gebhart/patrepeval huggingface dataset:
A Monoclonal Antibody with Broad Reactivity to Human Interferon‐α Subtypes Useful for Purification of Leukocyte‐Derived Interferon (1986)

A monoclonal antibody to human interferon-alpha, termed HT-1 antibody, with a broad reactivity to various subtypes of interferon-alpha was prepared. It bound and neutralized all of the four subtypes of E. coli-derived human recombinant interferon-alpha (alpha 1, alpha 2, alpha 4, and alpha 6) tested; it also neutralized human natural leukocyte interferon but only partially. Human interferon-beta and -gamma were not bound. The antibody conjugated to Sepharose beads retained over 90% of human leukocyte interferon induced by Sendai virus. The bound interferon was recovered by acid elution in good yields and in almost pure form (specific activity was about 2 X 10(8) international units/mg protein). The purified interferon showed, in SDS-polyacrylamide gel electrophoresis, an activity profile with major peaks in a mol. wt. range of 17,000-22,000, which completely agreed with the profile shown by polyclonal antibody-purified interferon. Such purified leukocyte interferon-alpha preparations containing most of the naturally occurring subtypes can be useful for clinical and other purposes.
An information-theoretic framework for resolving community structure in complex networks (2007)

To understand the structure of a large-scale biological, social, or technological network, it can be helpful to decompose the network into smaller subunits or modules. In this article, we develop an information-theoretic foundation for the concept of modularity in networks. We identify the modules of which the network is composed by finding an optimal compression of its topology, capitalizing on regularities in its structure. We explain the advantages of this approach and illustrate them by partitioning a number of real-world and model networks.
3-Aryl-2-Quinolone Derivatives:  Synthesis and Characterization of In Vitro and In Vivo Antitumor Effects with Emphasis on a New Therapeutical Target Connected with Cell Migration (2002)

Among 25 3-aryl-2-quinolone derivatives synthesized, the antitumor activity of some of them was characterized both in vitro and in vivo. In this series, no compound appeared to be cytotoxic in vitro, as was known by the colorimetric MTT assay carried out on 12 distinct human cancer cell lines obtained from the American Type Culture Collection. Indeed, the concentration values decreasing the growth of the 12 cell lines by at least 50% (IC(50) index) were always higher than 10(-5) M. We then made use of a computer-assisted phase-contrast videomicroscopy system to quantitatively determine in vitro the level of migration of living MCF-7 human breast cancer cells. For example, at 10(-7) M, compounds 7, 13, 16, and 28 markedly decreased the migration level of these MCF-7 human breast cancer cells. The in vivo determination of the maximum tolerated dose showed that all compounds tested were definitively nontoxic. When the nontoxic, antimigratory compound 16 was combined with either doxorubicin or etoposide, two cytotoxic compounds routinely used in the clinic, this led to additive in vivo benefits from this treatment (as compared to individual administrations of the drugs) when the MXT mouse mammary adenocarcinoma was used. Thus, nontoxic antimigratory compounds, including the 2-quinolone derivatives synthesized here, can actually improve the efficiency of antitumor treatment when combined with conventional cytotoxic agents.
Phase I study of the histone deacetylase inhibitor entinostat in combination with 13-cis retinoic acid in patients with solid tumours (2011)

The combination of entinostat with CRA was reasonably well tolerated. The recommended phase II doses are entinostat 4 mg m(-2) once weekly and CRA 1 mg kg(-1) per day. Although no tumour responses were seen, further evaluation of this combination is warranted.
Amyotrophic Lateral Sclerosis Mutant VAPB Causes a Nuclear Envelope Defect (2012)

A proline to serine mutation (P56S) in vesicle-associated membrane protein-associated protein B and C (VAPB) causes an autosomal dominant form of amyotrophic lateral sclerosis (ALS). We show that the mutation also causes a nuclear envelope defect. Transport of nucleoporins (Nups) and emerin (EMD) to the nuclear envelope is blocked, resulting in their sequestration in dilated cytoplasmic membranes. Simultaneous overexpression of the FFAT motif (two phenylalanine residues in an acidic track) antagonizes the effect of mutant VAPB and restores transport to the nuclear envelope. VAPB function is required for transport to the nuclear envelope, with knockdown of endogenous VAPB recapitulating this phenotype. Moreover, we identified the compartment into which the Nups and EMD were sequestered as the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC), with nuclear envelope membrane proteins transiting to the ERGIC before VAPB-dependent retrograde transport to the nuclear envelope.
Spectral Sparsification of Graphs (2011)

We introduce a new notion of graph sparsification based on spectral similarity of graph Laplacians: spectral sparsification requires that the Laplacian quadratic form of the sparsifier approximate that of the original. This is equivalent to saying that the Laplacian of the sparsifier is a good preconditioner for the Laplacian of the original. We prove that every graph has a spectral sparsifier of nearly linear size. Moreover, we present an algorithm that produces spectral sparsifiers in time $O(m\log^{c}m)$, where m is the number of edges in the original graph and c is some absolute constant. This construction is a key component of a nearly linear time algorithm for solving linear equations in diagonally dominant matrices. Our sparsification algorithm makes use of a nearly linear time algorithm for graph partitioning that satisfies a strong guarantee: if the partition it outputs is very unbalanced, then the larger part is contained in a subgraph of high conductance.
Demethylating Drugs as Novel Analgesics for Cancer Pain (2014)

Our study establishes the regulatory role of methylation in cancer pain. OPRM1 re-expression in cancer cells produces antinociception through cancer-mediated endogenous opioid secretion. Demethylating drugs have an analgesic effect that involves OPRM1.
Two-way global broadcast system architecture (2004)

The global broadcast system (GBS) implemented by the U.S. Department of Defense utilizes commercially-based digital video broadcast (DVB) technology to enable high-rate (10's of Mb/s), one-way, data dissemination to a large number of users. Currently, however, user terminals are limited to receive-only operation. For many users, a receive-only configuration is not adequate and a low to medium-rate (10's to 100's of kb/s) return channel is required for true network-centric operations and enhanced mission effectiveness. This paper describes a frequency re-use architecture that provides such return channel connectivity to a large number of users without requiring additional satellite bandwidth and with minimal interference to current receive-only users.
Glomerulonephritis in beta-thalassemia Hb-E disease: clinical manifestations, histopathologic studies and outcome. (1995)

We presented 8 patients with beta-thal/Hb E with glomerular diseases. Diverse glomerular lesions were seen, but diffuse endocapillary glomerulonephritis was the most common. The clinical manifestations of acute glomerulonephritis in beta-thal/Hb E differed from typical cases in the older age group, female preponderance, longer duration of edema, less hypertension, marked proteinuria, hypoalbuminemia and hypertriglyceridemia and also a longer period of recovery but their outcome was still favorable despite many risk factors of renal injury. Renal biopsy was necessary in doubtful cases to detect the correct diagnosis and give proper management. The association and mechanism of glomerulonephritis in these patients require further prospective study.
Growth Hormone-Releasing Factor from a Human Pancreatic Tumor That Caused Acromegaly (1982)

A 44 amino acid peptide with growth hormone-releasing activity has been isolated from a human tumor of the pancreas that had caused acromegaly. The primary structure of the tumor-derived peptide is H-Tyr-Ala-Asp-Ala-Ile-Phe-Thr-Asn-Ser-Tyr-Arg-Lys-Val-Leu-Gly-Gln-Leu-Ser-Ala- Arg-Lys-Leu-Leu-Gln-Asp-Ile-Met-Ser-Arg-Gln-Gln-Gly-Glu-Ser-Asn-Gln-Glu-Arg-Gly -Ala-Arg-Ala-Arg-Leu-NH2. The synthetic replicate has full biological activity in vitro and in vivo specifically to stimulate the secretion of immunoreactive growth hormone. The tumor-derived peptide is identical in biological activity and similar in physiochemical properties to the still uncharacterized growth hormone-releasing factor present in extracts of hypothalamic tissues.
A nonrecursive list compacting algorithm (1970)

A simple nonrecursive list structure compacting scheme or garbage collector suitable for both compact and LISP-like list structures is presented. The algorithm avoids the need for recursion by using the partial structure as it is built up to keep track of those lists that have been copied.
Determining permeability of tight rock samples using inverse modeling (1997)

Data from gas‐pressure‐pulse‐decay experiments have been analyzed by means of numerical simulation in combination with automatic model calibration techniques to determine hydrologie properties of low‐permeability, low‐porosity rock samples. Porosity, permeability, and Klinkenberg slip factor have been estimated for a core plug from The Geysers geothermal field, California. The experiments were conducted using a specially designed permeameter with small gas reservoirs. Pressure changes were measured as gas flowed from the pressurized upstream reservoir through the sample to the downstream reservoir. A simultaneous inversion of data from three experiments performed on different pressure levels allows for independent estimation of absolute permeability and gas permeability which is pressure‐dependent due to enhanced slip flow. With this measurement and analysis technique we can determine matrix properties with permeabilities as low as 10 −21 m 2 . In this paper we discuss the procedure of parameter estimation by inverse modeling. We will focus on the error analysis, which reveals estimation uncertainty and parameter correlations. This information can also be used to evaluate and optimize the design of an experiment. The impact of systematic errors due to potential leakage and uncertainty in the initial conditions will also be addressed. The case studies clearly illustrate the need for a thorough error analysis of inverse modeling results.
Stimulation of Medial Prefrontal Cortex Decreases the Responsiveness of Central Amygdala Output Neurons (2003)

In extinction of auditory fear conditioning, rats learn that a tone no longer predicts the occurrence of a footshock. Recent lesion and unit recording studies suggest that the medial prefrontal cortex (mPFC) plays an essential role in the inhibition of conditioned fear following extinction. mPFC has robust projections to the amygdala, a structure that is known to mediate the acquisition and expression of conditioned fear. Fear conditioning potentiates the tone responses of neurons in the basolateral amygdala (BLA), which excite neurons in the central nucleus (Ce) of the amygdala. In turn, the Ce projects to the brainstem and hypothalamic areas that mediate fear responses. The present study was undertaken to test the hypothesis that the mPFC inhibits conditioned fear via feedforward inhibition of Ce output neurons. Recording extracellularly from physiologically identified brainstem-projecting Ce neurons, we tested the effect of mPFC prestimulation on Ce responsiveness to synaptic input. In support of our hypothesis, mPFC prestimulation dramatically reduced the responsiveness of Ce output neurons to inputs from the insular cortex and BLA. