gebhart/patrepeval huggingface dataset:
Photoacoustic endoscopy (2009)

We have developed photoacoustic endoscopy with a miniaturized imaging probe. A light-guiding optical fiber, an ultrasonic sensor, and a mechanical scanning unit are integrated to enable circumferential sector scanning, which produces B-scan images. Biological tissues, including the gastrointestinal tract of a rat, have been imaged ex vivo or in situ.
Inhibition of receptor binding by high-affinity RNA ligands to vascular endothelial growth factor (1994)

The proliferation of new blood vessels (angiogenesis) is a process that accompanies many pathological conditions including rheumatoid arthritis and solid tumor growth. Among angiogenic cytokines that have been identified to date, vascular endothelial growth factor (VEGF) is one of the most potent. We used SELEX [systematic evolution of ligands by exponential enrichment; Tuerk, C., & Gold, L. (1990) Science 249, 505-510] to identify RNA ligands that bind to VEGF in a specific manner with affinities in the low nanomolar range. Ligands were selected from a starting pool of about 10(14) RNA molecules containing 30 randomized positions. Isolates from the affinity-enriched pool were grouped into six distinct families on the basis of primary and secondary structure similarities. Minimal sequence information required for high-affinity binding to VEGF is contained in 29-36-nucleotide motifs. Binding of truncated (minimal) high-affinity ligands to VEGF is competitive with that of other truncated ligands and heparin. Furthermore, truncated ligands from the six ligand families inhibit binding of [125I]VEGF to its cell-surface receptors. Oligonucleotide ligands described here represent an initial set of lead compounds in our ongoing effort toward the development of potent and specific VEGF antagonists.
Lymphotoxin-alpha beta heterotrimers are shed from the surface of activated human lymphocytes, circulate in serum, and are elevated in synovial fluid of rheumatoid arthritis patients (38.22) (2009)

Abstract Lymphotoxin, a trimeric cytokine in the tumor necrosis family, is expressed by activated T, B, and NK cells and is involved in inflammatory response signaling and secondary lymphoid organ architecture. Using a specific assay for human LTαβ which detects both LTα1β2 and LTα2β1 trimers but not LTα3, we show here that LTαβ is detected in culture supernatants of 293 cells transfected with human LTα and LTβ constructs, and in supernatants of primary activated human T lymphocytes. The levels of soluble LTαβ detected in culture supernatants of human CD4+ Th1 polarized lymphocytes treated with an inhibitor of ADAM17 (TACE) protease, were reduced 3-6 fold compared to supernatants from untreated cells. This suggests that LTαβ cleavage is carried out by TACE. A 26 KDa MW form of LTβ was detected in activated human T cell culture supernatant by Western blot analysis using an anti-LTβ-specific antibody. Soluble LTαβ was detected in serum from normal human donors and rheumatoid arthritis (RA) patients at levels of approximately 100 pg/mL. Soluble LTαβ was also detected in synovial fluid from RA patients at significantly higher levels than in synovial fluid from osteoarthritis patients. Cleavage of LTαβ trimers from the cell membrane and release into circulation has not been previously described. Soluble LTαβ may play a role as an inflammatory mediator of autoimmune disease. Research supported by Genentech Inc., S. San Francisco, CA
Preparation of micelle-forming polymer-drug conjugates (1992)

Adriamycin, a hydrophobic anticancer drug, was conjugated with poly(ethylene oxide)-poly(aspartic acid) block copolymers composed of various lengths of each block copolymer segment ranging from 1000 to 12,000 in molecular weight and from 10 to 80 units, respectively. Conjugation was achieved without precipitation by adjusting the ratio of adriamycin to aspartic acid residues of the block copolymer and the quantity of DMF used for the reaction. Thus obtained conjugates showed high water solubility irrespective of a large amount of the conjugated adriamycin. Furthermore, these conjugates were found to form micellar structures with a hydrophobic inner core and a hydrophilic outer shell. This micellar architecture may be utilized for effective drug targeting.
Simultaneous measurement of estrogen and progesterone receptors in tumor cytosols with use of 125I-labeled estradiol and of 3H-R5020. (1981)

