gebhart/patrepeval huggingface dataset:
Hairless is a nuclear receptor corepressor essential for skin function (2009)

The activity of nuclear receptors is modulated by numerous coregulatory factors. Corepressors can either mediate the ability of nuclear receptors to repress transcription, or can inhibit transactivation by nuclear receptors. As we learn more about the mechanisms of transcriptional repression, the importance of repression by nuclear receptors in development and disease has become clear. The protein encoded by the mammalian Hairless (Hr) gene was shown to be a corepressor by virtue of its functional similarity to the well-established corepressors N-CoR and SMRT. Mutation of the Hr gene results in congenital hair loss in both mice and men. Investigation of Hairless function both in vitro and in mouse models in vivo has revealed a critical role in maintaining skin and hair by regulating the differentiation of epithelial stem cells, as well as a putative role in regulating gene expression via chromatin remodeling.
Anti-idiotypic Antibody Vaccine for Type B Viral Hepatitis in Chimpanzees (1986)

Anti-idiotypic antibodies (anti-Id) that contain an internal image component that mimics the surface antigen of hepatitis B virus (HBsAg) were used to immunize chimpanzees. Four injections of the rabbit anti-Id preparation elicited an antibody response to HBsAg (anti-HBs). The antibody specificity appeared to be against the anti-Id, since the anti-Id immunogen was shown to bind the chimpanzee anti-HBs. Two chimpanzees immunized with the anti-Id, along with two control animals that were either untreated or received a nonimmune rabbit immunoglobulin G preparation, were challenged with infectious hepatitis B virus. Both control chimpanzees developed clinical and serological characteristics consistent with an active hepatitis B virus infection, whereas the two anti-Id treated chimpanzees were protected from infection. Since chimpanzees provide a relevant model of a human response to hepatitis B virus immunization and infection, these results indicate that anti-Id preparations such as that described here might be candidates for vaccines against human diseases.
Electrodeless dielectrophoresis: Impact of geometry and material on obstacle polarization (2015)

Insulator-based (electrodeless) dielectrophoresis (iDEP) is a promising particle manipulation technique, based on movement of matter in inhomogeneous fields. The inhomogeneity of the field arises because the excitatory field distorts at obstacles (posts). This effect is caused by accumulation of polarization charges at material interfaces. In this study, we utilize a multipole expansion method to investigate the influence of geometry and material on field distortion of posts with arbitrary cross-sections in homogeneous electric fields applied perpendicular to the longitudinal axis of the post. The post then develops a multipole parallel or anti parallel to the excitatory field. The multipoles intensity is defined by the post's structure and material properties and directly influences the DEP particle trapping potential. We analyzed posts with circular and rhombus-shaped cross-sections with different cross-sectional width-to-height ratios and permittivities for their polarization intensity, multipole position, and their particle trapping behavior. A trade-off between high maximum field gradient and high coverage range of the gradient is presented, which is determined by the sharpness of the post's edges. We contribute to the overall understanding of the post polarization mechanism and expect that the results presented will help optimizing the structure of microchannels with arrays of posts for electrodeless DEP application.
Ultrafiltration Membranes Composed of Highly Cross‐Linked Cationic Polymer Gel: the Network Structure and Superior Separation Performance (2011)

Ultrafiltration membranes with a thickness of several tens of nanometers are prepared from cross-linked poly(4-vinylpyridine) gel using a flat and smooth sacrificial layer of metal hydroxide nanostrands. The membranes have a network structure with pores sizes of approximately 2.0 ± 1.0 nm and can separate small proteins and organic dyes at a surprisingly high filtration rate. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Transcriptional control of liver regeneration (1996)

Determining what factors are responsible for initiating regeneration following partial hepatectomy or toxic damage, and how the liver maintains differentiated functions while the hepatocytes are undergoing cellular proliferation are central issues in understanding the molecular bases of liver regeneration. Examination of the transcriptional milieu in the regenerating liver provides clues to the answers to these questions. Growth factor-generated intracellular signals that trigger liver regeneration result in activation via posttranslational modifications of latent, normally inactive transcription factors that preexist in the liver. Two transcription factors that are activated by this mechanism include posthepatectomy factor/nuclear factor-kappa B) and Stat3. Because cytokines such as tumor necrosis factor-alpha (TNF-alpha), interleukin-l (IL-1), and IL-6 can induce these factors in the liver, the finding of activated Stat3 and PHF/NF-kappa B suggests that these cytokines may play a role in some aspects of growth regulation during liver regeneration. Rapidly induced transcription factors, Stat3, PHF/NF-kappa B, and others are responsible for activation of the primary growth response or immediate-early genes, which play a role in regulating later phases of cell growth in regenerating liver and other mitogen-activated cells. Immediate-early genes encode many members of diverse transcription factor families including the Jun-Fos-LRF-1, nuclear receptor, and myc families to name a few. In this way a transcriptional cascade is established during the G1 phase of liver regeneration. Coexisting with these induced factors are liver-specific transcription factors such as the CAAT enhancer binding proteins and hepatocyte nuclear factors, which may interact with growth-induced factors to help the liver maintain metabolic homeostasis during regeneration. As a result the liver is able to accomplish the goals of reestablishing its mass while it maintains its functional capacity during regeneration.
Graphene/Si-nanowire heterostructure molecular sensors (2014)

