gebhart/patrepeval huggingface dataset:
Gut Colonization of Mice withactA-Negative Mutant ofListeria monocytogenesCan Stimulate a Humoral Mucosal Immune Response (2001)

We used Listeria monocytogenes, a gram-positive, facultative intracellular bacterium, to study the gut mucosal immune responses following oral infection. We employed a germfree (GF) mouse model to try to accentuate the development of a humoral mucosal immune response in the gut, and we used oral colonization with one of the mutants, actA-negative (DeltaactA) L. monocytogenes, to restrict infection largely to the gut. The DeltaactA mutant was able to colonize the intestinal mucosa of formerly GF mice for long periods of time without causing disease while eliciting secretory immunoglobulin A (IgA) responses, as evidenced by gut tissue fragment culture assays. Flow cytometric analyses and immunohistochemical methods showed the development of only minimal germinal center reactions (GCR) in Peyer's patches and more robust GCR in mesenteric lymph nodes. Pronounced increases in total (natural) IgA production occurred in gut tissues by day 7 and were maintained for up to 90 days. Levels of specific IgA were modest in gut tissues on day 14, increased until day 76, and stabilized at day 90. We also observed a significant rise in serum IgA and IgG1 levels following oral infection by listeriae. Upon colonization, the organisms mainly infected the intestines and intestinal lumen, and we only sporadically observed few colony-forming bacteria in the liver and spleen. We observed a marked rise in IgA-secreting cells, including listeria-specific IgA antibody-secreting cells, in the lamina propria of the small intestine by enzyme-linked immunospot assays. To ascertain whether some of the IgA was specific for listeriae, we performed Western blot analysis to test the reactivity of IgA from fragment cultures to antigens in sonicates of L. monocytogenes. We detected IgA binding to antigenic proteins with molecular masses of 96, 60, 40, and 14 kDa in the Listeria sonicates.
Effect of Blood-Brain Barrier and Blood-Tumor Barrier Modification on Central Nervous System Liposomal Uptake (1993)

In this study of 25 central nervous system (CNS) tumor-bearing rats, the CNS biodistribution of intravenously administered, indium-labeled liposomes was investigated. In 16 animals, the blood-brain barrier and blood-tumor barrier were modified using intracarotid administration of etoposide. In control animals, analysis by autoradiography and well-counting experiments demonstrated uptake of liposomes in the tumor-bearing hemisphere (% injected dose/g tissue = 0.135) with minimal uptake in the non-tumor-bearing hemisphere (% injected dose/g tissue = 0.007), p < 0.01. Unilateral intracarotid etoposide administration enhanced liposome uptake in both hemispheres-0.215 and 0.023 (tumor-bearing and nontumor-bearing), respectively. The presence of meningeal tumor involvement in nontumor-implanted hemispheres increased liposomal uptake 10-fold. These findings may have clinical applicability in designing therapeutic protocols for the treatment of CNS tumors.
Measles virus P gene codes for two proteins (1985)

The entirety of the phosphoprotein gene of measles virus has been sequenced. The gene is composed of 1,657 nucleotides and specifies a 507-amino-acid protein (P). A second overlapping reading frame was predicted from the sequence and specifies a 186-amino-acid protein (C). Through the use of antisynthetic peptide antibodies, we show that both proteins are expressed in virally infected cells. Both proteins are expressed from a functionally bicistronic mRNA through independent initiation of ribosomes at the respective AUG codons. Using immunofluorescent microscopy, we localized the C protein in the nucleus and in cytoplasmic inclusions within the infected cells.
The Anatomy of A-, B-, and Z-DNA (1982)

Recent advances in DNA synthesis methods have made it possible to carry out single-crystal x-ray analyses of double-stranded DNA molecules of predetermined sequence, with 4 to 12 base pairs. At least one example has been examined from each of the three known families of DNA helix: A, B, and Z. Each family has its own intrinsic restrictions on chain folding and structure. The observed solvent positions in these crystal structures have confirmed earlier fiber and solution measurements, and have led to proposals explaining the transitions from B to A and from B to Z helices. Prospects are improving for an understanding of the mode of bending of DNA in chromatin, and the way in which specific DNA sequences are recognized by drug molecules and repressor proteins.
Reducing the peak-to-average power ratio in OFDMbycyclically shifting partial transmit sequences (2000)

