gebhart/patrepeval huggingface dataset:
Inhibition of Autoimmune Diabetes in Nonobese Diabetic Mice by Transgenic Restoration of H2-E MHC Class II Expression: Additive, But Unequal, Involvement of Multiple APC Subtypes (2001)

Transgenic restoration of normally absent H2-E MHC class II molecules on APC dominantly inhibits T cell-mediated autoimmune diabetes (IDDM) in nonobese diabetic (NOD) mice. We analyzed the minimal requirements for transgenic H2-E expression on APC subtypes (B lymphocytes vs macrophages/dendritic cells (DC)) to inhibit IDDM. This issue was addressed through the use of NOD stocks transgenically expressing high levels of H2-E and/or made genetically deficient in B lymphocytes in a series of genetic intercross and bone marrow/lymphocyte chimera experiments. Standard (H2-E(null)) NOD B lymphocytes exert a pathogenic function(s) necessary for IDDM. However, IDDM was inhibited in mixed chimeras where H2-E was solely expressed on all B lymphocytes. Interestingly, this resistance was abrogated when even a minority of standard NOD H2-E(null) B lymphocytes were also present. In contrast, in NOD chimeras where H2-E expression was solely limited to approximately half the macrophages/DC, an active immunoregulatory process was induced that inhibited IDDM. Introduction of a disrupted IL-4 gene into the NOD-H2-E transgenic stock demonstrated that induction of this Th2 cytokine does not represent the IDDM protective immunoregulatory process mediated by H2-E expression. In conclusion, high numbers of multiple subtypes of APC must express H2-E MHC class II molecules to additively inhibit IDDM in NOD mice. This raises a high threshold for success in future intervention protocols designed to inhibit IDDM by introduction of putatively protective MHC molecules into hemopoietic precursors of APC.
Distributed interference pricing with MISO channels (2008)

We study a distributed algorithm for adapting transmit beamforming vectors in a multi-antenna peer-to-peer wireless network. The algorithm attempts to maximize a sum of per-user utility functions, where each user's utility is a function of his transmission rate, or equivalently the received signal-to-interference plus noise ratio (SINR). This is accomplished by exchanging interference prices, each of which represents the marginal cost of interference to a particular user. Given the interference prices, users update their beamforming vectors to maximize their utility minus the cost of interference. For a two-user system, we show that this algorithm converges for a suitable class of utility functions. Convergence of the algorithm with more than two users is illustrated numerically.
Specific immunoglobulin E responses in ZAP‐70‐deficient patients are mediated by Syk‐dependent T‐cell receptor signalling (2001)

ZAP-70 deficiency is a rare primary immunodeficiency characterized by the absence of peripheral CD8+ T cells and defects in T-cell receptor (TCR) signalling. T cells in ZAP-70-deficient patients are assumed to have no helper functions for B-cell immunoglobulin synthesis, whereas the patients rarely have antigen-specific antibodies. We experienced a ZAP-70-deficient patient, who had immunoglobulin E (IgE) antibodies specific to food allergens, and we investigated the mechanisms of switching to IgE in the patient. Peripheral blood mononuclear cells from the patient did not proliferate upon stimulation with the antigens but produced distinct levels of interleukin-4 (IL-4). Cell sorting analysis indicated that the cells that produced IL-4 in response to the antigens were enriched in CD4+ T cells. Purified CD4+ T cells from the patient produced IL-4 and expressed CD40L upon stimulation with anti-CD3. Moreover, CD4+ T cells pretreated with anti-CD3 induced mature epsilon transcript on naive B cells. Since the results indicated that there remained sufficient T-cell receptor (TCR)-signalling in the patient's T cells to exert antigen-specific IgE switching on B cells, we next investigated the expression of the ZAP-70-homologous kinase Syk. Syk was present in high levels in patient's CD4+ T cells and was tyrosine-phosphorylated after TCR stimulation. Inhibition of Syk by piceatannol resulted in decreased production of IL-4 and expression of CD40L on patient's CD4+ T cells. Moreover, Syk was expressed on all human T-cell leukaemia virus (HTLV-1)-transformed T-cell lines derived from peripheral blood of the patient, whereas it was low or undetectable in control lines. It was therefore concluded that specific IgE responses in the patient were most likely to be mediated by Syk-dependent TCR-signalling.
Using salience to segment desktop activity into projects (2009)

