gebhart/patrepeval huggingface dataset:
HIV viral dynamics. (1996)

Here, I discuss the theoretical basis of the steady state model of HIV infection as well as its important consequences for understanding and controlling HIV pathogenesis. These include the significance of genetic variation and the establishment and evolution of the virus quasispecies, the evolution of resistance of the virus to antiviral therapy, and the theoretical and practical significance of virus load measurements. Emphasis is on discussion of recent developments as well as areas where our understanding still has significant gaps.
A cell surface chondroitin sulfate proteoglycan, immunologically related to CD44, is involved in type I collagen-mediated melanoma cell motility and invasion. (1992)

The metastatic spread of tumor cells occurs through a complex series of events, one of which involves the adhesion of tumor cells to extracellular matrix (ECM) components. Multiple interactions between cell surface receptors of an adherent tumor cell and the surrounding ECM contribute to cell motility and invasion. The current studies evaluate the role of a cell surface chondroitin sulfate proteoglycan (CSPG) in the adhesion, motility, and invasive behavior of a highly metastatic mouse melanoma cell line (K1735 M4) on type I collagen matrices. By blocking mouse melanoma cell production of CSPG with p-nitrophenyl beta-D-xylopyranoside (beta-D-xyloside), a compound that uncouples chondroitin sulfate from CSPG core protein synthesis, we observed a corresponding decrease in melanoma cell motility on type I collagen and invasive behavior into type I collagen gels. Melanoma cell motility on type I collagen could also be inhibited by removing cell surface chondroitin sulfate with chondroitinase. In contrast, type I collagen-mediated melanoma cell adhesion and spreading were not affected by either beta-D-xyloside or chondroitinase treatments. These results suggest that mouse melanoma CSPG is not a primary cell adhesion receptor, but may play a role in melanoma cell motility and invasion at the level of cellular translocation. Furthermore, purified mouse melanoma cell surface CSPG was shown, by affinity chromatography and in solid phase binding assays, to bind to type I collagen and this interaction was shown to be mediated, at least in part, by chondroitin sulfate. Additionally we have determined that mouse melanoma CSPG is composed of a 110-kD core protein that is recognized by anti-CD44 antibodies on Western blots. Collectively, our data suggests that interactions between a cell surface CD44-related CSPG and type I collagen in the ECM may play an important role in mouse melanoma cell motility and invasion, and that the chondroitin sulfate portion of the proteoglycan seems to be a critical component in mediating this effect.
A critical role for vesicle‐associated membrane protein‐7 in exocytosis from human eosinophils and neutrophils (2006)

Our observations indicate for the first time a critical role for VAMP-7 in both eosinophil and neutrophil mediator release.
A catabolic block does not sufficiently explain how 2-deoxy-d-glucose inhibits cell growth (2008)

The glucose analogue 2-deoxy-D-glucose (2-DG) restrains growth of normal and malignant cells, prolongs the lifespan of C. elegans, and is widely used as a glycolytic inhibitor to study metabolic activity with regard to cancer, neurodegeneration, calorie restriction, and aging. Here, we report that separating glycolysis and the pentose phosphate pathway highly increases cellular tolerance to 2-DG. This finding indicates that 2-DG does not block cell growth solely by preventing glucose catabolism. In addition, 2-DG provoked similar concentration changes of sugar-phosphate intermediates in wild-type and 2-DG-resistant yeast strains and in human primary fibroblasts. Finally, a genome-wide analysis revealed 19 2-DG-resistant yeast knockouts of genes implicated in carbohydrate metabolism and mitochondrial homeostasis, as well as ribosome biogenesis, mRNA decay, transcriptional regulation, and cell cycle. Thus, processes beyond the metabolic block are essential for the biological properties of 2-DG.
The H+-Sucrose Cotransporter NtSUT1 Is Essential for Sugar Export from Tobacco Leaves1 (1998)