An adaptation of the work by Huber and Muller on partial transmit sequences (PTSs) for the reduction of the peak-to-average power ratio (PAPR) in orthogonal frequency division multiplexing (OFDM) is described. The new variation combines cyclic shifts of the inverse fast Fourier transform (IFFT) sub-block output with PTSs. The performance of the new scheme is slightly better than that of a PTS scheme for the same number of comparisons and avoids the need for complex multipliers when the number of phase rotations is greater than 4.
FIRST Forensic Internet Replay Sequencing Tool (2009)

This paper discusses the design and development of a tool that can be used by digital forensic investigators to display a visual recreation of Web browsing sessions based on the browser cache stored on a suspectpsilas hard drive. Frequently, a forensic investigator will search a Web browser cache to learn about the browsing habits of a suspect. The data gathered from the cache will be used to support a case in a civil or criminal proceeding. Thus, the investigator must have a method to clearly convey the information learned from the investigation of the cache. Currently, tools exist that can parse the browser cache to determine the Uniform Resource Locaters (URLs) visited by the suspect and the times that the URLs were visited. While this data indicates the browsing habits of the suspect, a list of URLs and timestamps is not easily understood by non-information technology professionals. The goal is to construct a tool that will assemble a visual slideshow that recreates, as closely as possible, a suspectpsilas browsing experience. This recreation will help provide investigators and other interested parties with an accurate understanding of the suspectpsilas intentions while browsing the Web.
Direct implantation and serial transplantation of human acute lymphoblastic leukemia in hamsters, SB-2. (1968)

Summary Human acute lymphoblastic leukemia cells have been established as a serially transplantable lymphosarcoma in newborn Syrian hamsters by the direct inoculation of cells from the peripheral blood of a boy in the terminal stages of lymphosarcoma. The experimental neoplasm, currently in its 70th serial passage, is metastatic and occasionally progresses to frank leukemia. In later passages, it has become transplantable in the newborn hamster every 10–12 days. Immunofluorescence evidence indicates that it is still composed of human cells after continued passage in the experimental host. Cytogenetic examination shows the cells to be of male human karyotype. Electron-microscopic examination reveals them to be free of morphologically recognizable virus.
An Investigation of Driver Discomfort and Related Seat Design Factors in Extended-Duration Driving (1991)

&lt;div class="htmlview paragraph"&gt;A study of automotive seating comfort and related design factors was conducted, utilizing subjective techniques of seat comfort assessment and objective measures of the seat/subject interaction. Eight male subjects evaluated four different test seats during a short-term seating session and throughout a three-hour driving simulation. For the latter, subjects operated a static laboratory driving simulator, performing body-area discomfort evaluations at thirty-minute intervals. Cross-modality matching (CMM), a subjective assessment technique in which a stimulus is rated by matching to the level of another stimulus, was used during the long-term driving simulation to evaluate discomfort. Subject posture, muscle activity in the lower back and abdomen, and pressure levels at key support locations on the seat were monitored. In addition, a sonic digitizing system was used to record seat indentation contours and to characterize the subjects' spinal contours.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The rights, welfare, and informed consent of the volunteer subjects who participated in this study were observed under guidelines established by the U.S. Department of Health, Education, and Welfare Policy (now Health and Human Services) on Protection of Human Subjects and accomplished under medical research design protocol standards approved by the Committee to Review Grants for Clinical Research and Investigation Involving Human Beings, Medical School, The University of Michigan.&lt;/div&gt;
Targeting folate receptor alpha for cancer treatment (2016)

Promising targeted treatments and immunotherapy strategies in oncology and advancements in our understanding of molecular pathways that underpin cancer development have reignited interest in the tumor-associated antigen Folate Receptor alpha (FRα). FRα is a glycosylphosphatidylinositol (GPI)-anchored membrane protein. Its overexpression in tumors such as ovarian, breast and lung cancers, low and restricted distribution in normal tissues, alongside emerging insights into tumor-promoting functions and association of expression with patient prognosis, together render FRα an attractive therapeutic target. In this review, we summarize the role of FRα in cancer development, we consider FRα as a potential diagnostic and prognostic tool, and we discuss different targeted treatment approaches with a specific focus on monoclonal antibodies. Renewed attention to FRα may point to novel individualized treatment approaches to improve the clinical management of patient groups that do not adequately benefit from current conventional therapies.
The Brave New World of clinical cancer research: Adaptive biomarker‐driven trials integrating clinical practice with clinical research (2015)

