gebhart/patrepeval huggingface dataset:
Human Leukocyte Antigen Matching Estimations in a Hypothetical Bank of Human Embryonic Stem Cell Lines in the Japanese Population for Use in Cell Transplantation Therapy (2006)

Human embryonic stem (hES) cell lines are of great potential in cell transplantation therapy. However, recipients of such allogeneic transplants probably need treatment with immunosuppressants. Recently, Taylor et al. [Lancet 2005;366:2019-2025] proposed banking of hES cell lines and estimated the required number of hES cell lines for beneficial human leukocyte antigen (HLA) matching in the U.K. population. Here, we carried out such an estimation in the Japanese population. We calculated the proportion of patients who can find at least one HLA-matched donor at three loci of HLA-A, -B, and -DR. With a bank of hES cell lines from 170 randomly selected donated embryos, 80% of patients were expected to find at least one hES cell line with a single mismatch at one HLA locus or a better match. Furthermore, 80% of patients are expected to find at least one donor with complete matching at the three HLA loci if parthenogenetic homozygous hES cell lines are established from 55 randomly selected donated oocytes. The relatively low ethnic diversity of the Japanese population may have resulted in a high success rate in beneficial matching. Moreover, parthenogenetic hES cell lines can greatly reduce the number required for a higher degree of HLA matching.
Selective epitaxial growth silicon bipolar transistors for material characterization (1988)

In development of the epitaxial lateral overgrowth (ELO) bipolar transistor, devices were fabricated in silicon selective epitaxial growth (SEG). These devices were used to electrically characterize the quality of the SEG material. Three silicon bipolar transistors, with almost identical doping profiles and geometries were simultaneously fabricated on the same wafer and their electrical characteristics compared. The three transistors were located in the substrate, a single SEG layer, and a double (interrupted growth) SEG layer. The SEG silicon was grown in a reduced-pressure RF-heated pancake-type epitaxial reactor at 950 degrees C and 150 torr. The transistors were tested for junction ideality factors, junction reverse-bias leakage currents, and forward DC current gain. Test results indicated the excellent device quality of the SEG material relative to the substrate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Role of sympathetic activity in controlling the expression of vascular endothelial growth factor in brown fat cells of lean and genetically obese rats (1999)

The thermogenic activity of brown adipose tissue (BAT) is heavily dependent on high perfusion, through its dense vascular system. Angiogenesis must go hand-in-hand with BAT functions, but little is known about the factors controlling it. In the present study we demonstrate that: (a) vascular endothelial growth factor (VEGF) is synthesised and released in brown adipocytes in culture; (b) VEGF mRNA isoforms and protein appear in dispersed mature brown adipocytes and whole tissue; (c) VEGF expression is increased in BAT from cold-exposed rats, and in cultured brown adipocytes exposed to noradrenaline and the beta3-adrenoceptor agonists; (e) BAT from genetically obese (falfa) rats exhibits reduced expression of VEGF as well as a change in the ratio of mRNA isoforms. It is concluded that sympathetic control of VEGF expression via noradrenaline acting on beta3-adrenoceptors plays a major role in developmental and adaptive angiogenesis, and defects in this contribute to the reduced thermogenic capacity of BAT in genetic obesity.
Stimulation of osteogenic differentiation in human osteoprogenitor cells by pulsed electromagnetic fields: an in vitro study (2010)

PEMF exposure of differentiating human BMSCs enhanced mineralization and seemed to induce differentiation at the expense of proliferation. The osteogenic stimulus of PEMF was confirmed by the up-regulation of several osteogenic marker genes in the PEMF treated group, which preceded the deposition of mineral itself. These findings indicate that PEMF can directly stimulate osteoprogenitor cells towards osteogenic differentiation. This supports the theory that PEMF treatment may recruit these cells to facilitate an osteogenic response in vivo.
Single-Crystal-to-Single-Crystal Topochemical Polymerizations of a Terminal Diacetylene:  Two Remarkable Transformations Give the Same Conjugated Polymer (2003)

