gebhart/patrepeval huggingface dataset:
Electrical, optical and fluidic through-silicon vias for silicon interposer applications (2011)

Modern high-performance computing systems and data centers are implemented as many-core server systems. Current state of the art data centers have server racks with pluggable boards where each board has many multi-core processors and memory units. These boards are connected via electrical or optical cables. In such systems, communication bandwidth between the high-speed microprocessor cores and the memory is limited. To leverage full performance of these powerful chips, it is required to provide high memory bandwidth as well as effective power delivery and heat removal solutions. To address these challenges in high performance computing systems, we present a 3D packaging solution that includes a novel silicon interposer with electrical, optical, and fluidic (trimodal) interconnects and through-silicon vias (TSVs). The electrical TSVs in the silicon interposer enable power and signal delivery from motherboard to chips stacked on top of the interposer. The optical TSVs in the silicon interposer can provide ultra-high bandwidth communication between chips on different silicon interposers through motherboard level optical links. The fluidic TSVs enable a coolant to be routed from the motherboard to the chips on the silicon interposer. We have fabricated and characterized polymer-clad electrical TSVs (for low stress) with diameter that meets ITRS projections for high-performance computing systems. Using the same polymer used for the cladding of electrical TSVs, we have fabricated and characterized optical TSVs adjacent to electrical TSVs. Spin coating of the photodefinable polymer for electrical and optical TSVs is done in single step. Fabrication of fluidic TSVs can be done using the same cladding as that of the polymer-clad electrical TSVs without electroplating the copper. This leaves behind an empty polymer-clad via which can be used as a fluidic TSV.
Mobilization of early hematopoietic progenitor cells with BB-10010: a genetically engineered variant of human macrophage inflammatory protein- 1 alpha (1995)

BB-10010 is a genetically engineered variant of human macrophage inflammatory protein-1 alpha with improved solution properties. We show here that it mobilizes stem cells into the peripheral blood. We investigated the mobilizing effects of BB-10010 on the numbers of circulating 8-day spleen colony-forming units (CFU-S8), CFU-S12, and progenitors with marrow repopulating ability (MRA). A single subcutaneous dose of BB-10010 caused a twofold increase in circulating numbers of CFU-S8, CFU-S12, and MRA 30 minutes after dosing. We also investigated the effects of granulocyte colony-stimulating factor (G-CSF) and the combination of G-CSF with BB-10010 on progenitor mobilization. Two days of G-CSF treatment increased circulating CFU-S8, CFU-S12, and MRA progenitors by 25.7-, 19.8-, and 27.7-fold. A single administration of BB-10010 after 2 days of G-CSF treatment increased circulating CFU-S8, CFU-S12, and MRA even further to 38-, 33-, and 100-fold. Splenectomy resulted in increased circulating progenitor numbers but did not change the pattern of mobilization. Two days of treatment with G-CSF then increased circulating CFU-S8, CFU-S12, and MRA by 64-, 69-, and 32-fold. A single BB-10010 administration after G-CSF treatment further increased them to 85-, 117-, and 140-fold, respectively, compared with control. We conclude that BB-10010 causes a rapid increase in the number of circulating hematopoietic progenitors and further enhances the numbers induced by pretreatment with G-CSF. BB-10010 preferentially mobilized the more primitive progenitors with marrow repopulating activity, releasing four times the number achieved with G-CSF alone. Translated into a clinical setting, this improvement in progenitor cell mobilization may enhance the efficiency of harvest and the quality of grafts for peripheral blood stem cell transplantation.
A Human Monoclonal Antibody Recognizing a Surface Antigen on Stomach Cancer Cells (1989)