Clinical trials are the final links in the chains of knowledge and for determining the roles of therapeutic advances. Unfortunately, in an important sense they are the weakest links. This article describes two designs that are being explored today: platform trials and basket trials. Both are attempting to merge clinical research and clinical practice.
An Array Immunosensor for Simultaneous Detection of Clinical Analytes (1998)

A fluorescence-based immunosensor has been developed for simultaneous analysis of multiple samples. A patterned array of recognition elements immobilized on the surface of a planar waveguide is used to "capture" analyte present in samples; bound analyte is then quantified by means of fluorescent detector molecules. Upon excitation of the fluorescent label by a small diode laser, a CCD camera detects the pattern of fluorescent antigen:antibody complexes on the sensor surface. Image analysis software correlates the position of fluorescent signals with the identity of the analyte. This immunosensor was used to detect physiologically relevant concentrations of staphylococcal enterotoxin B (SEB), F1 antigen from Yersinia pestis, and D-dimer, a marker of sepsis and thrombotic disorders, in spiked clinical samples.
ACTIVATED CASPASE-1 IS NOT A CENTRAL MEDIATOR OF INFLAMMATION IN THE COURSE OF ISCHEMIA-REPERFUSION1 (2001)

These findings suggest that activated caspase-1 and its inflammatory products are involved in, but not crucial to, the induction of inflammation after renal ischemia-reperfusion. Hence, apart from caspase-1, other (combinations of) activated caspases are likely to be more prominently involved in renal reperfusion injury.
Multiplexing of miniaturized planar antibody arrays for serum protein profiling – a biomarker discovery in SLE nephritis (2014)

In the quest to decipher disease-associated biomarkers, miniaturized and multiplexed antibody arrays may play a central role in generating protein expression profiles, or protein maps, of crude serum samples. In this conceptual study, we explored a novel, 4-times larger pen design, enabling us to, in a unique manner, simultaneously print 48 different reagents (antibodies) as individual 78.5 μm(2) (10 μm in diameter) sized spots at a density of 38,000 spots cm(-2) using dip-pen nanolithography technology. The antibody array set-up was interfaced with a high-resolution fluorescent-based scanner for sensitive sensing. The performance and applicability of this novel 48-plex recombinant antibody array platform design was demonstrated in a first clinical application targeting SLE nephritis, a severe chronic autoimmune connective tissue disorder, as the model disease. To this end, crude, directly biotinylated serum samples were targeted. The results showed that the miniaturized and multiplexed array platform displayed adequate performance, and that SLE-associated serum biomarker panels reflecting the disease process could be deciphered, outlining the use of miniaturized antibody arrays for disease proteomics and biomarker discovery.
A Phase I trial of h-ras antisense oligonucleotide ISIS 2503 administered as a continuous intravenous infusion in patients with advanced carcinoma (2001)

ISIS 2503, an antisense oligonucleotide against H-ras, was well tolerated as a single agent at doses up to 10.0 mg/kg/day by 14-day continuous intravenous infusion. Several patients had stabilization of disease, suggesting that ISIS 2503 had some tumor growth inhibitory effects and future trials of ISIS 2503 in combination with chemotherapy should be considered.
Molecular cloning of a Pseudomonas syringae pv. syringae gene cluster that enables Pseudomonas fluorescens to elicit the hypersensitive response in tobacco plants (1988)