We describe a dual-isotope assay for measuring the concentration of estrogen receptors and progesterone receptors in tumor cytosols. The concentrations of these receptors are derived from separate Scatchard-plot analyses of a single dextran-coated charcoal assay that incorporates both radioiodinated estradiol and tritiated R5020 as the labeled ligands. The two isotopes, radioiodine and tritium, are easily measured with a liquid-scintillation counter. The concentrations of estrogen and progesterone receptors derived from the dual-label assay are identical to values derived from the respective single-label assays. Moreover, values obtained from an assay with dextran-coated charcoal that incorporates radioiodinated estradiol are identical to those obtained from an assay in which tritiated estradiol is used as the labeled ligand. The dual-isotope assay requires both less time and less tissue.
Cyproheptadine Treatment of Sexual Dysfunction Induced by Serotonin Reuptake Inhibitors (1995)

Treatment of serotonin reuptake inhibitors (SRIs) is associated with sexual dysfunction. The cause of this dysfunction is unclear but may be related to stimulation of the serotonergic system. In the present article, we describe seven patients in whom iatrogenic sexual dysfunction induced by SRIs was treated with cyproheptadine, a 5HT-2 antagonist with antihistaminergic and adrenolytic properties. Seven obsessive-compulsive male patients, aged 29-54 years, who developed sexual dysfunction following treatment with SRIs (fluoxetine, fluvoxamine, and clomipramine) were instructed to take cyproheptadine (4-12 mg) 1-2 h before commencing sexual activity. Five of the seven patients displayed improvement in sexual function, although the improvement was transitory in two. The two remaining patients did not respond. All patients exhibited sedation on the day following cyproheptadine administration. Our preliminary observation suggests that some patients with sexual dysfunction associated with SRI treatment, mainly decreased libido and anorgasmia, may benefit from cyproheptadine administration. The role of 5HT-2 antagonists in SRI-induced sexual dysfunction merits further investigation.
Scalable reader-writer locks (2009)

We present three new reader-writer lock algorithms that scale under high read-only contention. Many previous reader-writer locks suffer significant degradation when many readers attempt to acquire the lock concurrently, even though they are all allowed to hold the lock at the same time. In contrast, our locks scale almost perfectly when there is only read contention on a 4-chip system with a total of 256 hardware threads.
16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates (2000)

Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmental, veterinary, and clinical sources. For 159 isolates (89.8%) there was at least one sequence in GenBank that yielded a similarity score of > or =97%, and for 139 isolates (78.5%) there was at least one sequence in GenBank that yielded a similarity score of > or =99%. These similarity score values were used to defined identification at the genus and species levels, respectively. For isolates identified to the species level, conventional identification failed to produce accurate results because of inappropriate biochemical profile determination in 76 isolates (58.7%), Gram staining in 16 isolates (11.6%), oxidase and catalase activity determination in 5 isolates (3.6%) and growth requirement determination in 2 isolates (1.5%). Eighteen isolates (10.2%) remained unidentifiable by 16S rDNA sequence analysis but were probably prototype isolates of new species. These isolates originated mainly from environmental sources (P = 0.07). The 16S rDNA approach failed to identify Enterobacter and Pantoea isolates to the species level (P = 0.04; odds ratio = 0.32 [95% confidence interval, 0.10 to 1.14]). Elsewhere, the usefulness of 16S rDNA sequencing was compromised by the presence of 16S rDNA sequences with >1% undetermined positions in the databases. Unlike phenotypic identification, which can be modified by the variability of expression of characters, 16S rDNA sequencing provides unambiguous data even for rare isolates, which are reproducible in and between laboratories. The increase in accurate new 16S rDNA sequences and the development of alternative genes for molecular identification of certain taxa should further improve the usefulness of molecular identification of bacteria.
Scaffold Role of a Mitogen-activated Protein Kinase Phosphatase, SKRP1, for the JNK Signaling Pathway (2002)

Stress-activated protein kinase (SAPK) pathway-regulating phosphatase 1 (SKRP1) has been identified as a member of the mitogen-activated protein kinase (MAPK) phosphatase (MKP) family that interacts physically with the MAPK kinase (MAPKK) MKK7, a c-Jun N-terminal kinase (JNK) activator, and inactivates the MAPK JNK pathway. Although these findings indicated that SKRP1 contributes to the precise regulation of JNK signaling, it remains to be elucidated how SKRP1 is integrated into this pathway. We report that SKRP1 also plays a scaffold role for the JNK signaling, judged by the following observations. SKRP1 selectively formed the stable complexes with MKK7 but not with MKK4 and biphasically regulated the MKK7 activity and MKK7-induced gene transcription in vivo. Co-precipitation analysis between SKRP1 and MKK7-activating MAPKK kinases (MAPKKKs) revealed that SKRP1 also interacted with the MAPKKK, apoptosis signal-regulating kinase 1 (ASK1), but not with MAP kinase kinase kinase 1 (MEKK1). Consistent with these findings, SKRP1 expression increased the ASK1-MKK7 complexes in a dose-dependent manner and specifically enhanced the activation of MKK7 by ASK1. Thus, our findings are, to our knowledge, the first evidence to show that an MKP also functions as a scaffold protein for the particular MAPK signaling.
Frustratingly Short Attention Spans in Neural Language Modeling (2017)

Neural language models predict the next token using a latent representation of the immediate token history. Recently, various methods for augmenting neural language models with an attention mechanism over a differentiable memory have been proposed. For predicting the next token, these models query information from a memory of the recent history which can facilitate learning mid- and long-range dependencies. However, conventional attention mechanisms used in memory-augmented neural language models produce a single output vector per time step. This vector is used both for predicting the next token as well as for the key and value of a differentiable memory of a token history. In this paper, we propose a neural language model with a key-value attention mechanism that outputs separate representations for the key and value of a differentiable memory, as well as for encoding the next-word distribution. This model outperforms existing memory-augmented neural language models on two corpora. Yet, we found that our method mainly utilizes a memory of the five most recent output representations. This led to the unexpected main finding that a much simpler model based only on the concatenation of recent output representations from previous time steps is on par with more sophisticated memory-augmented neural language models.
Correction: High-Throughput Profiling of Anti-Glycan Humoral Responses to SIV Vaccination and Challenge (2013)

Recent progress toward an HIV vaccine highlights both the potential of vaccines to end the AIDS pandemic and the need to boost efficacy by incorporating additional vaccine strategies. Although many aspects of the immune response can contribute to vaccine efficacy, the key factors have not been defined fully yet. A particular area that may yield new insights is anti-glycan immune responses, such as those against the glycan shield that HIV uses to evade the immune system. In this study, we used glycan microarray technology to evaluate anti-glycan antibody responses induced by SIV vaccination and infection in a non-human primate model of HIV infection. This comprehensive profiling of circulating anti-glycan antibodies found changes in anti-glycan antibody levels after both vaccination with the Ad5hr-SIV vaccine and SIV infection. Notably, SIV infection produced generalized declines in anti-glycan IgM antibodies in a number of animals. Additionally, some infected animals generated antibodies to the Tn antigen, which is a cryptic tumor-associated antigen exposed by premature termination of O-linked glycans; however, the Ad5hr-SIV vaccine did not induce anti-Tn IgG antibodies. Overall, this study demonstrates the potential contributions that glycan microarrays can make for HIV vaccine development.
Lattices that admit logarithmic worst-case to average-case connection factors (2007)

We exhibit an average-case problem that is as hard as finding γ(n)-approximate shortest nonzero vectors in certain n-dimensional lattices in the worst case, for γ(n) = O(√log n). The previously best known factor for any non-trivial class of lattices was γ(n) = Õ(n).
Polymer‐Supported and Free‐Standing Metal–Organic Framework Membrane (2012)

Thrive on a polymer: A polymer-supported method is developed and used to prepare well-intergrown and free-standing metal–organic framework (MOF) membranes. By using this method, a stainless steel net/PMMA–PMAA-supported HKUST-1 membrane was fabricated and applied in gas separation. Results indicated that such a membrane has a high separation factor to H2/N2, H2/CH4, H2/CO2 gas mixtures (see figure).
Differential Expression of Fibroblast Growth Factor Receptors 1 to 4 and Ligand Genes in Late Fetal and Early Postnatal Rat Lung (1998)