Host-guest chemistry was used to prepare a cocrystal of a dipyridyl substituted oxalamide host and a resorcinol derivative of a terminal diacetylene. X-ray crystallography revealed that the molecules assemble into a triple-helix with the diacetylene functionalities aligned in the center of the helix. Upon heating, the diacetylenes polymerize to give the corresponding polymer. In a second experiment, the X-ray structure of the crystalline hydrate of the same diacetylene also showed a suitable alignment of the diacetylene functionalities. These crystals polymerize at only 50 degrees C with the C1 carbon end of the diacetylene undergoing an unprecedented 2.4 A inward swinging movement. This results in a remarkable 9% increase in crystal density. These are the first structurally characterized polymerizations of any terminal diacetylene. A detailed comparison of the two sets of structural changes offers an interesting insight into the precise trajectories of polymerization reactions.
The BALB/c secondary response to the Sb site of influenza virus hemagglutinin. Nonrandom silent mutation and unequal numbers of VH and Vk mutations. (1990)

We have determined the nucleotide sequences of the expressed VH and Vk genes from 13 secondary (2 degrees) hemagglutinin (HA) (Sb) specific hybridomas derived from a single mouse. These antibodies share an Id, H37-68 (68Id) that dominates the 2 degrees HA(Sb) response in this mouse, but is rare or absent from 2 degrees responses of other mice. We find that these antibodies derive from five clones. The H chains of these antibodies are encoded by a single VH gene joined to a variety of DH and JH genes. The length of complementarity-determining region (CDR) 3 and sequence of the D-J junction are restricted, suggesting selection on CDR3 of the H chain. The L chains are more diverse. In the presented examples, they are encoded by the Vk21C and Vk21E genes and a Vk9 gene, and are joined to Jk1, 2, or 4. Each antibody is extensively mutated. The nature and distribution of the mutations suggests that 68Id-producing cells have been selected by Ag, although there are differences regarding the domain (VH, Vk, or both) in which mutations were selected. The implications of these findings on the idiosyncratic nature of the 68Id antibody response to HA(Sb) are discussed. There are two unusual characteristics regarding somatic mutation in these hybridomas. Whereas the expressed VH and Vk21 genes appear to have accumulated mutations at a high rate (1 to 1.5 x 10(-3)/base pairs/division, the expressed Vk9 genes appear to have accumulated mutations at a 5 to 15-fold lower rate than the expressed VH genes in the same cells. There is also a surprisingly high number of parallel silent somatic mutations in the VH genes, of which all but one are clustered to a 28-bp region in framework region 2 and CDR 2-encoding segments. The probability that this could have occurred by a random mutational process is essentially zero.
Low-dose deoxycoformycin in the treatment of hairy cell leukemia (1986)

Ten patients with progressive hairy cell leukemia were treated with 2′deoxycoformycin (dCF) by intravenous bolus (4 mg/m2) given every other week. All ten patients are evaluable for response and nine of the ten patients have achieved a complete remission. In addition to clearing of hairy cells from the bone marrow, eight patients had resolution of their monocytopenia. Seven of the nine patients remain in unmaintained remission with a median duration of 6.2 months. Two patients have had relapse in the bone marrow alone and continue to have normal peripheral blood counts. They are being followed without treatment. Toxicity was minimal at this low dose with one patient having a mild reversible reduction in creatinine clearance. Four other patients had reversible neutropenia. There were no significant infections associated with treatment. Low-dose deoxycoformycin administered intravenously every other week represents an extremely effective treatment for hairy cell leukemia.
Binding of a histidine-rich peptide toPorphyromonas gingivalis (1991)

Porphyromonas gingivalis 381 cells were incubated with 125I-histidine-rich polypeptide (histatin) 5 in the presence or absence of unlabeled histatin 5, to evaluate the histatin-binding capacity of the cells. The binding of histatin 5 was rapid, reversible, saturable and specific. The number of histatin 5-binding sites per cell was 3,600, and the dissociation constant (Kd) was in the order of 10(-6) M. These findings suggest that histatin interacts with certain bacterial cells through specific binding sites on their surface, and will allow the development of a histatin radioreceptor assay.
Thermography basket catheter: In vivo measurement of the temperature of atherosclerotic plaques for detection of vulnerable plaques (2003)

We have developed an intravascular thermography basket catheter to measure the temperature of the vessel wall to locate foci of inflammation. Our 3 Fr thermography basket catheter is a thermocouple-based catheter made of a nitinol expandable and externally controllable basket system loaded with nine small and flexible built-in thermosensors. It is equipped with real-time data acquisition software with a thermal resolution of 0.0001 degrees C and a sampling rate of 20 readings per second. In 10 inbred cholesterol-fed dogs with femoral (but not carotid) atherosclerosis, we found foci of warmth on the surface of atherosclerotic but not disease-free regions (P < 0.05). Marked temperature heterogeneity was also observed in the aortas of atherosclerotic Watanabe rabbits but not in normal rabbits. The catheters showed satisfactory accuracy, reproducibility, and safety. If confirmed in further studies, it has the potential to be utilized in detection of vulnerable plaques.
Comparison of three whole seed near‐infrared analyzers for measuring quality components of canola seed (1994)

Abstract Whole seed near‐infrared (NIR) analyzers are capable of high‐speed compositional analysis of oilseed commodities. This study compared the PerCon Inframatic 8144 (Perten Instruments, North America Inc., Reno, NV), the Tecator Infratec 1225 (Tecator AB, Hoganas, Sweden) and the NIR‐Systems 6500 (NIR Systems, Inc., Silver Spring, MD) analyzers for measurement of oil, protein, chlorophyll and glucosinolates in intact canola seed of composite samples from the Grain Research Laboratory's (Winnipeg, Manitoba, Canada) annual Western Canada Harvest Surveys (1985–1989) for assembly of calibration and prediction sets. No significant differences were found between the three instruments for oil [standard error of prediction (SEP 0.43–0.55%)], protein (SEP 0.35–0.42%) and glucosinolates (SEP 2.4–3.8 mM/g). Neither the Tecator nor the PerCon instruments were effective for determining chlorophyll. By combining oil content and fatty acid composition data to give an estimate of the total level of each fatty acid in the sample, high correlations were obtained for total saturates, linolenic acid, and linoleic acid although the RPD (ratio of the S.E. of prediction to the S.D. of the original data) values were not high enough to enable routine use of the method to predict results.
The Hypoxia-Inducible Factor 2α N-Terminal and C-Terminal Transactivation Domains Cooperate To Promote Renal Tumorigenesis In Vivo (2007)

Hypoxia-inducible factor (HIF) is a heterodimeric transcription factor, consisting of an alpha subunit and a beta subunit, that controls cellular responses to hypoxia. HIFalpha contains two transcriptional activation domains called the N-terminal transactivation domain (NTAD) and the C-terminal transactivation domain (CTAD). HIFalpha is destabilized by prolyl hydroxylation catalyzed by EglN family members. In addition, CTAD function is inhibited by asparagine hydroxylation catalyzed by FIH1. Both hydroxylation reactions are linked to oxygen availability. The von Hippel-Lindau tumor suppressor protein (pVHL) is frequently mutated in kidney cancer and is part of the ubiquitin ligase complex that targets prolyl hydroxylated HIFalpha for destruction. Recent studies suggest that HIF2alpha plays an especially important role in promoting tumor formation by pVHL-defective renal carcinoma cells among the three HIFalpha paralogs. Here we dissected the relative contribution of the two HIF2alpha transactivation domains to hypoxic gene activation and renal carcinogenesis and investigated the regulation of the HIF2alpha CTAD by FIH1. We found that the HIF2alpha NTAD is capable of activating both artificial and naturally occurring HIF-responsive promoters in the absence of the CTAD. Moreover, we found that the HIF2alpha CTAD, in contrast to the HIF1alpha CTAD, is relatively resistant to the inhibitory effects of FIH1 under normoxic conditions and that, perhaps as a result, both the NTAD and CTAD cooperate to promote renal carcinogenesis in vivo.
An Improved Clinical Model of Orthotopic Pancreatic Cancer in Immunocompetent Lewis Rats (2001)

The study of pancreatic cancer (PaCa) requires orthotopic, clinically relevant animal models. The aims of this study were to establish an orthotopic model of ductal pancreatic adenocarcinoma in immunocompetent Lewis rats and to develop a scoring system to quantify local tumor infiltration and distant metastasis. Cells (10(7)) of the rat ductal PaCa cell line DSL-6A/C1 were injected s.c. into donor rats. After 8 weeks, either three (IPL-3) or five (IPL-5) fragments (1 mm3) of the resulting s.c. tumors were microsurgically implanted into the pancreas of recipient rats. In another series of animals, 10(7) DSL-6A/C1 cells were directly injected (INJ) into the pancreas. All animals were monitored daily until death or for 16 weeks. At autopsy, volume of primary tumors and ascites, local and systemic tumor spread, and histologic phenotype were assessed. IPL-5 resulted in significantly larger tumors (12,224 +/- 1,933 mm3), more local infiltration and systemic spread (score: 18.3 +/- 2.0 points), severe clinical tumor disease, and lethality (50%) in comparison to the other induction techniques (IPL-3: 283 +/- 115 mm3/3.5 +/- 0.8 points/0; INJ: 752 +/- 207 mm3/4.3 +/- 0.8 points/8%). Histologic examination revealed moderately to well-differentiated ductal tumors, surrounded by dense stroma. Intraperitoneal tumor dissemination in the INJ group occurred simultaneous with primary tumor growth, indicating PaCa cell spread during injection. Orthotopic implantation of five DSL-6A/C1 tumor fragments into the rat pancreas provides a valid clinical model of ductal pancreatic adenocarcinoma in immunocompetent rodents for preclinical treatment studies. The dissemination score we used permitted quantification of local and systemic tumor spread.
Improving nonstoquastic quantum annealing with spin-reversal transformations (2021)

Nonstoquastic Hamiltonians are hard to simulate due to the sign problem in quantum Monte Carlo simulation. It is, however, unclear whether nonstoquasticity can lead to advantage in quantum annealing. Here we show that $YY$ interactions between the qubits make the adiabatic path during quantum annealing, and therefore the performance, dependent on spin-reversal transformations. With the right choice of spin-reversal transformation, a nonstoquastic Hamiltonian with $YY$ interaction can outperform stoquastic Hamiltonians with similar parameters. We introduce an optimization protocol to determine the optimal transformation and discuss the effect of suboptimality.
Terminating Spatial Hierarchies by A Priori Bounding Memory (2007)

We consider the efficient top-down construction of spatial hierarchies for accelerating ray tracing and present a new termination criterion that allows for a priori fixing the memory footprint of the data structure. The resulting simplification of memory management makes algorithms shorter, more efficient, and more widely applicable, especially when considering hardware implementations and kd-trees. Even the on demand construction of parts of the hierarchy becomes close to trivial. In addition it proves to be the case that the hierarchy construction time easily can be predicted by the size of the provided memory block. This in turn allows for automatically balancing construction and ray tracing time in order to minimize the total time needed to render a frame from scratch.
Fabricating Simple Wax Screen-Printing Paper-Based Analytical Devices To Demonstrate the Concept of Limiting Reagent in Acid–Base Reactions (2018)

In this article, a low-cost, simple, and rapid fabrication of paper-based analytical devices (PADs) using a wax screen-printing method is reported here. The acid–base reaction is implemented in the simple PADs to demonstrate to students the chemistry concept of a limiting reagent. When a fixed concentration of base reacts with a gradually increasing concentration of acid, a dramatic demonstration allows students to discover the limiting reagent by naked eyes observing the color change from phenolphthalein as an indicator. This demonstration is not only a new approach to enhancing students’ learning of the chemistry concept of the limiting reagent, but also presents potential applications of PADs into all levels of chemistry from middle school through college classes.
Correlation of interleukin‐6 production and disease activity in polymyalgia rheumatica and giant cell arteritis (1993)

Increased production of IL-6, but not TNF alpha, is a characteristic finding in patients with PMR or GCA. Corticosteroids rapidly suppress IL-6 production but do not correct the underlying mechanism inducing the increased IL-6 production. The close correlation of plasma IL-6 concentrations with clinical symptoms suggests a direct contribution of this cytokine to the disease manifestations and presents the possibility that monitoring IL-6 levels would be useful in making decisions on adjustment of corticosteroid dosage in individual patients.
Human immunodeficiency virus type 1 Tat does not transactivate mature trans-acting responsive region RNA species in the nucleus or cytoplasm of primate cells (1991)

