.1) occurring as part of a simple karyotype in 1 tumor and as part of a complex karyotype in the other, the latter from a postchemotherapy specimen. Both tumors harbored trisomy 8 and lacked any other known sarcoma-associated translocation. No EWS or SYT rearrangements were detected by RT-PCR or FISH. The tumors had small round cell morphology with a distinctive constellation of histologic features including extensive geographic necrosis, mild nuclear pleomorphism with coarse chromatin and prominent nucleoli, clear cell areas, and focal myxoid matrix. Only focal staining for CD99 was present in each tumor. Two had very focal cytokeratin staining. All tumors were negative for desmin, myogenin, TLE-1, and S100 protein, whereas nuclear INI-1 staining was retained. The tumors were highly aggressive, and all patients died of disseminated disease within 16.8 months. CIC-DUX4 sarcoma represents a novel translocation-associated sarcoma with distinctive histopathologic features and rapid disease progression.
DNA-mediated gene transfer without carrier DNA. (1981)

DNA-mediated gene transfer is a procedure which uses purified DNA to introduce new genetic elements into cells in culture. The standard DNA-mediated gene transfer procedure involves the use of whole cell DNA as carrier DNA for the transfer. We have modified the standard DNA-mediated gene transfer procedure to transfer the Herpes simplex virus type 1 thymidine kinase gene (TK) into TK- murine recipient cells in the absence of whole cell carrier DNA. The majority (8/10) of carrier-free transformant lines expressed the TK+ phenotype stably, in sharp contrast to our results with carrier-containing DNA-mediated gene transfer. There was a wide range in donor DNA content among independent transformants. Further analysis on one transformant line using DNA restriction digests and in situ hybridization provided evidence that, in the absence of whole cell carrier DNA, multiple donor DNA sequences became integrated at a single chromosomal site.
Constitutive nuclear localization of Janus kinases 1 and 2 (1996)

Both GH and the GH receptor have been reported to undergo rapid nuclear translocation. Janus kinases (JAK) 1 and 2 have been implicated in GH receptor signaling, and both of these kinases are phosphorylated by GH stimulation. In this report, we have investigated the subcellular distribution of JAK1 and JAK2. Both JAK1 and JAK2 exhibit a nucleocytoplasmic distribution by immunocytochemistry in unstimulated serum deprived CHO cells stably transfected with rat GH receptor complementary DNA (cDNA). The nucleocytoplasmic localization of JAK2 was verified by immunogold electron microscopy in both rat liver hepatocytes and CHO cells stably transfected with rat GH receptor cDNA. Nucleocytoplasmic localization of JAK2 was also verified by transient tranfection of CHO cells with a Haemophilus influenzae haemagglutinin (HA) epitope tagged JAK2 expression plasmid and subsequent localization of HA immunoreactivity. Western blot analysis of purified nuclear extracts revealed the presence of immunoreactive JAK1 at 130 kDa and immunoreactive JAK2 at 128 kDa. No change in the nuclear content of JAK1 or JAK2 was observed upon ligand stimulation of GH receptor cDNA transfected cells with 100 nM human GH for 5, 10, 15, 30, or 60 min. GH stimulation caused, however, the appearance of tyrosine phosphorylated 42- and 44-kDa proteins as well as tyrosine phosphorylated JAK2 in the nucleus. The constitutive nuclear localization of the Janus Kinases is suggestive of a novel nuclear role for JAK family members, in addition to their described cytosolic function and presents an interesting challenge to the subcellular site of hormone action.
Managing network security — The unpredictability of defence (1998)

Over the last few years, computing has changed to an almost purely networked environment, but the technical aspects of information protection have not kept up. As a result, the success of information security programmes has increasingly become a function of our ability to make prudent management decisions about organizational activities. This series of articles takes a management view of protection and seeks to reconcile the need for security with the limitations of technology.
Overexpression of a p-glycoprotein in hepatocellular carcinomas from woodchuck hepatitis virus-infected woodchucks (Marmota monax) (1996)

