gebhart/patrepeval huggingface dataset:
Small and big Hodgkin-Reed-Sternberg cells of Hodgkin lymphoma cell lines L-428 and L-1236 lack consistent differences in gene expression profiles and are capable to reconstitute each other (2017)

The hallmark of classical Hodgkin lymphoma (cHL) is the presence of giant, mostly multinucleated Hodgkin-Reed-Sternberg (HRS) cells. Whereas it has recently been shown that giant HRS cells evolve from small Hodgkin cells by incomplete cytokinesis and re-fusion of tethered sister cells, it remains unsolved why this phenomenon particularly takes place in this lymphoma and what the differences between these cell types of variable sizes are. The aim of the present study was to characterize microdissected small and giant HRS cells by gene expression profiling and to assess differences of clonal growth behavior as well as susceptibility toward cytotoxic intervention between these different cell types to provide more insight into their distinct cellular potential. Applying stringent filter criteria, only two differentially expressed genes between small and giant HRS cells, SHFM1 and LDHB, were identified. With looser filter criteria, 13 genes were identified to be differentially overexpressed in small compared to giant HRS cells. These were mainly related to energy metabolism and protein synthesis, further suggesting that small Hodgkin cells resemble the proliferative compartment of cHL. SHFM1, which is known to be involved in the generation of giant cells, was downregulated in giant RS cells at the RNA level. However, reduced mRNA levels of SHFM1, LDHB and HSPA8 did not translate into decreased protein levels in giant HRS cells. In cell culture experiments it was observed that the fraction of small and big HRS cells was adjusted to the basic level several days after enrichment of these populations via cell sorting, indicating that small and big HRS cells can reconstitute the full spectrum of cells usually observed in the culture. However, assessment of clonal growth of HRS cells indicated a significantly reduced potential of big HRS cells to form single cell colonies. Taken together, our findings pinpoint to strong similarities but also some differences between small and big HRS cells.
Assignment of the gene coding for the T3-delta subunit of the T3-T-cell receptor complex to the long arm of human chromosome 11 and to mouse chromosome 9. (1985)

The gene encoding the 20-kDa glycoprotein of the T3-T-cell receptor complex (T3-delta chain) has been mapped to human chromosome 11 by hybridization of a T3-delta cDNA clone (pPGBC#9) to DNA from a panel of human-rodent somatic cell hybrids. In Southern blotting experiments with DNAs of somatic cell hybrids that contained segments of chromosome 11, we were able to assign the T3-delta gene to the distal portion of the long arm of human chromosome 11 (11q23-11qter). By use of a newly developed cDNA clone (pPEM-T3 delta) that codes for the murine T3-delta chain, the mouse T3-delta gene was mapped on chromosome 9. The importance of the T3-delta map position and its relationship to the other genes on the long arm of human chromosome 11 and to those on mouse chromosome 9 is discussed.
Diffusion of Glucose and Glucitol in Microporous and Mesoporous Silicate/Aluminosilicate Catalysts (1996)

The effective diffusivities of glucose and its linear analog glucitol were measured by a liquid chromatographic technique at 30 °C within water-filled silica and aluminosilicate catalysts of mean pore size ranging from 7.4 to 116 Å. For glucose, the effective diffusivity decreased from 1.08 × 10-6 to 1.77 × 10-9 cm2/s as the mean pore size decreased from 116 to 7.4 Å. All values were significantly lower than the molecular diffusivity of 7.02 × 10-6 cm2/s. The effective diffusivities for glucitol were three times lower than those for glucose over the same pore size range due to differences in solute size, structure, and solute−adsorbent interactions. The 8.6 Å glucose molecule was able to diffuse into the 7.4 Å Y-zeolite pore, possibly as its acyclic form. However, the 9.7 Å glucitol molecule could not diffuse into the Y-zeolite pore. The reduced diffusivity was correlated to the reduced pore diameter using the Ternan model.
Low-resistance Ohmic conduction across compound semiconductor wafer-bonded interfaces (1995)