Lymph-node lymphocytes of a patient with stomach cancer were fused with the mouse-human heterohybridoma, HM-5. A clone (2F9) was isolated that showed stable production of an IgM antibody reactive with NUGC-4 stomach cancer cell line. This antibody reacted predominantly with a cell surface antigen on cell lines originating from gastro-intestinal cancer and adenocarcinoma of lung, whereas it was not generally reactive with other types of cancers, or with normal kidney cells or fibroblasts. Biotin-labeled 2F9 antibody clearly stained cell smears and the nude mouse tumor of NUGC-4, but it did not show a positive reaction with stomach cancer tissues obtained from more than 10 patients, indicating that the antigen detected is very weakly expressed on tumor cells or on a limited number of stomach cancers. The antigen shed from NUGC-4 cell line was detected in the culture supernatant. 2F9 antibody precipitated a glycoprotein with a molecular weight of over 200 kilodaltons as well as a possible glycolipid, from NUGC-4 cells labeled with [3H]glucosamine or [35S]-H2SO4. Periodic acid treatment of the tissue section decreased reactivity with 2F9 antibody, but heat, neuraminidase or protease treatment did not. These results suggested that the epitope is present on a carbohydrate moiety not containing sialic acid, and that a part of the antigen molecule is sulfated.
IL-4-producing CD8+ T cell clones can provide B cell help. (1995)

Interactions between CD4+ T cells and B cells are mediated by both soluble factors and cell surface molecules. The Ag-independent interaction between the CD40 ligand, expressed on activated T cells, and its CD40 receptor, expressed on B cells, enhances B cell proliferation in response to IL-4 stimulation. The expression of the CD40 ligand is induced on CD4+ T cells by stimulation with Ag-pulsed APC or mitogens. Here, we show that at least some IL-4-producing murine CD8+ T cell clones can be induced to express the CD40 ligand when stimulated with anti-CD3 mAb. Additionally, such activated CD8+ IL-4-producing clones potentiate the proliferative response of small resting B cells to IL-4 and induce Ig secretion by small resting B cells to IL-4 and IL-5. Proliferation of small resting B cells cultured with IL-4 in the presence of activated IL-4-producing CD8+ murine T cell clones appeared to be mediated by the expression of the CD40 ligand on the T cell because an anti-CD40 ligand mAb inhibited this proliferative response. A conventional murine CD8+ CTL clone, which did not produce IL-4 or express CD40 ligand upon activation, did not potentiate proliferation of small resting B cells exposed to IL-4. Thus, under some circumstances, CD8+ T cells that are able to express CD40 ligand may be able to provide B cell help.
Photolabile chelators for the rapid photorelease of divalent cations. (1988)

The properties of a recently synthesized photolabile chelator for divalent cations are described, the affinity of which for Ca2+ changes by some 5 orders of magnitude on illumination. The compound 1-(2-nitro-4,5-dimethoxyphenyl)-N,N,N',N'-tetrakis[(oxycarbonyl)me thyl]-1,2-ethanediamine (DM-nitrophen) binds Ca2+ (Kd approximately 5.0 x 10(-9) M) and Mg2+ (Kd approximately 2.5 x 10(-6) M) with relatively high affinities. On exposure of the DM-nitrophen-Ca2+ complex to UV light in the 350-nm range, the chelator is cleaved yielding iminodiacetic products with a much lower affinity for Ca (Kd approximately 3 x 10(-3) M) and the free [Ca2+] increases. The quantum yield for Ca2+ release is 0.18. In experiments with chemically skinned skeletal muscle fibers, a fully relaxed fiber equilibrated with DM-nitrophen-Ca2+ complex produced maximal contraction after a single flash from a frequency-doubled ruby laser (347 nm). Half-maximal tension was achieved in approximately 40 ms, some 5 times faster than that obtained after a rapid solution change from a Ca2+-free to a Ca2+-containing solution. In experiments with resealed human erythrocyte ghosts, irradiation of ghosts containing the DM-nitrophen-Ca2+ complex activates a Ca2+-dependent K+ efflux pathway, which is not observed in the absence of illumination. DM-nitrophen is sufficiently stable and photolabile to be used as a caged Ca (or caged Mg) for the rapid photoinitiation of divalent cation-dependent processes over a wide concentration range with a significant increase in temporal resolution over conventional mixing methods.
Cell Counter, Blood (2006)

Abstract This article discussed the basic principles of hematology with emphasis on humans. Enumeration of cell population distribution in peripheral blood is examined using optical, electrooptical and light scattering techniques. As seen, such experimental modalities can be automated and the resulting hematology analyzers can be used for clinical application. Even though the exact strategy of cell counting varies between various manufacturers of automated cell counters, performance standards for such instrumentation have been established by the National Committee for Clinical Laboratory Standard (NCCLS) and the International Council for Standardization in Hematology (ICSH). The parameters evaluated here include (1) accuracy in measurement within a single batch and between batches of blood samples; (2) carryover of parameters between consecutive samples; (3) linearity or the ability to get similar measurements when the sample is diluted to different levels before being read; and (4) clinical sensitivity or the specificity and efficiency with which flags are generated during analysis to detect abnormal readouts.
Central sleep apnea. (1992)

The critical issue in considering the diagnosis and management of CSA is to determine the physiologic process underlying the disorder. CSA includes a pathophysiologically and clinically heterogeneous group of disorders that can be divided into two main groups on the basis of the awake PaCO2: a hypercapnic group, in whom the disorder is related to central alveolar hypoventilation or neuromuscular disease, and a nonhypercapnic group, in whom there is no identifiable underlying disorder. The common feature of these two groups is recurrent episodes of central apnea during sleep related to withdrawal of the wakefulness drive to breathing. In the hypercapnic group the clinical history is dominated by recurrent episodes of respiratory failure and its complications, with the sleep disturbance being a secondary feature. CSA in these patients is simply an exaggeration, by sleep, of their hypoventilation disorder. Treatment in most cases involves mechanical assisted ventilation during sleep, which can be very effective in reversing CSA and respiratory failure. In contrast, idiopathic CSA is characterized by a tendency to hyperventilation. This tendency is reinforced during sleep by recurrent arousals, which tend to propagate the CSA. Unlike hypercapnic CSA, idiopathic CSA is a relatively benign condition in which cardiorespiratory failure is not a feature. Treatment of this disorder is problematic, but the use of nocturnal nasal CPAP appears to be quite effective.
IL-9 Deficiency Promotes Pulmonary Th17 Response in Murine Model of Pneumocystis Infection (2018)

Although similar basic clearance of <i>Pneumocystis</i> organisms was achieved in both WT and IL-9<sup>-/-</sup> PCP mice, IL-9 deficiency could lower <i>Pneumocystis</i> organism burden and promote pulmonary Th17 cells response in the early stage of infection.
Predicting Future User Actions by Observing Unmodified Applications (2000)

Intelligent user interfaces often rely on modified applications and detailed application models. Such modifications and models are expensive to build and maintain. We propose to automatically model the use of unmodified applications to solve this problem. We observe a user&amp;apos;s interactions with the application&amp;apos;s interface and from these observations infer a state space which the user navigates and the stochastic policy he or she follows. ONISI, the algorithm presented here, builds this state space implicitly and on-line, and uses it to predict future user actions. Trials with real users show that this algorithm predicts the next user action significantly better than another current algorithm. Content Areas: plan recognition, human computer interaction, automated modeling, software agents
Mechanism of Pulmonary Conversion of Anglotensin II to Angiotensin II in the Dog (1971)

The mechanism of conversion of angiotensin I to angiotensin II was studied in vivo in the pulmonary circulation of the intact anesthetized dog and in vitro in plasma by using L-Leu-anglotensin I, D-Leu-angiotensin I, and des-Leu-angiotensin I which had been synthesized by the solid-phase technique. None of the peptides were active in the rabbit aortic strip preparation; D-Leu-angiotensin I and des-Leu-angiotensin I gave less than 5% of the pressor response of L-Leu-angiotensin I in the pentolinium-treated rat. D-Leu-angiotensin I and des-Leu-angiotensin I were not converted to angiotensin II when incubated with diluted human or dog plasma or partially purified converting enzyme from dog plasma. In a single pulmonary circulation time, following injection of a 20-nmole bolus of L-Leu-angiotensin I into the dog right ventricle, 56% of the material recovered had been converted to angiotensin II, as measured by radioimmunoassay. Conversion was accompanied by a rise in mean blood pressure of 30 mm Hg. After injection of equimolar amounts of D-Leu-angiotensin I and des-Leu-angiotensin I, no generation of angiotensin II and no pressor response occurred. These observations indicate that pulmonary conversion in vivo and plasma conversion in vitro occur via a dipepridylcarboxypeptidase and that a D-amino acid at the C-terminus prevents conversion.
Constructing transcriptional regulatory networks (2005)