Wafer-scale graphene/Si-nanowire (Si-NW) array heterostructures for molecular sensing have been fabricated by vertically contacting single-layer graphene with high-density Si NWs. Graphene is grown in large scale by chemical vapour deposition and Si NWs are vertically aligned by metal-assisted chemical etching of Si wafer. Graphene plays a key role in preventing tips of vertical Si NWs from being bundled, thereby making Si NWs stand on Si wafer separately from each other under graphene, a critical structural feature for the uniform Schottky-type junction between Si NWs and graphene. The molecular sensors respond very sensitively to gas molecules by showing 37 and 1280% resistance changes within 3.5/0.15 and 12/0.15 s response/recovery times under O2 and H2 exposures in air, respectively, highest performances ever reported. These results together with the sensor responses in vacuum are discussed based on the surface-transfer doping mechanism.
Diversity of endophytic bacteria in ginseng and their potential for plant growth promotion (2010)

Endophytic bacteria have been found in virtually every plant studied, where they colonize the internal tissues of their host plant and can form a range of different beneficial relationships. The diversity of bacterial endophytes associated with ginseng plants of varying age levels in Korea was investigated. Fifty-one colonies were isolated from the interior of ginseng stems. Although a mixed composition of endophyte communities was recovered from ginseng based on the results of 16S rDNA analysis, bacteria of the genus Bacillus and Staphylococcus dominated in 1-year-old and 4-year-old plants, respectively. Phylogenetic analysis revealed four clusters: Firmicutes, Actinobacteria, α-Proteobacteria, and γ-Proteobacteria, with Firmicutes being predominant. To evaluate the plant growth promoting activities, 18 representative isolates were selected. Amplification of nifH gene confirmed the presence of diazotrophy in only two isolates. Half of the isolates solubilized mineral phosphate. Except four, all the other endophytic isolates produced significant amounts of indole acetic acid in nutrient broth. Iron sequestering siderophore production was detected in seven isolates. Isolates E-I-3 (Bacillus megaterium), E-I-4 (Micrococcus luteus), E-I-8 (B. cereus), and E-I-20 (Lysinibacillus fusiformis) were positive for most of the plant growth promoting traits, indicating their role in growth promotion of ginseng.
Repeated BCG vaccination is more effective than a single dose in preventing diabetes in non-obese diabetic (NOD) mice. (1997)

Stimulation of the non-obese diabetic (NOD) mouse immune-system with a single bacillus Calmette-Guerin (BCG) vaccination can inhibit the development of diabetes. The optimal dose, and the time and number of vaccinations is still to be clarified. In this study we evaluated the protective effect of repeated BCG vaccinations on preventing diabetes in NOD mice. 17/32 (53%) of the control group, 8/31 (26%) of the single vaccine-treated (at age 35 days) mice, and 7/23 (30%) of the single vaccine-treated (at age 90 days) mice developed diabetes, and none of the repeated BCG vaccination (at age 35 & 90 days, n = 14) animals developed the disease, up to 250 days of age (p < 0.05, compared with controls and each of the single-vaccination groups). While the severity of insulitis was lower in repeatedly BCG-treated mice at age 120 days as compared with controls and single BCG-vaccination groups, we could not detect significant differences in the Intracellular adhesion molecule-1 (ICAM-1) expression between the various groups. There were no differences in weight gain and blood hematocrit between the different groups. Our report demonstrates that repeated BCG vaccination is safe and more effective than a single dose in preventing type I diabetes in NOD mice. This data should be considered in planning new human trials with BCG.
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations (2009)

Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From approximately 3 million reads derived from a single Illumina Genome Analyzer lane, approximately 94% (approximately 50,500) target sites can be observed with at least one read. The uniformity of coverage was also greatly improved; up to 93% and 57% of all targets fell within a 100- and 10-fold coverage range, respectively. Alleles at >400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%-100%. We detected >500 SNPs not currently in dbSNP, 362 of which were in targeted CpG locations. Transitions in CpG sites were at least 13.7 times more abundant than non-CpG transitions. Fractions of polymorphic CpG sites are lower in CpG-rich regions and show higher correlation with human-chimpanzee divergence within CpG versus non-CpG sites. This is consistent with the hypothesis that methylation rate heterogeneity along chromosomes contributes to mutation rate variation in humans. Our success suggests that targeted CpG resequencing is an efficient way to identify common and rare genetic variations. In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation.
FORMATION OF HELICAL SUPER STRUCTURE FROM SINGLE-WALLED BILAYERS BY AMPHIPHILES WITH OLIGO-l-GLUTAMIC ACID-HEAD GROUP (1984)