Human immunodeficiency virus (HIV)-encoded transactivator Tat is essential for viral gene expression and replication. By interacting with a nascent RNA stem-loop called the trans-acting responsive region (TAR). Tat increases rates of initiation and/or elongation of HIV transcription. Several reports have also suggested that Tat has additional effects on mature HIV RNA species including modification of primary transcripts in the nucleus and their increased translation in the cytoplasm. These posttranscriptional effects are most pronounced in the Xenopus oocyte. To investigate directly whether Tat has similar effects on viral transcripts in cells that are permissive for HIV replication, we cotransfected and microinjected human and monkey cells with Tat and TAR in the form of DNA or RNA. Whereas Tat transactivated TAR DNA targets, it did not transactivate TAR RNA targets in the nucleus of microinjected cells or in the cytoplasm of transfected cells. We conclude that in cells permissive for viral replication, Tat exerts its effect primarily at the level of HIV transcription.
Length-dependent gametic CAG repeat instability in the Huntington's disease knock-in mouse (1999)

The CAG repeats in the human Huntington's disease (HD) gene exhibit striking length-dependent intergenerational instability, typically small size increases or decreases of one to a few CAGs, but little variation in somatic tissues. In a subset of male transmissions, larger size increases occur to produce extreme HD alleles that display somatic instability and cause juvenile onset of the disorder. Initial efforts to reproduce these features in a mouse model transgenic for HD exon 1 with 48 CAG repeats revealed only mild intergenerational instability ( approximately 2% of meioses). A similar pattern was obtained when this repeat was inserted into exon 1 of the mouse Hdh gene. However, lengthening the repeats in Hdh to 90 and 109 units produced a graded increase in the mutation frequency to >70%, with instability being more evident in female transmissions. No large jumps in CAG length were detected in either male or female transmissions. Instead, size changes were modest increases and decreases, with expansions typically emanating from males and contractions from females. Limited CAG variation in the somatic tissues gave way to marked mosaicism in liver and striatum for the longest repeats in older mice. These results indicate that gametogenesis is the primary source of inherited instability in the Hdh knock-in mouse, as it is in man, but that the underlying repeat length-dependent mechanism, which may or may not be related in the two species, operates at higher CAG numbers. Moreover, the large CAG repeat increases seen in a subset of male HD transmissions are not reproduced in the mouse, suggesting that these arise by a different fundamental mechanism than the small size fluctuations that are frequent during gametogenesis in both species.
Peripheralization of hemopoietic progenitors in primates treated with anti-VLA4 integrin. (1993)

Interaction of hemopoietic cells with the elements of the underlying bone marrow stroma, the unique site of their "homing" in adult individuals, is essential for sustained normal hemopoiesis. However, the specific molecules responsible for homing and for the continuing interaction of hemopoietic cells with the bone marrow stromal cells in vivo, or those involved in progenitor/stem cell trafficking through the bloodstream, have not been defined. A large repertoire of adhesion receptors, especially of the integrin family, appear to play a prominent role in promoting adhesion of hemopoietic stem cells to cultured marrow stromal cells in vitro. To test the functional role of cytoadhesion molecules in vivo, we treated primates systemically with either anti-alpha 4- or anti-beta 2-integrin antibodies, whose antigens are found in the majority of hemopoietic progenitors and in many differentiated cells. We found that anti-alpha 4 (anti-VLA4, anti-CD49d) but not anti-beta 2 (anti-CD18) treatment selectively mobilized progenitors into the bloodstream (up to 200-fold). Peripheralization involved erythroid, myeloid, and mixed progenitors; was detectable 24 hr after a single anti-VLA4 injection; and lasted beyond the days of treatment. Anti-VLA4 treatment additively augmented peripheralization of progenitors in animals with a preceding course of granulocyte-colony-stimulating factor. These data provide insight on the involvement of VLA4 antigens in the in vivo trafficking of progenitors and are of relevance to collection of peripheral blood stem cells for transplantation.