In many species translocation of sucrose from the mesophyll to the phloem is carrier mediated. A sucrose/H+-symporter cDNA, NtSUT1, was isolated from tobacco (Nicotiana tabacum) and shown to be highly expressed in mature leaves and at low levels in other tissues, including floral organs. To study the in vivo function of NtSUT1, tobacco plants were transformed with a SUT1 antisense construct under control of the cauliflower mosaic virus 35S promoter. Upon maturation, leaves of transformants expressing reduced amounts of SUT1 mRNA curled downward, and strongly affected plants developed chloroses and necroses that led to death. The leaves exhibited impaired ability to export recently fixed 14CO2 and were unable to export transient starch during extended periods of darkness. As a consequence, soluble carbohydrates accumulated and photosynthesis was reduced. Autoradiographs of leaves show a heterogenous pattern of CO2 fixation even after a 24-h chase. The 14C pattern does not change with time, suggesting that movement of photosynthate between mesophyll cells may also be impaired. The affected lines show a reduction in the development of the root system and delayed or impaired flowering. Taken together, the effects observed in a seed plant (tobacco) demonstrate the importance of SUT1 for sucrose loading into the phloem via an apoplastic route and possibly for intermesophyll transport as well.
Microstructure of erbium-implanted Si (1991)

A study is presented of the relation between microstructure and 1.54 μm photoluminescence (PL) in high-energy ion-implantated Er in Si as a function of implant dose, energy, and temperature and subsequent anneal. Transmission electron microscopy (TEM) of material implanted at 500 keV and ≳100 °C and annealed at 900 °C to activate the Er PL suggests the solubility of Er in Si to be ≊1.3±0.4× 1018 cm−3 at 900 °C. Precipitates take the form of platelets (probably ErSi2) ≊100–300 Å in diameter and ≊10 Å thick. The 1.54 μm PL saturates at ≊5× 1017 cm−3, before the apparent solubility limit. Layers in which the Si is fully amorphized and subsequently regrown by solid phase epitaxy during an anneal show increased Er incorporation in the crystalline Si but segregation at the amorphous-crystalline interface. In buried amorphous layers regrown from top and bottom, segregation leads to a line of high Er concentration near the center of the layer: Regrowth from a single interface leads to a segregation pileup of Er at the interface until the precipitation threshhold is reached.
Character-level incremental speech recognition with recurrent neural networks (2016)

In real-time speech recognition applications, the latency is an important issue. We have developed a character-level incremental speech recognition (ISR) system that responds quickly even during the speech, where the hypotheses are gradually improved while the speaking proceeds. The algorithm employs a speech-to-character unidirectional recurrent neural network (RNN), which is end-to-end trained with connectionist temporal classification (CTC), and an RNN-based character-level language model (LM). The output values of the CTC-trained RNN are character-level probabilities, which are processed by beam search decoding. The RNN LM augments the decoding by providing long-term dependency information. We propose tree-based online beam search with additional depth-pruning, which enables the system to process infinitely long input speech with low latency. This system not only responds quickly on speech but also can dictate out-of-vocabulary (OOV) words according to pronunciation. The proposed model achieves the word error rate (WER) of 8.90% on the Wall Street Journal (WSJ) Nov'92 20K evaluation set when trained on the WSJ SI-284 training set.
Complement activation by polysaccharide of lipopolysaccharide: an important virulence determinant of salmonellae (1983)

Salmonellae with differences only in the O-antigenic polysaccharide of their lipopolysaccharide were previously shown to differentially activate complement via the alternative pathway, causing them to be ingested at different rates by the mouse macrophage-like cell line J774. We now show that this mechanism could explain the different virulence of these strains in vivo. Mouse peritoneal macrophages (thioglycolate induced) ingest these salmonellae at rates that are inversely proportional to the known virulence of the organisms and virtually identical to the rates observed with J774. As with J774, complement is required for this differential uptake, since serum was required and heating (56 degrees C for 30 min) or zymosan treatment of the serum destroyed activity. The known receptor for nonreducing terminal mannose-, fucose-, N-acetylglucosamine, and glucose-containing glyco-proteins did not participate, since uptake was not inhibited by high concentrations of mannan. When clearance of bacteria from the bloodstream of mice was measured, the least virulent organism was cleared very much faster than the most virulent organism, in confirmation of earlier data. When complement in the mice was destroyed by pretreatment with cobra venom factor, the clearance of the least virulent strain was greatly reduced, whereas the very slow clearance of the most virulent strain was unaffected. These data strongly support the hypothesis that when bacteria have polysaccharide in lipopolysaccharide that activates complement efficiently, the bacteria will be phagocytosed, whereas if the polysaccharide activates complement poorly, the bacteria escape ingestion and may cause disease.
Production and Characterization of Monoclonal Antibody to a Melanoma Specific Glycoprotein (1981)