Data are presented demonstrating low-resistance Ohmic conduction across interfaces formed by high-temperature (750–1000 °C) compound semiconductor wafer bonding. Unipolar junctions formed by wafer bonding surfaces consisting of In0.5Ga0.5P/In0.5Ga0.5P, GaP/GaP, GaP/In0.5Ga0.5P, and In0.5Ga0.5P/GaAs are shown to exhibit low-resistance Ohmic conduction for both p- and n-isotype junctions. The achievement of these properties is demonstrated to be critically dependent upon the crystallographic alignment of the bonded wafer surfaces, irrespective of the lattice mismatch between the surfaces. Specifically, we show that the surface orientation of the bonded surfaces must be nominally matched while simultaneously maintaining rotational alignment of the wafers.
TOC: Localizing wireless rechargeable sensors with time of charge (2014)

Wireless rechargeable sensor network is a promising platform for long-term applications such as inventory management, supply chain monitoring and so on. For these applications, sensor localization is one of the most fundamental challenges. Different from traditional sensor node, wireless rechargeable sensor has to be charged above a voltage level by the wireless charger in order to support its sensing, computation and communication operations. In this work, we consider the scenario where a mobile charger stops at different positions to charge sensors, and propose a novel localization design that utilizes the unique Time of Charge (TOC) sequences among wireless rechargeable sensors. Specifically, we introduce two efficient region dividing methods, Inter-node Division and Inter-area Division, to exploit TOC differences from both temporal and spatial dimensions to localize individual sensor nodes. To further optimize the system performance, we introduce both an optimal charger stop planning algorithm for single sensor case and a suboptimal charger stop planning algorithm for the generic multisensor scenario with a provable performance bound. We have extensively evaluated our design by both testbed experiments and large-scale simulations. The experiment and simulation results show that by as less as 5 stops, our design can achieve sub-meter accuracy and the performance is robust under various system conditions.
BRCA1 and BRCA2 mutations and the risk for colorectal cancer (2014)

Women who carry a BRCA1 or BRCA2 mutation are at high risk of breast and ovarian cancer, and may be at moderately increased risk of other cancer types. This review examines studies to date that have evaluated the risk of BRCA1 and BRCA2 mutations for colorectal cancer. Accurate knowledge of colorectal cancer risk in BRCA1/2 carriers is important, because colonoscopy screening can prevent colorectal cancer through the removal of adenomatous polyps. Most studies that have identified an increased risk for colorectal cancer in BRCA1/2 mutation carriers were in high-risk cancer families, while studies that found no association were conducted in specific populations and involved the analysis of founder mutations. A recent prospective study of 7015 women with a BRCA1 or BRCA2 mutation identified significant fivefold increased risk of colorectal cancer among BRCA1 mutation carriers younger than 50 years [standardized incidence ratio (SIR): 4.8; 95% CI: 2.2-9], but not in women with a BRCA2 mutation or in older women. Based on this evidence, women with BRCA1 mutations should be counseled about their increased risk for early-onset colorectal cancer, and offered colonoscopy at 3- to 5-year intervals between the ages of 40 and 50 years, and should follow population guidelines thereafter.
Open treatment of abdominal septic catastrophies (1983)

Abstract From 1973 to 1981, a total of 30 patients undergoing reoperative surgery for serious septic complications were treated without closure of the abdominal cavity. The open wound was covered with gauze soaked in saline. Intraabdominal abscesses could then be evacuated directly, if necessary, under slight general anesthesia in the patient's own bed. Reperitonealization and excess growth of granulation tissue was seen within 2 weeks. Sixteen patients survived. In 10 of these, the wound healed secondarily without any other treatment. In the remaining 6, split‐skin grafts or a pedicled flap was necessary. In 4 patients the abdominal wall almost reestablished itself. The remaining 12 patients showed larger or smaller defects with negligible problems. Patients with severe abdominal sepsis, associated with necrotic wound edges, multiple laparotomies, and multiple organ failures should have the abdominal cavity left completely open.
Resonant nonlinear magneto-optical effects in atoms (2002)

The authors review the history, current status, physical mechanisms, experimental methods, and applications of nonlinear magneto-optical effects in atomic vapors. They begin by describing the pioneering work of Macaluso and Corbino over a century ago on linear magneto-optical effects (in which the properties of the medium do not depend on the light power) in the vicinity of atomic resonances. These effects are then contrasted with various nonlinear magneto-optical phenomena that have been studied both theoretically and experimentally since the late 1960s. In recent years, the field of nonlinear magneto-optics has experienced a revival of interest that has led to a number of developments, including the observation of ultranarrow (1-Hz) magneto-optical resonances, applications in sensitive magnetometry, nonlinear magneto-optical tomography, and the possibility of a search for parity- and time-reversal-invariance violation in atoms.
How Does Synaptotagmin Trigger Neurotransmitter Release? (2008)