Knowledge workers must manage large numbers of simultaneous, ongoing projects that collectively involve huge numbers of resources (documents, emails, web pages, calendar items, etc). An activity database that captures the relationships among projects, resources, and time can drive a variety of tools that save time and increase productivity. To maximize net time savings, we would prefer to build such a database automatically, or with as little user effort as possible. In this paper, we present several sets of features and algorithms for predicting the project associated with each action a user performs on the desktop. Key to our methods is salience, the notion that more recent activity is more informative. By developing novel features that represent salience, we were able to learn models that outperform both a simple benchmark and an expert system tuned specifically for this task on real-world data from five users.
Bioconversion for Production of Renewable Transportation Fuels in the United States (1994)

Ideally, the scope of this introductory chapter would encompass all of the major issues that face bioconversion technology for fuel production in the United States, both technical and social. This is, obviously, a far more ambitious scope than can actually be covered in the space allotted here. For many of the social and political issues presented here, I make no claims of expertise. My perspective is presented strictly as that -- my own perspective on issues facing bioconversion technology development. I will be satisfied if I am able to provide a flavor for some of the bigger issues and to give the technical audience of this book an appreciation for the broad range of opportunities and challenges that face the research community in this area.
Effects of human recombinant tumor necrosis factor- <i>alpha</i> and interleukin 1 on the synthesis of glycosaminoglycan and DNA in cultured rat costal chondrocytes. (1988)

We examined effects of human rTNF alpha on the synthesis of glycosaminoglycan and DNA in cultured rat costal chondrocytes. The effects of human recombinant IL-1 alpha and IL-1 beta were also given attention. rTNF alpha, as well as rIL-1 alpha and rIL-1 beta, decreased the incorporation of [35S]sulfate into glycosaminoglycan to about 10% of the levels in the control. The half-maximal doses of rTNF alpha, rIL-1 alpha or rIL-1 beta required for the suppression of glycosaminoglycan synthesis (by rTNF alpha, rIL-1 alpha, and rIL-1 beta) were 2 ng/ml, 30 ng/ml, or 5 ng/ml, respectively. rTNF alpha stimulated incorporation of [3H]thymidine in the chondrocytes in a dose- and time-dependent manner. DNA synthesis was increased to about threefold over the control cultures in the presence of 1 microgram/ml rTNF alpha for 72 hr. The stimulatory effect of rTNF alpha on DNA synthesis was observed in both subconfluent and confluent cultures, whereas rIL-1 alpha and rIL-1 beta had no stimulatory activity on DNA synthesis. The addition of rTNF alpha to the cultures of chondrocytes stimulated DNA synthesis, even in medium containing no fetal calf serum. The fetal calf serum acted synergistically with rTNF alpha in increasing DNA synthesis. We propose that both TNF and IL-1 may be involved in inflammatory diseases of cartilage, and that TNF alpha, but not IL-1, may have some physiologic growth factor function for chondrocytes.
Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas aeruginosa: sequencing and identification of a locus for heme d1 biosynthesis (1997)

The primary structure of an nir gene cluster necessary for production of active dissimilatory nitrite reductase was determined from Pseudomonas aeruginosa. Seven open reading frames, designated nirDLGHJEN, were identified downstream of the previously reported nirSMCF genes. From nirS through nirN, the stop codon of one gene and the start codon of the next gene were closely linked, suggesting that nirSMCFDLGHJEN are expressed from a promoter which regulates the transcription of nirSM. The amino acid sequences deduced from the nirDLGH genes were homologous to each other. A gene, designated nirJ, which encodes a protein of 387 amino acids, showed partial identity with each of the nirDLGH genes. The nirE gene encodes a protein of 279 amino acids homologous to S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase from other bacterial strains. In addition, NirE shows 21.0% identity with NirF in the N-terminal 100-amino-acid residues. A gene, designated nirN, encodes a protein of 493 amino acids with a conserved binding motif for heme c (CXXCH) and a typical N-terminal signal sequence for membrane translocation. The derived NirN protein shows 23.9% identity with nitrite reductase (NirS). Insertional mutation and complementation analyses showed that all of the nirFDLGHJE genes were necessary for the biosynthesis of heme d1.
Current understanding of HIV-associated neurocognitive disorders pathogenesis (2011)