An immunogen consisting of a 4M urea extract derived from human melanoma cells (M14), that was devoid of HLA-A.BX, HLA-DR antigens and fibronectin was adsorbed to lens culinaris lectin-Sepharose 4B and used to immunize mice for production of monoclonal antibody to a melanoma-specific glycoprotein. Screening for hybridomas secreting antibodies to melanoma associated antigens was facilitated by use of a solid phase target antigen of chemically defined medium of melanoma cells (CDM). Use of these procedures allowed us to select 40 hybridomas secreting antibody which recognized determinants on melanoma cells not found on lymphoid cells. Further characterization of one of these hybridomas, 9.2.27, indicated that the antibody it secreted recognized a 240K dalton glycoprotein found on all melanoma cell lines tested but not on carcinoma, lymphoid, or fibroblastoid cultures. These results demonstrate the utility of soluble antigen preparations devoid of strongly immunogenic non tumor-specific molecules in the elicitation of tumor specific antibody. Preliminary results suggest that immunogens of this kind are superior to intact melanoma cells for production of tumor specific hybridomas.
Cs2AgBiX6 (X = Br, Cl): New Visible Light Absorbing, Lead-Free Halide Perovskite Semiconductors (2016)

The double perovskites Cs2AgBiBr6 and Cs2AgBiCl6 have been synthesized from both solid state and solution routes. X-ray diffraction measurements show that both compounds adopt the cubic double perovskite structure, space group Fm3̅m, with lattice parameters of 11.2711(1) Å (X = Br) and 10.7774(2) Å (X = Cl). Diffuse reflectance measurements reveal band gaps of 2.19 eV (X = Br) and 2.77 eV (X = Cl) that are slightly smaller than the band gaps of the analogous lead halide perovskites, 2.26 eV for CH3NH3PbBr3 and 3.00 eV for CH3NH3PbCl3. Band structure calculations indicate that the interaction between the Ag 4d-orbitals and the 3p/4p-orbitals of the halide ion modifies the valence band leading to an indirect band gap. Both compounds are stable when exposed to air, but Cs2AgBiBr6 degrades over a period of weeks when exposed to both ambient air and light. These results show that halide double perovskite semiconductors are potentially an environmentally friendly alternative to the lead halide perovskite semiconductors.
Animal models of human tumor suppressor genes (2000)

While advances in science and technology have increased options for treating breast cancer, current social trends have changed the way people deal with this disease. Women in the United States are no longer simply passive patients, but rather they are survivors, advocates and activists who are speaking up for themselves and speaking out for issues relevant to the treatment and prevention of breast cancer.
Deblurring random time-varying blur (1989)

The problem of restoring a constant image distorted by a system of random time-varying point-spread functions is studied. The restoration is based on a finite number of images that are observed in a finite period of time. Two features distinguish this problem. The first is that of the signal-noise dependency, and the second is the availability of large amounts of data. The Wiener criterion approach is used to solve the signal-noise-dependency problem. The problem of data size is also alleviated. For the case of time-space separability, a Karhunen-Loève transformation is used to reduce the computations to the size of a single-frame problem. For the case in which the noise is stationary in time and in space, a solution based on the direct form of the Wiener filter is presented. The amount of computations here is reduced considerably by the use of fast Fourier transforms and circulant matrix approximations whenever they are valid.
Diversity of light chain variable region sequences among rabbit antibodies elicited by the same antigens. (1975)