The leading cause of human hepatocellular carcinomas (HCCs) is hepatitis B virus (HBV) infection. Woodchucks infected with a closely related hepadnavirus, woodchuck hepatitis virus (WHV), serve as a model for HBV because woodchucks chronically infected with WHV also develop hepatocellular carcinomas. Increased expression of p-glycoprotein (pgp) in human HCCs is a common obstacle in successful cancer chemotherapy. Pgps are encoded by a family of multidrug-resistance (MDR) genes. Livers from uninfected and WHV-infected woodchucks were examined to determine if pgp was expressed in HCCs and if there was a difference in expression between HCCs and nonneoplastic liver. A 170-kd protein was identified by Western blot in HCCs, whereas, constitutive pgp was not detected in normal liver taken from the same animals in 3 of 3 cases. Immunolocalization of the pgp with a panel of monoclonal antibodies revealed intensification of staining in 7 of 20 foci and 12 of 22 HCCs from six animals. Using primers for the human MDR1 gene, a single product was detected by reverse-transcribed polymerase chain reaction (RT-PCR) from HCCs. We have shown an increase in pgp in HCCs compared with normal liver from WHV-infected woodchucks. This is the first example of the induction of a pgp in a naturally hepadnavirus infected rodent system. It suggests the woodchuck can be a useful model for the study of the acquisition of resistance to chemotherapeutic agents in virally induced HCCs. (Hepatology 1996 Apr;23(4):662-8)
Potent gene regulatory and antiproliferative activities of 20-methyl analogues of 1,25 dihydroxyvitamin D3 (1996)

The biological active form of vitamin D3, 1,25-dihydroxyvitamin D3 (VD), regulates cellular growth and differentiation. This provides the hormone with an interesting therapeutic potential. However, hypercalcemia is a side effect, which is caused by VD's classical action, the regulation of calcium homeostasis. This made the need for VD analogues with selectively increased cell regulatory properties. Studies with 20-epi analogues pointed out the importance of the carbon-20 position and led to the development of 20-methyl derivatives of VD. In this report the biological properties of the compounds ZK161422 and ZK157202, which are 20-methyl- and 20-methyl-23-eneanalogues, respectively, have been analyzed in comparison with VD. Both compounds show about 2-fold lower affinity to the VD receptor (VDR) than VD. However, compared to VD, their antiproliferative effect is up to 30-fold higher on human peripheral blood mononuclear cells and even up to 300-fold higher on human breast cancer MCF-7 cells. Whereas the hypercalcemic effect for ZK157202 is also increased 10-fold, ZK161422 has the same calcium-mobilizing potency as VD. Moreover, ZK161422, but not ZK157202, showed preference for gene activation from a promoter carrying a VD response element with a palindromic arrangement of two hexameric receptor binding sites spaced by 9 nucleotides (IP9) rather than for activation from a response element formed by a direct repeat spaced by 3 nucleotides (DR3). This observation supports a model, in which promoter selectivity reflects the selectively increased antiproliferative effect of VD analogues.
Respiratory Syncytial Virus NS1 Protein Colocalizes with Mitochondrial Antiviral Signaling Protein MAVS following Infection (2012)

Respiratory syncytial virus (RSV) nonstructural protein 1(NS1) attenuates type-I interferon (IFN) production during RSV infection; however the precise role of RSV NS1 protein in orchestrating the early host-virus interaction during infection is poorly understood. Since NS1 constitutes the first RSV gene transcribed and the production of IFN depends upon RLR (RIG-I-like receptor) signaling, we reasoned that NS1 may interfere with this signaling. Herein, we report that NS1 is localized to mitochondria and binds to mitochondrial antiviral signaling protein (MAVS). Live-cell imaging of rgRSV-infected A549 human epithelial cells showed that RSV replication and transcription occurs in proximity to mitochondria. NS1 localization to mitochondria was directly visualized by confocal microscopy using a cell-permeable chemical probe for His(6)-NS1. Further, NS1 colocalization with MAVS in A549 cells infected with RSV was shown by confocal laser microscopy and immuno-electron microscopy. NS1 protein is present in the mitochondrial fraction and co-immunoprecipitates with MAVS in total cell lysatesof A549 cells transfected with the plasmid pNS1-Flag. By immunoprecipitation with anti-RIG-I antibody, RSV NS1 was shown to associate with MAVS at an early stage of RSV infection, and to disrupt MAVS interaction with RIG-I (retinoic acid inducible gene) and the downstream IFN antiviral and inflammatory response. Together, these results demonstrate that NS1 binds to MAVS and that this binding inhibits the MAVS-RIG-I interaction required for IFN production.
Uncovering the essential genes of the human malaria parasite <i>Plasmodium falciparum</i> by saturation mutagenesis (2018)

Severe malaria is caused by the apicomplexan parasite <i>Plasmodium falciparum.</i> Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of <i>P. falciparum</i> in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 <i>Plasmodium</i>-conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity.
Differential infection patterns of CD4+ T cells and lymphoid tissue viral burden distinguish progressive and nonprogressive lentiviral infections (2012)