Abstract Double-chain alkyl amphiphiles with oligo-l-glutamic acid-head group were prepared. These compounds were dispersed in water at pH 8 to 9 to form bilayer aggregates, in which helical and hollow structures were contained. New CD bands were observed in the solution.
Enriched Odor Exposure Increases the Number of Newborn Neurons in the Adult Olfactory Bulb and Improves Odor Memory (2002)

In the mammalian forebrain, most neurons originate from proliferating cells in the ventricular zone lining the lateral ventricles, including a discrete area of the subventricular zone (SVZ). In this region, neurogenesis continues into adulthood. Most of the cells generated in the SVZ are neuronal precursors with progeny that migrate rostrally along a pathway known as the rostral migratory stream before they reach the main olfactory bulb (MOB) where they differentiate into local interneurons. The olfactory system thus provides an attractive model to investigate neuronal production and survival, processes involving interplay between genetic and epigenetic influences. The present study was conducted to investigate whether exposure to an odor-enriched environment affects neurogenesis and learning in adult mice. Animals housed in either a standard or an odor-enriched environment for 40 d were injected intraperitoneally with bromodeoxyuridine (BrdU) to detect proliferation among progenitor cells and to follow their survival in the MOB. The number of BrdU-labeled neurons was not altered 4 hr after a single BrdU injection. In contrast, the number of surviving progenitors 3 weeks after BrdU injection was markedly increased in animals housed in an enriched environment. This effect was specific because enriched odor exposure did not influence hippocampal neurogenesis. Finally, we showed that adult mice housed in odor-enriched cages display improved olfactory memory without a change in spatial learning performance. By maintaining a constitutive turnover of granule cells subjected to modulation by environmental cues, ongoing bulbar neurogenesis could be associated with improved olfactory memory.
Development of Automatic Test Facilities for Pneumatic Devices (1998)

The manufacture and overhaul of safety-critical braking equipment demands reliable and repeatable testing equipment to verify compliance with test specifications. Historically, testing of pneumatic devices has been conducted on a purpose-built apparatus, fitted with numerous cocks, clamps and analogue gauges. Such test racks require regular maintenance and calibration and require high levels of operator skill. This paper describes the progress made by Westinghouse Brakes Australia in the development of automatic, computer controlled test racks which increase repeatability, traceability, reliability and simplify troubleshooting. The potential for this technology to be adapted to a unit for the automatic testing of brake equipment on railway wagons is also discussed.
A recombinant retrovirus encoding alkaline phosphatase confirms clonal boundary assignment in lineage analysis of murine retina. (1992)

Recombinant retroviruses encoding the histochemically detectable enzyme beta-galactosidase have been used to investigate lineage in the vertebrate nervous system. Identification of the descendants of individual progenitors is straightforward when progeny cells are arranged in a reproducible, clustered pattern, but difficulties in interpretation arise when progeny migrate extensively and/or in an irregular pattern. To better resolve clonal boundaries, additional histochemical marker viruses that engender distinctive reaction products can be used in combination with lacZ-bearing viruses. To this end, we have created a retrovirus vector, DAP, encoding an easily assayable enzyme, human placental alkaline phosphatase. DAP was found to be at least as useful as a lacZ-encoding retrovirus (e.g., BAG) with respect to high viral titer, stability of expression, and in identification of infected cells in vivo. Moreover, it was found to be neutral with respect to postnatal rodent retinal development and offered superior staining characteristics relative to lacZ. Coinfection of rodent retina with DAP and BAG allowed an examination of the clonal nature of radial arrays of labeled retinal cells that previously had been described as products of a single infected progenitor. Of 1100 radial arrays examined for the presence of both DAP- and BAG-infected cells, only 1.2% were the result of infection with more than one virus.
Pronuclear Microinjection and Oviduct Transfer Procedures for Transgenic Mouse Production (2013)

Transgenic mouse technology is a powerful method for studying gene function and creating animal models of human diseases. Currently, the most widely used method for generating transgenic mice is the pronuclear microinjection method. In this method, a transgenic DNA construct is physically microinjected into the pronucleus of a fertilized egg. The injected embryos are subsequently transferred into the oviducts of pseudopregnant surrogate mothers. A portion of the mice born to these surrogate mothers will harbor the injected foreign gene in their genomes. These procedures are technically challenging for most biomedical researchers. Inappropriate experimental procedures or suboptimal equipment setup can substantially reduce the efficiency of transgenic mouse production. In this chapter, we describe in detail our microinjection setup as well as our standard microinjection and oviduct transfer procedures.
A novel Fc-engineered monoclonal antibody to CD37 with enhanced ADCC and high proapoptotic activity for treatment of B-cell malignancies (2011)