We report the complete variable region sequences of three homogeneous rabbit antibody light chains and the partial sequences of five others. Wehn these are compared to other published rabbit light chain sequences, two regions of markedly increased variability are revealed, which are homologous in position to the first and third hypervariable regions of murine and human myeloma light chains. In addition, there is increased variability among the first three residues at the aminoterminal end. A hypervariable region homologous to that identified at positions 50 to 56 in myeloma light chains is not present in these rabbit antibody light chains. The available three-dimensional models of Fab fragments based on x-ray crystallography indicate that neither the amino-terminal portion of the light chain nor the region homologous to positions 50 to 56 forms a part of the combining site. Comparison of the hypervariable regions among six light chains from antibodies to Type III pneumococcal polysaccharide and among four from antibodies to Type VIII pneumococcal polysaccharide suggests that a large number of different sequences may be found in antibodies specific for these relatively simple antigens. Certain residues outside of the hypervariable regions are invariant in the rabbit light chains and correspond to residues that are required for proper chain folding in human and murine myeloma light chains, indicating that the general conformation of myeloma light chains is the same as that of light chains of elicited antibodies.
EFFECT OF SOLVENTS ON EXTRACTION AND CARRIER FACILITATED TRANSPORT OF LITHIUM IONS BY POLYETHYLENE GLYCOLS (1999)

Article EFFECT OF SOLVENTS ON EXTRACTION AND CARRIER FACILITATED TRANSPORT OF LITHIUM IONS BY POLYETHYLENE GLYCOLS was published on November 1, 1999 in the journal Main Group Metal Chemistry (volume 22, issue 11).
Human Cytomegalovirus Vaccine Based on the Envelope gH/gL Pentamer Complex (2014)

Human Cytomegalovirus (HCMV) utilizes two different pathways for host cell entry. HCMV entry into fibroblasts requires glycoproteins gB and gH/gL, whereas HCMV entry into epithelial and endothelial cells (EC) requires an additional complex composed of gH, gL, UL128, UL130, and UL131A, referred to as the gH/gL-pentamer complex (gH/gL-PC). While there are no established correlates of protection against HCMV, antibodies are thought to be important in controlling infection. Neutralizing antibodies (NAb) that prevent gH/gL-PC mediated entry into EC are candidates to be assessed for in vivo protective function. However, these potent NAb are predominantly directed against conformational epitopes derived from the assembled gH/gL-PC. To address these concerns, we constructed Modified Vaccinia Ankara (MVA) viruses co-expressing all five gH/gL-PC subunits (MVA-gH/gL-PC), subsets of gH/gL-PC subunits (gH/gL or UL128/UL130/UL131A), or the gB subunit from HCMV strain TB40/E. We provide evidence for cell surface expression and assembly of complexes expressing full-length gH or gB, or their secretion when the corresponding transmembrane domains are deleted. Mice or rhesus macaques (RM) were vaccinated three times with MVA recombinants and serum NAb titers that prevented 50% infection of human EC or fibroblasts by HCMV TB40/E were determined. NAb responses induced by MVA-gH/gL-PC blocked HCMV infection of EC with potencies that were two orders of magnitude greater than those induced by MVA expressing gH/gL, UL128-UL131A, or gB. In addition, MVA-gH/gL-PC induced NAb responses that were durable and efficacious to prevent HCMV infection of Hofbauer macrophages, a fetal-derived cell localized within the placenta. NAb were also detectable in saliva of vaccinated RM and reached serum peak levels comparable to NAb titers found in HCMV hyperimmune globulins. This vaccine based on a translational poxvirus platform co-delivers all five HCMV gH/gL-PC subunits to achieve robust humoral responses that neutralize HCMV infection of EC, placental macrophages and fibroblasts, properties of potential value in a prophylactic vaccine.
Defined Conditions for the Isolation and Expansion of Basal Prostate Progenitor Cells of Mouse and Human Origin (2015)