Neurotransmitter release at synapses involves a highly specialized form of membrane fusion that is triggered by Ca(2+) ions and is optimized for speed. These observations were established decades ago, but only recently have the molecular mechanisms that underlie this process begun to come into view. Here, we summarize findings obtained from genetically modified neurons and neuroendocrine cells, as well as from reconstituted systems, which are beginning to reveal the molecular mechanism by which Ca(2+)-acting on the synaptic vesicle (SV) protein synaptotagmin I (syt)-triggers rapid exocytosis. This work sheds light not only on presynaptic aspects of synaptic transmission, but also on the fundamental problem of membrane fusion, which has remained a puzzle that has yet to be solved in any biological system.
Facile synthetic route to cone-shaped phosphorylated [CH2P(O)Ph2] calix[4]arenes (1995)

Selective incorporation of one, two or four CH2P(O)Ph2 substituents at specific sites in para-tert-butylcalix[4] arene was achieved using NaH and an appropriate alkylating agent; the tetrasubstituted compound (structure established by X-ray crystallography) was quantitatively reduced to the corresponding tetraphosphine L6 which, by reaction with [{Pd(C6H4CH2NMe2-o)Cl}2], gave access to the tetranuclear complex [{Pd(C6H4CH2NMe2-o)Cl}4L6].
miR-181a/b significantly enhances drug sensitivity in chronic lymphocytic leukemia cells via targeting multiple anti-apoptosis genes (2012)

MicroRNAs (miRNAs) have been shown to play critical roles in regulating the progress of leukemia. We performed miRNA expression profile in six Chinese patients with chronic lymphocytic leukemia (CLL), and in peripheral B cells from pooled 30 healthy donors, using a platform containing 866 human miRNAs. The most frequent changes in miRNAs in CLL cells included downregulation of miR-126, miR-572, miR-494, miR-923, miR-638, miR-130a, miR-181a and miR-181b and up-regulation of miR-29a, miR-660, miR-20a, miR-106b, miR-142-5p, miR-101, miR-30b, miR-34a, miR-let-7f, miR-21 and miR-155. Among the miRNAs down-regulated in CLL cells, we showed that miR-181a/b expression levels were significantly lower in poor prognostic subgroups defined by unmutated immunoglobulin heavy chain variable status and p53 aberrations. Furthermore, under-expression of miR-181a and miR-181b was associated with shorter overall survival and treatment-free survival in CLL patients. We further evaluated fludarabine-induced apoptosis after transfection of primary CLL cells from 40 patients with miR-15a, miR-16-1, miR-34a, miR-181a and miR-181b mimics. Transfection of miR-34a, miR-181a and miR-181b mimics into CLL cells from p53 wild-type patients led to significant increase in apoptosis compared with miRNA control. However, enforced expression of these miRNAs had no effect on B-CLL cells from p53-attenuated patients. We further demonstrated that miR-181a and miR-181b inhibiting BCL-2, MCL-1 and X-linked inhibitor of apoptosis protein by direct binding to 3'UTR. Thus, these results suggest that miR-181a/b may play important roles in the pathogenesis of CLL and may provide a possible therapeutic avenue and a sensitive indicator of the activity of the p53 axis in CLL.
Anti-SIRPα antibodies as a potential new tool for cancer immunotherapy (2017)

Tumor cells are thought to evade immune surveillance through interaction with immune cells. Much recent attention has focused on the modification of immune responses as a basis for new cancer treatments. SIRPα is an Ig superfamily protein that inhibits phagocytosis in macrophages upon interaction with its ligand CD47 expressed on the surface of target cells. Here, we show that SIRPα is highly expressed in human renal cell carcinoma and melanoma. Furthermore, an anti-SIRPα Ab that blocks the interaction with CD47 markedly suppressed tumor formation by renal cell carcinoma or melanoma cells in immunocompetent syngeneic mice. This inhibitory effect of the Ab appeared to be mediated by dual mechanisms: direct induction of Ab-dependent cellular phagocytosis of tumor cells by macrophages and blockade of CD47-SIRPα signaling that negatively regulates such phagocytosis. The antitumor effect of the Ab was greatly attenuated by selective depletion not only of macrophages but also of NK cells or CD8<sup>+</sup> T cells. In addition, the anti-SIRPα Ab also enhances the inhibitory effects of Abs against CD20 and programmed cell death 1 (PD-1) on tumor formation in mice injected with SIRPα-nonexpressing tumor cells. Anti-SIRPα Abs thus warrant further study as a potential new therapy for a broad range of cancers.
(A)BC excinuclease: the Escherichia coli nucleotide excision repair enzyme (1992)

Nucleotide excision repair is the major pathway for removing damage from DNA. (A)BC excinuclease is the nuclease activity which initiates nucleotide excision repair in Escherichia coli. In this review, we focus on current understanding of the structure-function of the enzyme and the reaction mechanism of the repair pathway. In addition, recent biochemical studies on preferential repair of actively transcribed genes in E. coli are summarized.
Theoretical Study of Reactivity of Ge(II)-hydride Compound: Comparison with Rh(I)-Hydride Complex and Prediction of Full Catalytic Cycle by Ge(II)-hydride (2013)

The reaction of a Ge(II) hydride compound HC{CMeArN}2GeH (Ar = 2,6-iPr2C6H3) 1 with 2,2,2-trifluoroacetophenone (CF3PhCO) is theoretically investigated with density functional theory and spin-component-scaled second-order Møller-Plesset methods. This reaction easily occurs with moderate activation barrier and considerably large exothermicity, to afford a Ge(II) alkoxide 2 through a four-membered transition state. In the transition state, the charge transfer from the Ge-H σ-bonding molecular orbital (MO) to the C═O π*-antibonding MO of CF3PhCO plays an important role. Acetone ((CH3)2CO) and benzophenone (Ph2CO) are not reactive for 1, because their π*-antibonding MOs exist at higher energy than that of CF3PhCO. Though 2 is easily formed, the catalytic hydrogenation of CF3PhCO by 1 is difficult because the reaction of 2 with a dihydrogen molecule needs a large activation energy. On the other hand, our calculations clearly show that the catalytic hydrogenation of ketone by cis-RhH(PPh3)24 easily occurs, as expected. The comparison of catalytic cycle between 1 and 4 suggests that the strong Ge-O bond of 2 is the reason of the very large activation energy for the hydrogenation by 1. To overcome this defect, we investigated various reagents and found that the catalytic cycle can be completed with the use of SiF3H. The product is silylether CF3PhCHOSiF3, which is equivalent to alcohol because it easily undergoes hydrolysis to afford CF3PhCHOH. The similar catalytic cycles are also theoretically predicted for hydrosilylations of CO2 and imine. This is the first theoretical prediction of the full catalytic cycle with a heavier main-group element compound.
Cloning and functional expression of Dfurin2, a subtilisin-like proprotein processing enzyme of Drosophila melanogaster with multiple repeats of a cysteine motif. (1992)

Production of a variety of regulatory eukaryotic proteins, such as growth factors and polypeptide hormones, often involves endoproteolytic processing of proproteins at cleavage sites consisting of paired basic residues. The first known mammalian proprotein processing enzyme with such specificity is the human fur gene product furin. Structurally and functionally, furin is related to the subtilisin-like serine endoprotease kexin (EC 3.4.21.61) of yeast Saccharomyces cerevisiae; unlike kexin, it contains a cysteine-rich region with an unknown function. Here, we describe cloning and sequencing of a 5.8-kbp cDNA of the Dfur2 gene, a fur-like gene of Drosophila melanogaster, which we found expressed during various stages of development. This Dfur2 cDNA has an open reading frame for a 1680-residue protein, called Dfurin2. Dfurin2 contains similar protein domains as mammalian furin, however, it has an extended amino-terminal region and its cysteine-rich region is much larger than that of mammalian furin. Because of this latter phenomenon, we were able to identify a particular cysteine motif that was repeated multiple times in Dfurin2 but present only twice in mammalian furin. Furthermore, we show that Dfur2 encodes an endoproteolytic enzyme with specificity for paired basic amino acid residues as, in cotransfection experiments, correct cleavage was demonstrated of the precursor of the von Willebrand factor but not of a cleavage mutant. Finally, Dfur2 was mapped to region 14C of the X chromosome of D. melanogaster.
Intracerebral Administration of Adeno-Associated Viral Vector Serotype rh.10 Carrying Human SGSH and SUMF1 cDNAs in Children with Mucopolysaccharidosis Type IIIA Disease: Results of a Phase I/II Trial (2014)

Mucopolysaccharidosis type IIIA is a severe degenerative disease caused by an autosomal recessive defect of a gene encoding a lysosomal heparan-N-sulfamidase, the N-sulfoglycosamine sulfohydrolase (SGSH), the catalytic site of which is activated by a sulfatase-modifying factor (SUMF1). Four children (Patients 1-3, aged between 5.5 and 6 years; Patient 4 aged 2 years 8 months) received intracerebral injections of an adeno-associated viral vector serotype rh.10-SGSH-IRES-SUMF1 vector in a phase I/II clinical trial. All children were able to walk, but their cognitive abilities were abnormal and had declined (Patients 1-3). Patients 1-3 presented with brain atrophy. The therapeutic vector was delivered in a frameless stereotaxic device, at a dose of 7.2×10(11) viral genomes/patient simultaneously via 12 needles as deposits of 60 μl over a period of 2 hr. The vector was delivered bilaterally to the white matter anterior, medial, and posterior to the basal ganglia. Immunosuppressive treatment (mycophenolate mofetil and tacrolimus) was initiated 15 days before surgery and maintained for 8 weeks (mycophenolate mofetil) or throughout follow-up (tacrolimus, with progressive dose reduction) to prevent elimination of transduced cells. Safety data collected from inclusion, during the neurosurgery period and over the year of follow-up, showed good tolerance, absence of adverse events related to the injected product, no increase in the number of infectious events, and no biological sign of toxicity related to immunosuppressive drugs. Efficacy analysis was necessarily preliminary in this phase I/II trial on four children, in the absence of validated surrogate markers. Brain atrophy evaluated by magnetic resonance imaging seemed to be stable in Patients 1 and 3 but tended to increase in Patients 2 and 4. Neuropsychological evaluations suggested a possible although moderate improvement in behavior, attention, and sleep in Patients 1-3. The youngest patient was the most likely to display neurocognitive benefit.
A High-Yielding Preparation of β-Ketonitriles (2006)

[reaction: see text] beta-Ketonitriles are important precursors for a wide variety of biologically active heterocycles. A facile procedure for the high-yielding acylation of nitrile anions with unactivated esters to provide beta-ketonitriles is reported. The procedure is successful with enolizable and nonenolizable esters as well as hindered nitrile anions.
Controlled Fabrication of Fluorescent Barcode Nanorods (2010)

We report a novel technique for generating polymer fluorescent barcode nanorods by reactive ion etching of polymer multilayer films using nonclose-packed (ncp) colloidal microsphere arrays as masks. The fluorescent polymer multilayer films were spin-coated on a substrate, and ncp microsphere arrays were transferred onto these films. The exposed polymers were then etched away selectively, leaving color-encoded nanorods with well-preserved fluorescent properties. By modifying the spin-coating procedure, the amount of polymer in each layer could be tuned freely, which determined the relative fluorescence intensity of the barcode nanorods. These nanorod arrays can be detached from the substrate to form dispersions of coding materials. Moreover, the shape of the nanorods is controllable according to the different etching speeds of various materials, which also endows the nanorods with shape-encoded characters. This method offers opportunities for the fabrication of novel fluorescent barcodes which can be used for detecting and tracking applications.
Enhanced RSSI-Based Real-Time User Location Tracking System for Indoor and Outdoor Environments (2007)

Existing researches on location tracking focus either entirely on indoor or entirely on outdoor by using different devices and techniques. Several solutions have been proposed to adopt a single location sensing technology that fits in both situations. This paper aims to track a user position in both indoor and outdoor environments by using a single wireless device with minimal tracking error. RSSI (received signal strength indication) technique together with enhancement algorithms is proposed to cater this solution. The proposed RSSI-based tracking technique is divided into two main phases, namely the calibration of RSSI coefficients (deterministic phase) and the distance along with position estimation of user location by iterative trilateration (probabilistic phase). A low complexity RSSI smoothing algorithm is implemented to minimize the dynamic fluctuation of radio signal received from each reference node when the target node is moving. Experiment measurements are carried out to analyze the sensitivity of RSSI. The results reveal the feasibility of these algorithms in designing a more accurate real-time position monitoring system.
The Scottish economy [September 2000] (2000)

This section presents forcasting for the Scottish economy within differing sectors.