The tetraspanin CD37 is widely expressed in B-cell malignancies and represents an attractive target for immunotherapy with mAbs. We have chimerized a high-affinity mouse Ab to CD37 and engineered the CH2 domain for improved binding to human Fcγ receptors. The resulting mAb 37.1 showed high intrinsic proapoptotic activity on malignant B cells accompanied by homotypic aggregation. Furthermore, the Ab-mediated high Ab-dependent cell-mediated cytotoxicity (ADCC) on lymphoma and primary CLL cells. mAb 37.1 strongly depleted normal B cells as well as spiked B-lymphoma cells in blood samples from healthy donors as well as malignant B cells in blood from CLL patients. In all assays, mAb 37.1 was superior to rituximab in terms of potency and maximal cell lysis. A single dose of mAb CD37.1 administered to human CD37-transgenic mice resulted in a reversible, dose-dependent reduction of peripheral B cells. In a Ramos mouse model of human B-cell lymphoma, administration of mAb 37.1 strongly suppressed tumor growth. Finally, a surrogate Fc-engineered Ab to macaque CD37, with in vitro proapoptotic and ADCC activities very similar to those of mAb 37.1, induced dose-dependent, reversible B-cell depletion in cynomolgus monkeys. In conclusion, the remarkable preclinical pharmacodynamic and antitumor effects of mAb 37.1 warrant clinical development for B-cell malignancies.
Glycosyltransferase‐Catalyzed Synthesis of Thiooligosaccharides (2004)

Eine Alternative zur chemischen Synthese: Thiooligosaccharide, gebildet aus den zugehörigen Kohlenhydratthiolen und Zuckernucleotid-Donoren durch Inkubation mit Glycosyltransferasen, sind stabil gegen Glycosylhydrolasen und könnten als Antigene mit verlängerter Bioverfügbarkeit eingesetzt werden.
Hepatocyte nuclear factor 1 alpha is expressed in a hamster insulinoma line and transactivates the rat insulin I gene. (1992)

Systematic mutational analysis previously identified two primary regulatory elements within a minienhancer (-247 to -198) of the rat insulin I promoter that are critical for transcriptional activity. The Far box (-241 to -232) and the FLAT element (-222 to -208) synergistically upregulate transcription and, together, are sufficient to confer tissue-specific and glucose-responsive transcriptional activity on a heterologous promoter. Detailed analysis of the FLAT element further revealed that, in addition to the positive regulatory activity it mediates in tandem with the Far box, it is a site for negative regulatory control. A portion of the FLAT element bears considerable sequence similarity to the consensus binding site for hepatocyte nuclear factor 1 alpha (HNF1 alpha; LF-B1) a liver-enriched homeodomain-containing transcription factor. Here we show that the HNF1-like site within the FLAT element exhibited positive transcriptional activity in both HepG2 and HIT cells and bound similar, but distinguishable, nuclear protein complexes in the respective nuclear extracts. Screening of a hamster insulinoma cDNA library with a PCR-derived probe encompassing the DNA-binding domain of rat HNF1 alpha resulted in isolation of a hamster HNF1 alpha (hHNF1 alpha) cDNA homolog. Specific antiserum identified the HNF1 alpha protein as one component of a specific FLAT-binding complex in HIT nuclear extracts. Expression of the hHNF1 alpha cDNA in COS cells resulted in transactivation of reporter constructs containing multimerized segments of the rat insulin I minienhancer. Thus, HNF1 alpha, one component of a DNA-binding complex involved in transcriptional regulation of the rat insulin I gene, may play a significant role in nonhepatic as well as hepatic gene transcription.
Resizable, Scalable, Concurrent Hash Tables (2011)

We present algorithms for shrinking and expanding a hash table while allowing concurrent, wait-free, linearly scalable lookups. These resize algorithms allow the hash table to maintain constant-time performance as the num-ber of entries grows, and reclaim memory as the number of entries decreases, without delaying or disrupting read-ers. We implemented our algorithms in the Linux kernel, to test their performance and scalability. Benchmarks show lookup scalability improved 125x over reader-writer locking, and 56 % over the current state-of-the-art for Linux, with no performance degradation for lookups during a resize. To achieve this performance, this hash table imple-mentation uses a new concurrent programming method-ology known as relativistic programming. In particular, we make use of an existing synchronization primitive which waits for all current readers to finish, with little to no reader overhead; careful use of this primitive allows ordering of updates without read-side synchronization or memory barriers. 1