Biological networks are the representation of multiple interactions within a cell, a global view intended to help understand how relationships between molecules dictate cellular behavior. Recent advances in molecular and computational biology have made possible the study of intricate transcriptional regulatory networks that describe gene expression as a function of regulatory inputs specified by interactions between proteins and DNA. Here we review the properties of transcriptional regulatory networks and the rapidly evolving approaches that will enable the elucidation of their structure and dynamic behavior. Several recent studies illustrate how complementary approaches combine chromatin immunoprecipitation (ChIP)-on-chip, gene expression profiling, and computational methods to construct blueprints for the initiation and maintenance of complex cellular processes, including cell cycle progression, growth arrest, and differentiation. These approaches should allow us to elucidate complete transcriptional regulatory codes for yeast as well as mammalian cells.
Cancer Sequencing Gets a Little More Personal (2010)

In this Perspective, we discuss a paper in this issue of Science Translational Medicine, in which Leary and colleagues present a new method based on massive, parallel, and near-complete sequencing of individual tumor genomes. Their findings support the notion that cancer genomes house a spectrum of genetic alterations, many of which are unique to the individual tumor. More validation and a reduction in cost are required for this approach to become common in clinics.
A yeast RNA-hybrid system for the detection of RNA–RNA interactions in vivo (2005)

RNA-RNA interactions play a crucial role at many different levels of the cellular metabolism such as plasmid replication control, viral encapsidation, or transcriptional and translational regulation. Therefore, methods are necessary to investigate the molecular determinants of given interactions, including their stabilities, or to screen for new interacting partners. We designed an RNA-hybrid system in S. cerevisiae, based on the yeast three-hybrid system. In this setup, the activation of a reporter gene is dependent on the interaction of two RNAs. A loop-loop interaction similar to the dimerization initiation site of the HIV genome was used as a model system, demonstrating that in this novel RNA-hybrid system only cognate RNAs promote the activation of the reporter gene. Levels of reporter activation correlate well with interaction stabilities determined in vitro by UV melting analyses, suggesting that conditions used for the analysis of in vitro structural stabilities translate well into the intracellular environment. Furthermore, the system was applicable for a screen against a test library. Nine out of ten selected clones were identified as predicted interaction partners for the bait RNA. In summary, we present a yeast reporter system depending on RNA-RNA interactions, which can be used alternatively for analysis of known interactions or for screening libraries in search for new interaction partners.
A practical concurrent binary search tree (2010)

We propose a concurrent relaxed balance AVL tree algorithm that is fast, scales well, and tolerates contention. It is based on optimistic techniques adapted from software transactional memory, but takes advantage of specific knowledge of the the algorithm to reduce overheads and avoid unnecessary retries. We extend our algorithm with a fast linearizable clone operation, which can be used for consistent iteration of the tree. Experimental evidence shows that our algorithm outperforms a highly tuned concurrent skip list for many access patterns, with an average of 39% higher single-threaded throughput and 32% higher multi-threaded throughput over a range of contention levels and operation mixes.
Purification and characterization of heparan sulphate proteoglycan from bovine brain (1999)

A heparan sulphate proteoglycan was purified from adult bovine brain tissues and its structure was characterized. The major heparan sulphate proteoglycan from whole bovine brain had a molecular mass of >200 kDa on denaturing SDS/PAGE and a core protein size of 66 kDa following the removal of glycosaminoglycan chains. Fractionation on DEAE-Sephacel showed that this proteoglycan consisted of three major forms having high, intermediate and low overall charge. All core proteins were identical in size and reacted with heparan sulphate proteoglycan-stub antibody and an antibody made to a synthetic peptide based on rat glypican. The three forms of proteoglycans had identical peptide maps and their amino acid compositional analysis did not match any of the known glypicans. The internal sequence of a major peptide showed only 37.5% sequence similarity with human glypican 5. The glycosaminoglycan chain sizes of the three forms of this proteoglycan, determined after beta-elimination by PAGE, were identical. The disaccharide compositional analysis on the heparan sulphate chains from the three forms of the proteoglycan, determined by treatment with a mixture of heparin lyases followed by high-resolution capillary electrophoresis, showed that they differed primarily by degree of sulphation. The most highly sulphated proteoglycan isolated had a disaccharide composition similar to heparan sulphate glycosaminoglycans found in brain tissue. Based on their sensitivity to low pH nitrous acid treatment, the N-sulphate groups in these proteoglycans were found to be primarily in the smaller glycosaminoglycan chains. The heparan sulphate proteoglycans were also heavily glycosylated with O-linked glycans and no glycosylphosphatidylinositol anchor could be detected.
Suppression of fibrosarcoma metastasis by elevated expression of manganese superoxide dismutase. (1994)