Nonhuman primate natural hosts for simian immunodeficiency viruses (SIV) develop a nonresolving chronic infection but do not develop AIDS. Mechanisms to explain the nonprogressive nature of SIV infection in natural hosts that underlie maintained high levels of plasma viremia without apparent loss of target cells remain unclear. Here we used comprehensive approaches (ie, FACS sorting, quantitative RT-PCR, immunohistochemistry, and in situ hybridization) to study viral infection within subsets of peripheral blood and lymphoid tissue (LT) CD4(+) T cells in cohorts of chronically SIV-infected rhesus macaques (RMs), HIV-infected humans, and SIVsmm-infected sooty mangabeys (SMs). We find: (1) infection frequencies among CD4(+) T cells in chronically SIV-infected RMs are significantly higher than those in SIVsmm-infected SMs; (2) infected cells are found in distinct anatomic LT niches and different CD4(+) T-cell subsets in SIV-infected RMs and SMs, with infection patterns of RMs reflecting HIV infection in humans; (3) T(FH) cells are infected at higher frequencies in RMs and humans than in SMs; and (4) LT viral burden, including follicular dendritic cell deposition of virus, is increased in RMs and humans compared with SMs. These data provide insights into how natural hosts are able to maintain high levels of plasma viremia while avoiding development of immunodeficiency.
Microporous Magnesium and Manganese Formates for Acetylene Storage and Separation (2007)

Acetylene sorption of microporous metal formates M(HCOO)2 (M = Mg and Mn) was investigated. Measurements of acetylene sorption at 196, 275, and 298 K showed a Type I isotherm with quick saturation at low pressures, and 50-75 cm3 g(-1) uptake at 1.0 atm. The single-crystal X-ray structure analysis of the acetylene-adsorbed metal formates revealed that acetylene molecules occupy two independent positions in the zigzag channels of the frameworks with a stoichiometry of M(HCOO)2 x 1/3C2H2, which is consistent with the gas sorption experiments. No specific interaction except van der Waals interactions between the adsorbed acetylene molecules and the walls of the frameworks was found. Sorption properties of other gases, including CO2, CH4, N2, O2, and H2, were also investigated. When the temperature was increased to 298 K, the amount of adsorbed acetylene was still above 60 cm3 g(-1) for Mg(HCOO)2 and 50 cm3 g(-1) for Mn(HCOO)2, whereas the uptake of other gases decreased substantially. The microporous metal formates may thus be useful not only for the storage of acetylene but also its separation from other gases at room or slightly higher temperatures.
Potent Fibrinolytic Enzyme from a Mutant of <i>Bacillus </i><i>s</i><i>ubtilis</i> IMR-NK1 (2000)

A mutant of Bacillus subtilis IMR-NK1, which is used for the production of domestic "natto" in Taiwan, produced high fibrinolytic enzyme activity by solid-state fermentation using wheat bran as medium. In addition, a strong fibrinolytic enzyme was purified from the cultivation media. The purified enzyme was almost homogeneous, as examined by SDS-PAGE and capillary electrophoresis. The enzyme had an optimal pH of 7.8, an optimal temperature of 55 degrees C, and a K(m) of 0.15% for fibrin hydrolysis. The molecular mass estimated by gel filtration was 31.5 kDa, and the isoelectric point estimated by isoelectric focusing electrophoresis was 8.3. The enzyme also showed activity for hydrolysis of fibrinogen, casein, and several synthetic substrates. Among the synthetic substrates, the most sensitive substrate was N-succinyl-Ala-Ala-Pro-Phe-pNA. PMSF and NBS almost completely inhibited the activity of the enzyme. These results indicate that the enzyme is a subtilisin-like serine protease, similar to nattokinase from Bacillus natto.
Development of GP-2 and five zymogens in the fetal and young pig: biochemical and immunocytochemical evidence of an atypical zymogen granule composition in the fetus. (1996)