Prevention and treatment of HAND requires strategies aimed at suppressing CNS HIV replication and effects of systemic and CNS inflammation in aging and substance-abusing HIV populations. Use of improved CNS-penetrating ART must be accompanied by evaluation of potential ART neurotoxicity.
HIV Vaccines Based on Novel MULV-HIV Fusion Proteins. (1999)

Abstract : We have continued our efforts to characterize the immunological properties of the Vl/V2 domain of HIV-l gp120. Studies with human sera and with antibodies isolated from immunized animals have shown that the Vl/V2 domain contains highly conserved epitopes that can act as potent neutralizing targets for a broad range of primary HIV-l isolates. We have prepared two prototype immunogens, based on the Case-A2 and SF-162 isolates. The Case-A2 isolate contains the clade B V2 consensus sequence, and this antigen induces highly cross reactive anti-V1/V2 antibodies in both rats and macaques that possess potent cross-neutralizing activity for several primary HIV-1 isolates. Our studies to date have shown that while the V1/V2 domain remains an intriguing target for viral neutralization and a candidate for HIV vaccine development, additional modification of the V1/V2 fusion proteins is needed to improve their specifications and efficiencies as vaccines capable of inducing relevant neutralizing responses.
<i>adg2‐1</i> represents a missense mutation in the ADPG pyrophosphorylase large subunit gene of <i>Arabidopsis thaliana</i> (1997)

Arabidopsis mutants affecting ADPG pyrophosphorylase (ADGase) activity can be divided into two complementation groups, adg1 and adg2. Previous biochemical studies of adg2-1 mutant indicated that mutant plants do not accumulate ADGase large subunit protein and that ADGase small subunits assemble as homotetramers. This suggested that the ADG2 gene may encode the large subunit of ADGase. In this paper, it is shown that adg2-1 mutant plants accumulate near wild-type levels of transcripts encoding both the large and small subunits of ADGase. However, by RFLP analysis and complementation of adg2-1 with the ADGase large subunit gene, we show that the adg2-1 mutant does represent a mutation of the ADGase large subunit gene. Sequence analysis of the adg2-1 allele revealed a missense mutation. The results therefore suggest either that the missense mutation affects the stability of the ADGase large subunit protein or that it prevents assembly of the large subunit into holoenzyme.
Haloperidol and Ziprasidone for Treatment of Delirium in Critical Illness (2018)

The use of haloperidol or ziprasidone, as compared with placebo, in patients with acute respiratory failure or shock and hypoactive or hyperactive delirium in the ICU did not significantly alter the duration of delirium. (Funded by the National Institutes of Health and the VA Geriatric Research Education and Clinical Center; MIND-USA ClinicalTrials.gov number, NCT01211522 .).
Nasolacrimal Drainage System Obstruction from Radioactive Iodine Therapy for Thyroid Carcinoma (2002)

Ophthalmic complications of (131)I therapy, including ocular dryness, have been recently investigated and described. However, nasolacrimal drainage system obstruction (NDSO), complicating (131)I therapy, has not been previously well appreciated or characterized. One of our patients developed bilateral complete nasolacrimal duct obstruction after (131)I therapy that prompted awareness of this potential complication. Over 16 months, 423 patients with epithelial-derived thyroid cancer were provided routine clinical care; 390 of these patients had received (131)I ablation or therapy, and 10 patients subsequently reported epiphora. All had evidence of NDSO disease after a mean cumulative (131)I dose of 17,279 +/- 2,923 MBq (467 +/- 79 mCi), with a mean individual (131)I dose of 6,660 +/- 555 MBq (180 +/- 15 mCi). Symptoms appeared 6.5 +/- 1.4 (range, 3-16) months after the last (131)I dose, whereas the mean time from symptom onset to correct diagnosis was 18 +/- 5 months. A causal relationship between (131)I administration and NDSO is strongly suspected. Patients reporting epiphora should be evaluated promptly by an oculoplastic surgeon.
Production in Escherichia coli of human thymosin beta 4 as chimeric protein with human tumor necrosis factor. (1989)