A mouse fibrosarcoma cell line (FSa-II), which exhibits low endogenous levels of manganese superoxide dismutase, was transfected with a human manganese superoxide dismutase complementary DNA. Fifty clones were screened for manganese superoxide dismutase activity by the superoxide dismutase activity gel assay. Activity of the positive clones was measured by the nitro blue tetrazolium-reduction assay in the presence of cyanide. Three cell lines exhibiting a range of activity were chosen to be transplanted into syngeneic mice. The results indicated that the metastasis rate for all transfected cells was significantly less than that of control cells.
Preparation of a novel psoralen containing deoxyadenosine building block for the facile solid phase synthesis of psoralen-modified oligonucleotides for a sequence specific crosslink to a given target sequence (1989)

4,5',8-Trimethylpsoralen was attached to the C8-position of deoxyadenosine via a sulfur atom and a five carbon atom linker. The modified deoxyadenosine was then converted to a protected phosphoramidite and used as unusual as a building block for solid phase oligodeoxyribonucleotide synthesis. The efficiency of the photoreaction of a psoralen-modified oligonucleotide to a complementary matrix strand reached more than 90% within a 1 hour irradiation time at a wavelength of 345 nm.
Targeting Mnks for Cancer Therapy (2012)

Deregulation of protein synthesis is a common event in human cancer and a key player in translational control is eIF4E. Elevated expression levels of eIF4E promote cancer development and progression. Recent findings suggest that eIF4E activity is a key determinant of the PI3K/Akt/mTOR and Ras/Raf/MEK/ERK mediated tumorigenic activity and targeting eIF4E should have a major impact on these pathways in human cancer. The function of eIF4E is modulated through phosphorylation of a conserved serine (Ser209) by Mnk1 and Mnk2 downstream of ERK. While the phosphorylation event is necessary for oncogenic transformation, it seems to be dispensable for normal development. Hence, pharmacologic Mnk inhibitors may provide non-toxic and effective anti-cancer strategy. Strong circumstantial evidence indicates that Mnk inhibition presents attractive therapeutic potential, but the lack of selective Mnk inhibitors has so far confounded pharmacological target validation and clinical development.
Isolation and reconstitution of the high‐affinity choline carrier (1989)

Monoclonal antibodies, which block the high-affinity uptake of choline in synaptosomal ghosts, have been used to purify a membrane polypeptide (80 kDa) from insect synaptosomal membranes. This isolated protein was found to catalyse the sodium-dependent, hemicholinium-sensitive accumulation of choline after reconstitution into liposomes, thus, apparently represents the high-affinity choline transporter.
Combinatorial Screening for Enzyme-Mediated Coupling. Tyrosinase-Catalyzed Coupling To Create Protein−Chitosan Conjugates (2001)

In nature, tyrosinase-generated o-quinones are commonly involved in processes that lead to functional biomaterials. These biomaterials are chemically complex and have been difficult to analyze. Furthermore, the cascade of reactions involving o-quinones is poorly understood, and it has been difficult to mimic ex vivo for materials processing. We report the use of a combinatorial approach to learn how tyrosinase and low molecular weight phenolic precursors can be used to generate biologically active protein-polysaccharide conjugates. Specifically, we screened various phenolic coupling precursors and various reaction conditions for the coupling of proteins onto the polysaccharide chitosan. Several natural phenols were identified as appropriate precursors for the coupling of polyhistidine tagged organophosphorus hydrolase (His-OPH) onto chitosan films. OPH activity was retained upon coupling and subsequent studies indicated that the histidine tag was not necessary for coupling. Using conditions identified for His-OPH coupling, we observed that various biologically active proteins (cytochrome c, OPH, and His-CAT) could be coupled onto chitosan films. The glycosylated protein horseradish peroxidase was not effectively coupled onto chitosan under the conditions studied. In all cases studied, we observed that coupling required a phenolic precursor, suggesting that tyrosinase is unable to couple by reaction with surface tyrosyl residues of the target protein. In conclusion, this study illustrates a combinatorial approach for the "discovery" of conditions to couple biologically active proteins onto chitosan through natural, quinone-based processes.