To characterize fibroblast growth factor (FGF) gene expression in the late fetal (days E18 to E22) and early postnatal lung (days P0 to P28), when the alveolar region undergoes extensive growth and reorganization, we analyzed the expression of four FGF receptors and six ligands. FGF receptor 1 (FGFR1) RNA levels were first low (E18) before rising late in the postnatal period (P28). FGFR2 RNA levels were detected early (at E18) and then increased (E20-P0) before falling (P2) to below later postnatal levels (P6 to P28). FGFR3 RNA levels were low at first (E18) and then increased, with peak levels in the days after birth (P2 to P10). FGFR4 RNA levels, barely detected in fetal lung (E18 to E22), increased at birth (P0) and remained high postnatally (P2 to P28). In fetal lung, FGF2 (basic FGF) RNA expression levels were low and FGF1 (acidic FGF) RNA levels were not detected: low RNA levels of each ligand were detected postnatally (P7 to P28). FGF3 to 5 and FGF7 RNA were not detected in fetal or postnatal lung. With in situ hybridization, predominantly the smooth muscle cells of large vessels expressed FGFR1 and 4 mRNA; the epithelial cells of large airways expressed FGFR1, 2, and 4; and alveolar cells expressed FGFR2, 3, and 4. Analysis of protein expression first identified FGF2 localized to the basement membrane of large airways and branching epithelial buds, to mesenchymal cells associated with buds, to the putative smooth muscle cells of large airways and vessels, and to pleural- and mesenchymal-associated cells (E18). Immediately before birth, this pattern of expression persisted (E20 to E22), with FGF2 also being expressed by putative smooth muscle cells of smaller airways and vessels (E22). After birth (P0 to P28), FGF2 expression remained relatively high in the smooth muscle cells of large and small vessels and in pleural cells; in airway smooth muscle cells and in most cells in the alveolar region, however, although FGF2 expression persisted in some cells, its intensity decreased with time.
Autoimmune response to U1 small nuclear ribonucleoprotein (U1 snRNP) associated with cytomegalovirus infection (2001)

The induction of autoantibodies to U1 small nuclear ribonucleoprotein (U1 snRNP) complexes is not well understood. We present evidence that healthy individuals with cytomegalovirus (CMV) infection have an increased frequency and quantity of antibodies to ribonucleoprotein, directed primarily against the U1-70k protein. A significant association between the presence of antibodies to CMV and antibodies to the total RNP targeted by the immune response to the spliceosome (to both the Sm and RNP; Sm/RNP) was found for patients with systemic lupus erythematosus (SLE) but not those with mixed connective-tissue disease. CMV thus may play a role in inducing autoimmune responses in a subset of patients with systemic lupus erythematosus.
Cytokine mRNA levels in mononuclear blood cells from patients with multiple sclerosis (1994)

We determined the cytokine messenger RNA (mRNA) expression pattern of blood mononuclear cells in 45 patients with the relapsing-remitting form of MS and 32 patients with other neurologic diseases. Using a semiquantitative polymerase chain reaction method, we detected significantly higher levels of tumor necrosis factor-alpha and lymphotoxin mRNA in patients with relapsing compared to those with stable disease (p < 0.001), but transforming growth factor-beta and interleukin-10 mRNA expressions were higher in patients with stable disease.
Fiber-Wireless Networks and Subsystem Technologies (2009)