We have produced thymosin beta 4 protein in Escherichia coli as a chimeric protein with tumor necrosis factor (TNF). The protein was abundantly expressed, was immunoreactive against both anti-thymosin beta 4 and anti-TNF antibodies, and retained cytotoxicity in a TNF assay using mouse L929 fibroblasts. This latter characteristic enabled the easy and simple purification of thymosin beta 4 merely by following the TNF activity. The chimeric protein was designed to have an Asp-Pro bridge between thymosin beta 4 and TNF which could be specifically cleaved under suitable acidic conditions to release the thymosin beta 4 from the chimeric protein. These results indicate that the expression system in E.coli of a chimeric protein composed of thymosin beta 4 and TNF is appropriate for obtaining an abundant amount of the beta 4 peptide, especially since its purification from tissues is usually difficult because of limited yield and obscurity of its biological activity.
Substance abuse in the perioperative setting (1995)

Published information and extensive anecdotal reports from perioperative nurses reveal an alarming amount of substance abuse in the perioperative setting. In addition to the familiar controlled substances (eg, narcotics, tranquilizers), practitioners must be familiar with the potential abuse of anesthesia induction agents such as ketamine, nitrous oxide, and general inhalation anesthetics. Perioperative nurses need to be aware of the problem of substance abuse in the perioperative setting, increase their knowledge of substance abuse practices, be alert to signs and symptoms of chemical dependency, and have plans for responding to reported substance abuse situations when on duty.
Graded expression of zinc-responsive genes through two regulatory zinc-binding sites in Zur (2011)

Zinc is one of the essential transition metals in cells. Excess or lack of zinc is detrimental, and cells exploit highly sensitive zinc-binding regulators to achieve homeostasis. In this article, we present a crystal structure of active Zur from Streptomyces coelicolor with three zinc-binding sites (C-, M-, and D-sites). Mutations of the three sites differentially affected sporulation and transcription of target genes, such that C- and M-site mutations inhibited sporulation and derepressed all target genes examined, whereas D-site mutations did not affect sporulation and derepressed only a sensitive gene. Biochemical and spectroscopic analyses of representative metal site mutants revealed that the C-site serves a structural role, whereas the M- and D-sites regulate DNA-binding activity as an on-off switch and a fine-tuner, respectively. Consistent with differential effect of mutations on target genes, zinc chelation by TPEN derepressed some genes (znuA, rpmF2) more sensitively than others (rpmG2, SCO7682) in vivo. Similar pattern of TPEN-sensitivity was observed for Zur-DNA complexes formed on different promoters in vitro. The sensitive promoters bound Zur with lower affinity than the less sensitive ones. EDTA-treated apo-Zur gained its DNA binding activity at different concentrations of added zinc for the two promoter groups, corresponding to free zinc concentrations of 4.5×10(-16) M and 7.9×10(-16) M for the less sensitive and sensitive promoters, respectively. The graded expression of target genes is a clever outcome of subtly modulating Zur-DNA binding affinities in response to zinc availability. It enables bacteria to detect metal depletion with improved sensitivity and optimize gene-expression pattern.
Monolithically integrated self-rolled-up tube based vertical coupler with planar waveguide – a new 3D photonic integration scheme (2015)

Self-rolled-up SiNx tube based vertical photonic couplers are monolithically integrated on top of planar ridge waveguides in various configurations. The coupling efficiency between the elements is >10 times higher than similar non-integrated device.
Binding and biologic characterization of recombinant human serum albumin-eTGFBR2 fusion protein expressed in CHO cells (2017)

Transforming growth factor-β1 (TGF-β1) signaling is involved in cell metabolism, growth, differentiation, carcinoma invasion and fibrosis development, which suggests TGF-β1 can be treated as a therapeutic target extensively. Because TGF-β1 receptor type α(TGFBR2) is the directed and essential mediator for TGF-β1 signals, the extracellular domain of TGFBR2 (eTGFBR2), binding partner for TGF-β1, has been produced in a series of expression systems to inhibit TGF-β1 signaling. However, eTGFBR2 is unstable with a short half-life predominantly because of enzymatic degradation and kidney clearance. In this study, a fusion protein consisting of human eTGFBR2 fused at the C-terminal of human serum albumin (HSA) was stably and highly expressed in Chinese Hamster Ovary (CHO) cells. The high and stable expression sub-clones with Ig kappa signal peptide were selected by Western blot analysis and used for suspension culture. After fed-batch culture over 8 d, the expression level of HSA-eTGFBR2 reached 180 mg/L. The fusion protein was then purified from culture medium using a 2-step chromatographic procedure that resulted in 39% recovery rate. The TGF-β1 binding assay revealed that HSA-eTGFBR2 could bind to TGF-β1 with the affinity constant (K<sub>D</sub> of 1.42 × 10<sup>-8</sup> M) as determined by the ForteBio Octet System. In addition, our data suggested that HSA-eTGFBR2 exhibited a TGF-β1 neutralizing activity and maintained a long-term activity more than eTGFBR2. It concluded that the overexpressing CHO cell line supplied sufficient recombinant human HSA-eTGFBR2 for further research and other applications.
FTY720 enhances the activation‐induced apoptosis of donor T cells and modulates graft‐<i>versus</i>‐host disease (2006)

FTY720 is a novel immunosuppressant that improves the outcomes after solid organ and bone marrow transplantation (BMT) due to the sequestration of T cells into LN. We tested the hypothesis that the sequestration of donor T cells in LN by FTY720 would enhance their interaction with host APC, thus causing a greater degree of activation-induced apoptosis of alloreactive T cells, and thereby resulting in a reduction of graft-vs.-host disease (GVHD). The short-term administration of FTY720 improved the recipient survival after allogeneic BMT. FTY720 treatment facilitated a rapid contraction of the donor T cell pool in association with an increased degree of apoptosis of donor T cells. The donor T cell reactivity to host alloantigens was diminished in host's LN and adoptive transfer of donor T cells isolated from LN of FTY720-treated recipients of allogeneic BMT induced less severe GVHD in secondary recipients than the transfer from controls. Caspase-dependent apoptosis was involved in this mechanism because FTY720-induced protection was abrogated when a pan-caspase inhibitor was administered. These findings thus demonstrate the presence of a novel mechanism by which FTY720 modulates the allogeneic T cell responses: namely, by the induction of activation-induced apoptosis of alloreactive T cells in LN.
AN INFRARED VIEW OF HIGH T<sub><font>c</font></sub> SUPERCONDUCTORS (1989)

Studies of the infrared properties of the high T c superconductors are reviewed, with particular emphasis on attempts to determine the energy gap by far infrared spectroscopy and on the properties of the strong absorption that occurs in the mid infrared. We argue that this mid-infrared absorption is a direct particle-hole excitation rather than a Holstein emission process. In addition, we conclude that although the energy gap is not easily observed, several recent experiments place it in the weak to moderate strong coupling range.
Producer-consumer communication in distributed shared memory multiprocessors (1999)

The shared memory abstraction supported by hardware based distributed shared memory (DSM) multiprocessors is an inherently consumer driven means of communication. When a process requires data, it retrieves them from the global shared memory. In distributed cache coherent systems, the data may reside in a remote memory module or in the producer's cache. Producer initiated mechanisms reduce communication latency by sending data to the consumer as soon as they are produced. We classify producer initiated mechanisms as implicit or explicit, according to whether the producer must know the identity of the consumer when data are transmitted. Explicit schemes include data forwarding and message passing. Implicit schemes include update based coherence, selective updates, and cache based locks. Several of these mechanisms are evaluated for performance and sensitivity to network parameters, using a common simulated architecture and a set of application kernel benchmarks. StreamLine, a cache based message passing mechanism, provides the best performance on the benchmarks with regular communication patterns. Forwarding write and cache based locks are also among the best performing producer initiated mechanisms. Consumer initiated prefetch, however, has good average performance and is the least expensive to implement.
Phosphorylation-Dependent Ubiquitination of Cyclin E by the SCF <sup>Fbw7</sup> Ubiquitin Ligase (2001)

Cyclin E binds and activates the cyclin-dependent kinase Cdk2 and catalyzes the transition from the G1 phase to the S phase of the cell cycle. The amount of cyclin E protein present in the cell is tightly controlled by ubiquitin-mediated proteolysis. Here we identify the ubiquitin ligase responsible for cyclin E ubiquitination as SCFFbw7 and demonstrate that it is functionally conserved in yeast, flies, and mammals. Fbw7 associates specifically with phosphorylated cyclin E, and SCFFbw7 catalyzes cyclin E ubiquitination in vitro. Depletion of Fbw7 leads to accumulation and stabilization of cyclin E in vivo in human and Drosophila melanogaster cells. Multiple F-box proteins contribute to cyclin E stability in yeast, suggesting an overlap in SCF E3 ligase specificity that allows combinatorial control of cyclin E degradation.