Methods to isolate and culture primary prostate epithelial stem/progenitor cells (PESCs) have proven difficult and ineffective. Here, we present a method to grow and expand both murine and human basal PESCs long term in serum- and feeder-free conditions. The method enriches for adherent mouse basal PESCs with a Lin(-)SCA-1(+)CD49f(+)TROP2(high) phenotype. Progesterone and sodium selenite are additionally required for the growth of human Lin(-)CD49f(+)TROP2(high) PESCs. The gene-expression profiles of expanded basal PESCs show similarities to ESCs, and NF-kB function is critical for epithelial differentiation of sphere-cultured PESCs. When transplanted in combination with urogenital sinus mesenchyme, expanded mouse and human PESCs generate ectopic prostatic tubules, demonstrating their stem cell activity in vivo. This novel method will facilitate the molecular, genomic, and functional characterization of normal and pathologic prostate glands of mouse and human origin.
Modular multiplication without trial division (1985)

Let <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper N greater-than 1"> <mml:semantics> <mml:mrow> <mml:mi>N</mml:mi> <mml:mo>&gt;</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> <mml:annotation encoding="application/x-tex">N &gt; 1</mml:annotation> </mml:semantics> </mml:math> </inline-formula>. We present a method for multiplying two integers (called <italic>N-residues</italic>) modulo <italic>N</italic> while avoiding division by <italic>N</italic>. <italic>N</italic>-residues are represented in a nonstandard way, so this method is useful only if several computations are done modulo one <italic>N</italic>. The addition and subtraction algorithms are unchanged.
Peptide-Based Strategy for siRNA Delivery into Mammalian Cells (2005)

The potential to control and alter gene expression constitutes an essential strategy in both fundamental and pharmaceutical research. The recent discovery of the RNA interference pathway in a wide variety of eukaryotic organisms has provided a novel means of characterizing gene function in mammalian cells and new perspectives in both molecular biology and future therapeutic developments (, , ). Short, interfering RNAs (siRNAs) constitute a powerful tool to silence gene expression posttranscriptionally (, , ). However, the major limitation of siRNA application, as for most antisense or nucleic acid-based strategies, remains their poor cellular uptake associated with low permeability of the cell membrane to nucleic acids (,). Several viral (, , , ) and nonviral (,) strategies have been proposed to improve the delivery of either siRNAs expressing vectors or synthetic siRNAs, both in cultured cells and in vivo (). So far, although siRNA transfection can be achieved with classical laboratory-cultured cell lines using lipid-based formulations, siRNA delivery remains a major challenge for many cell lines and there is still no reasonably efficient method for in vivo application (). The most efficient method for in vivo applications is the nonviral “hydrodynamic” tail-vein injection of mice with high doses of siRNA (, , ). Cell-penetrating peptides are powerful carriers for cellular uptake of a variety of macromolecules, including proteins, peptides, and oligonucleotides (, , , ). Several peptide-based strategies have been developed to improve the delivery of oligonucleotides both in vitro and in vivo using either covalent or complex approaches (, , ).
WWW: past, present, and future (1996)

The World Wide Web is simply defined as the universe of global network-accessible information. It is an abstract space within which people can interact, and it is chiefly populated by interlinked pages of text, images, and animations, with occasional sounds, videos, and three-dimensional worlds. The Web marks the end of an era of frustrating and debilitating incompatibility between computer systems. It has created an explosion of accessibility, with many potential social and economical impacts. The Web was designed to be a space within which people could work on a project. This was a powerful concept, in that: people who build a hypertext document of their shared understanding can refer to it at all times; people who join a project team can have access to a history of the team's activities, decisions, and so on; the work of people who leave a team can be captured for future reference; and a team's operations, if placed on the Web, can be machine-analyzed in a way that could not be done otherwise. The Web was originally supposed to be a personal information system and a tool for groups of all sizes, from a team of two to the entire world. People have rapidly developed new features for the Web, because of its tremendous commercial potential. This has made the maintenance of globalWeb interoperability a continuous task. This has also created a number of areas into which research must continue.