To uncover the mechanisms involved in the biogenesis of secretory granules, we studied development of the exocrine pancreas in the pig from the fetus up to the mature animal by following the enzyme activities and expression (Northern blot) of five zymogens and GP-2, the major protein of the granule membrane. Fetal pancreas mainly contained chymotrypsinogen and barely detectable amounts of amylase, trypsin, lipase, and elastase. GP-2 was not notably expressed before the Day 21 of life. Ultrastructural examination of the fetal tissue embedded in Epon with osmium postfixation or in Lowicryl at -20 degrees C without postfixation showed dense granules with an irregular shape but also showed that most granules had uncondensed contents, with the aspect of immature granules, or had a dense core surrounded by light material. With immunogold cytochemistry, the concentration of chymotrypsinogen was directly associated with the acquisition of electron density by the granule matrix. These observations suggest that fetal granules have a slower rhythm of zymogen condensation and an irregular shape that could be due to the particular composition of the matrix and the absence of GP-2. We conclude that, in the exocrine pancreas, secretory granules can be formed under various conditions, even with a matrix containing a ratio of components very different from that of the normal mature animal.
Speed adaptation control of a small-sized treadmill with state feedback controller (2010)

Variable velocity in treadmill training may play an important role in gait rehabilitation where a patient can practice variable walking velocity while the treadmill adjusts to it. In order to adjust the treadmill velocity to the subject's variable walking velocity, we have developed an automatic gait velocity adaptation algorithm implemented on a small-sized commercial treadmill (belt length of 1.2 m and width of 0.5 m) which is widely used at home and health centers. The control objective is to automatically adjust the treadmill velocity so that the subject's position is maintained within the track when the subject walks at a variable velocity. The subject's position with respect to a reference point is measured by a low-cost sonar sensor located on the back of the subject. Based on a encoder sensor measurement at the treadmill motor, a state feedback control algorithm with Kalman filter was implemented to determine the velocity of the treadmill. In order to reduce the unnatural inertia force felt by the subject, a predefined acceleration limit was applied, which generated smooth velocity trajectories. The experimental results demonstrate the effectiveness of the proposed method in providing successful velocity changes in response to variable velocity walking including starting (accelerating) and stopping (decelerating) periods of treadmill exercise without causing significant inertia force to the subject. In the pilot study with three subjects, users could change their walking velocity easily and naturally with small deviations during slow, medium, and fast walking. The proposed automatic velocity adaptation algorithm can potentially be applied to any locomotion interface in an economical way without having to use sophisticated and expensive sensors and larger treadmills.
A Study on the Control of Exotic Weed Mikania micrantha by Using Parasitic Cuscuta campestris (2003)

Parasite Cuscuta campestris Yunker was examined for controlling the growth and spread of harmful weed Mikania micrantha H.B.K.The experiments were carried out to estimate biomass production by sowing the seeds of M.micrantha in sample plots in Shenzhen Xianhu Botanic Garden where this weed grew densely,and for physiological study by cultivation of both plants in pots.The result exhibited that the leaf number,stem length,and biomass dry weight of individual of the host M.micrantha began to decrease after the host was parasitized for about 30days.Such decrease was obvious after2months of parasitism,so did the photosynthetic rate(P n ),transpiration rate(E),stomatal conductance(g s ),water use efficiency(WUE),chlorophyll content,and Fv /Fm.The parasite could spread rapidly extending to an area of20m 2 with longest distance of5m within2months.The parasite hampered the growth and reproduction of the host and depressed it even to die.It is suggested that C.campestris might be a promising plant for controlling this weed.
<em>Cura Personalis, Cura communitas</em>: Loving our neighbor in Covid-19 times (2020)

The months of November and December have given chilling notice that the pandemic is far from over.Worldwide the global case rates continued steadily upward, with daily new cases exceeding 700,000 for the first time, total confirmed cases surpassing 75 million, and deaths exceeding 1.6 million. 1After pushing back or being spared by the April-May COVID-19 onslaught France, Italy, Germany, Russia, the United Kingdom, and other countries experienced record daily highs for new cases and a steady increase in the cumulative death toll.In the U.S., nearly every state experienced new daily highs for confirmed cases. 2 By mid-December deaths were occurring at the rate of more than 75,000 per month.Nationwide nearly 17 million cases and more than 300,000 deaths had been reported.Parts of Latin America, North Africa, and the Middle East were also seeing new surges.With the exception of new outbreaks in India, Kenya, South Africa, Australia and a few other countries, Asia and sub-Saharan Africa maintained a relatively low incidence of COVD-19.Pandemic misinformation, fatigue, denial, and resistance -along with cooler weather -have created a perfect storm for regional and national surges. 3andemic fatigue occurred among the many who understood the reality of COVID-19 but were tiring of the efforts needed to keep themselves and their loved ones safe. 4,5Pandemic denial continued among those convinced reports of a pandemic were untrue and that masking, distancing, and other