Hybrid fiber-wireless networks incorporating WDM technology for fixed wireless access operating in the sub-millimeter-wave and millimeter-wave (mm-wave) frequency regions are being actively pursued to provide untethered connectivity for ultrahigh bandwidth communications. The architecture of such radio networks requires a large number of antenna base-stations with high throughput to be deployed to maximize the geographical coverage with the main switching and routing functionalities located in a centralized location. The transportation of mm-wave wireless signals within the hybrid network is subject to several impairments including low opto-electronic conversion efficiency, fiber chromatic dispersion and also degradation due to nonlinearities along the link. One of the major technical challenges in implementing such networks lies in the mitigation of these various optical impairments that the wireless signals experience within the hybrid network. In this paper, we present an overview of different techniques to optically transport mm-wave wireless signals and to overcome impairments associated with the transport of the wireless signals. We also review the different designs of subsystems for integrating fiber-wireless technology onto existing optical infrastructure.
Primary structure of human alpha 2-macroglobulin. IV. Primary structure of two large CNBr fragments, located in the COOH-terminal part and accounting for 337 residues. (1984)

The amino acid sequences have been determined for two CNBr fragments of human alpha 2-macroglobulin which, due to the presence of an uncleaved Hse-Thr bond, form an Mr = 40,000 fragment. These fragments are located in the COOH-terminal part of alpha 2-macroglobulin (CB21, residues 955-1185 and CB22, residues 1186-1291). CB21 contains one glucosamine-based carbohydrate group attached to Asn-14 and one internal disulfide bridge (Cys-102 bound to Cys-150). CB21 and CB22 account for 337 of the 1451 residues of the subunit of alpha 2-macroglobulin.
Insulin‐like growth factor‐1 stimulates regulatory T cells and suppresses autoimmune disease (2014)

The recent precipitous rise in autoimmune diseases is placing an increasing clinical and economic burden on health systems worldwide. Current therapies are only moderately efficacious, often coupled with adverse side effects. Here, we show that recombinant human insulin-like growth factor-1 (rhIGF-1) stimulates proliferation of both human and mouse regulatory T (Treg) cells in vitro and when delivered systemically via continuous minipump, it halts autoimmune disease progression in mouse models of type 1 diabetes (STZ and NOD) and multiple sclerosis (EAE) in vivo. rhIGF-1 administration increased Treg cells in affected tissues, maintaining their suppressive properties. Genetically, ablation of the IGF-1 receptor specifically on Treg cell populations abrogated the beneficial effects of rhIGF-1 administration on the progression of multiple sclerotic symptoms in the EAE model, establishing a direct effect of IGF-1 on Treg cell proliferation. These results establish systemically delivered rhIGF-1 as a specific, effective stimulator of Treg cell action, underscoring the clinical feasibility of manipulating natural tolerance mechanisms to suppress autoimmune disease.
Capillary Electrophoresis Combined with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry; Continuous Sample Deposition on a Matrix-precoated Membrane Target (1996)

Capillary electrophoresis (CE) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) were combined in an off-line arrangement to provide separation and mass analysis of peptide and protein mixtures in the attomole range. A membrane target, precoated with MALDI matrix, was used for the continuous deposition of effluent exiting from a CE device. A sample track was produced by linear movement of the target during the electrophoretic separation and this track was subsequently analyzed by MALDI/MS. The technique is effective for peptides and proteins, having limits of detection (signal-to-noise >3) of about 50 amol for neurotensin (1673 Da) and 250 amol for cytochrome c (12361 Da) and apomyoglobin (16951 Da). The electrophoretic separation achieved from the membrane target, as measured by theoretical plate numbers from the mass spectrometric data, can be as high as 80-90% of that achieved by on-line UV detection under optimal conditions, although band broadening occurs and with some loss of separation efficiency. Non-volatile buffers such as 10-50 mM phosphate can also be used in the electrophoresis process and directly deposited on the membrane. The use of post-source decay techniques is shown for peptides in the CE sample track in order to obtain sequence verification. The effectiveness of this method of integration of CE and MALDI/MS is demonstrated with both peptide and protein mixtures and with the analysis of a tryptic digest of a protein.
Position of exhalation port and mask design affect CO2 rebreathing during noninvasive positive pressure ventilation* (2003)

Facial-MEP with its exhalation port within the mask and the smallest mask volume demonstrated less rebreathed CO2 and a lower PDR than either the Facial-WS or Total Face masks. Additional studies are necessary to confirm if mask design can clinically affect patient's inspiratory effort during noninvasive positive pressure ventilation.