A cosmid clone isolated from a genomic library of Pseudomonas syringae pv. syringae 61 restored to all Tn5 mutants of this strain studied the ability to elicit the hypersensitive response (HR) in tobacco. Cosmid pHIR11 also enabled Escherichia coli TB1 to elicit an HR-like reaction when high levels of inoculum (10(9) cells per ml) were infiltrated into tobacco leaves. The cosmid, which contains a 31-kilobase DNA insert, was mobilized by triparental matings into Pseudomonas fluorescens 55 (a nonpathogen that normally causes no plant reactions), P. syringae pv. syringae 226 (a tomato pathogen that causes the HR in tobacco), and P. syringae pv. tabaci (a tobacco pathogen that causes the HR in tomato). The plant reaction phenotypes of all of the transconjugants were altered. P. fluorescens(pHIR11) caused the HR in tobacco and tomato leaves and stimulated an apparent proton influx in suspension-cultured tobacco cells that was indistinguishable from the proton influx caused by incompatible pathogenic pseudomonads. P. syringae pv. tabaci(pHIR11) and P. syringae pv. syringae 226(pHIR11) elicited the HR rather than disease symptoms on their respective hosts and were no longer pathogenic. pHIR11 was mutagenized with TnphoA (Tn5 IS50L::phoA). One randomly chosen mutant, pHIR11-18, no longer conferred the HR phenotype to P. fluorescens. The mutation was marker-exchanged into the genomes of P. syringae pv. syringae strains 61 and 226. The TnphoA insertions in the two pseudomonads abolished their ability to elicit any plant reactions in all plants tested. The results indicate that a relatively small portion of the P. syringae genome is sufficient for the elicitation of plant reactions.
Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB (2014)

Accumulating evidence implicates impairment of the autophagy-lysosome pathway in Alzheimer's disease (AD). Recently discovered, transcription factor EB (TFEB) is a molecule shown to play central roles in cellular degradative processes. Here we investigate the role of TFEB in AD mouse models. In this study, we demonstrate that TFEB effectively reduces neurofibrillary tangle pathology and rescues behavioral and synaptic deficits and neurodegeneration in the rTg4510 mouse model of tauopathy with no detectable adverse effects when expressed in wild-type mice. TFEB specifically targets hyperphosphorylated and misfolded Tau species present in both soluble and aggregated fractions while leaving normal Tau intact. We provide in vitro evidence that this effect requires lysosomal activity and we identify phosphatase and tensin homolog (PTEN) as a direct target of TFEB that is required for TFEB-dependent aberrant Tau clearance. The specificity and efficacy of TFEB in mediating the clearance of toxic Tau species makes it an attractive therapeutic target for treating diseases of tauopathy including AD.
A Hybrid Dynamic Load Balancing Approach for Cloud Storage (2012)

In the cloud storage, load balancing is a key issue. It would consume a lot of cost to maintain load information, since the system is too huge to timely disperse load. This paper presents a hybrid control strategy for load balancing. On the one hand the storage node cluster redistributes the load in its local range. On the other hand the system applies the overlapping structure to distribute the load to the global storage nodes by batch iteration approach. We also present a dynamic migrating strategy caused by two reasons: overload access or long response time in some storage nodes. Simulation results show that our approach can dramatically reduce the overall response time and better balance the global load.
Substrate overlap and functional competition between human nucleotide excision repair and Escherichia coli photolyase and (A)BC excision nuclease (1990)

Human cell free extract prepared by the method of Manley et al. (1980) carries out repair synthesis on UV-irradiated DNA. Removal of pyrimidine dimers by photoreactivation with DNA photolyase reduces repair synthesis by about 50%. With excess enzyme in the reaction mixture photolyase reduced the repair signal by the same amount even in the absence of photoreactivating light, presumably by binding to pyrimidine dimers and interfering with the binding of human damage recognition protein. Similarly, the UvrB subunit of Escherichia coli (A)BC excinuclease when loaded onto UV-irradiated or psoralen-adducted DNA inhibited repair synthesis by cell-free extract by 75-80%. The opposite was true also as HeLa cell free extract specifically inhibited the photorepair of a thymine dimer by DNA photolyase and its removal by (A)BC excinuclease. Cell-free extracts from xeroderma pigmentosum (XP) complementation groups A and C were equally effective in blocking the E. coli repair proteins, while extracts from complementation groups D and E were ineffective in blocking the E. coli enzyme. These results suggest that XP-D and XP-E cells are defective in the damage recognition subunit(s) of human excision nuclease.
The Theory of the Dynamic Vibration Absorber (1928)

Abstract The “vibration absorber” discussed in this paper consists of a small vibratory system tuned to the operating frequency of a larger machine and attached to it in a suitable location. When properly designed this will reduce the vibrations of the machine itself materially. The absorber, without damping, annihilates vibrations of its own frequency completely, but creates two other critical speeds in the machine system. Therefore it is suitable only for applications on constant-speed machinery. When damping is introduced into the absorber it constitutes a simple and efficient means of diminishing the vibrations of a machine of variable speed. An analysis of its operation in simple cases with and without damping is given in the paper, tests made on a model are described, and actual applications are discussed.
On-off control of flexible spacecraft with specified fuel usage (1997)

A method for generating on-off command profiles for flexible systems is presented. The command profiles move a system without residual vibration while using a specified amount of actuator fuel. Robustness to modeling errors can be incorporated into the design of the command signals. Techniques are presented which facilitate implementation and indicate prudent choices for the amount of fuel to be used. The method is compared to other command generation techniques that balance fuel usage and slew time.
Effect of impurities on the fixed charge of nanoscale HfO2 films grown by atomic layer deposition (2006)

Hf O 2 films were grown by atomic layer deposition using two different precursor chemistries—HfCl4 and tetrakis(diethylamido)hafnium (TDEAH) with H2O as the oxidant. Electrical measurements on capacitor structures fabricated using the films showed a 0.4V positive shift in the flatband voltage for the chloride-HfO2 with respect to the amide-derived HfO2, indicating a considerable negative fixed charge in the dielectric. Secondary ion mass spectrometry depth profiles of the gate stack showed that Cl segregated preferentially at the HfO2∕SiO2 interface for chloride-derived HfO2. In situ vacuum anneals of the HfCl4-derived films at 500°C did not affect the profile, indicating that Cl is stably bonded at that interface. A similar analysis of the TDEAH-derived HfO2 showed very low concentrations of C, N, and H impurities. A positive fixed charge of +4.5×1011∕cm2 was extracted for the amide-HfO2 whereas a negative fixed charge of −1.86×1012∕cm2 was estimated for the chloride-HfO2. Thus, Cl incorporation can significantly alter both the magnitude and sign of the fixed charge in the HfO2∕SiO2∕Si gate stacks.
First Examples of Transition-Metal Free Sonogashira-Type Couplings (2003)

[reaction: see text] We report here our observation that, using appropriate reaction conditions, the Sonogashira reaction can be performed without the need for transition-metal catalysts. Our approach involves the use of water as a solvent, poly(ethylene glycol) as a phase-transfer agent, and sodium hydroxide as a base. The methodology works, to differing extents, for aryl iodides and bromides.
Hepatocyte growth factor: molecular structure, roles in liver regeneration, and other biological functions. (1992)

Hepatocyte growth factor (HGF) is the most potent mitogen for mature hepatocytes and seems to act as a hepatotropic factor that has not been purified over the past 30 years. HGF was first purified from rat platelets in 1986. HGF is a hetrodimer molecule composed of 69-kDa alpha-subunit and 34-beta-subunit. In 1989, cDNAs of both human and rat HGF were cloned and primary structure of HGF was determined. HGF is derived from preproprecursor of of 728 amino acids, which is proteolytically processed to form mature HGF. The alpha-chain contains four kringle domains and it has 38% homology with plasmin. HGF mRNA and HGF activity increase markedly in the liver of rats after various liver injuries such as hepatitis, ischemia, physical crush, and partial hepatectomy. Production of HGF in the liver occurs in Kupffer cells and sinusoidal endothelial cells, but not in parenchymal hepatocytes. HGF mRNA is also markedly increased even in the intact lung, kidney, and spleen after injuries of the liver. Therefore, HGF may act as a trigger for liver regeneration through two mechanisms: a paracrine mechanism and an endocrine mechanism. Moreover, HGF mRNA increases markedly in the kidney after various renal injuries, thus it suggests that HGF may act not only as a hepatotropic factor but also as a renotropic factor. HGF receptor with a Kd of 20 to 30 pM is widely distributed in various epithelial cells including hepatocytes. HGF receptor was recently identified as the product of c-met protooncogene, which encodes a 190-kDa transmembrane protein possessing tyrosine kinase domain. HGF has recently been shown to be a pleiotropic factor. HGF stimulates growth of various epithelial cells, including renal tubular cells (Mitogen). It is worth noting that HGF strongly enhances motility of epithelial cells (Motogen) and induces epithelial tubule formation (Morphogen), while it strongly inhibits growth of several tumor cells. All these findings indicate that HGF may have important roles in organogenesis, morphogenesis, carcinogenesis, as well as in organ regeneration.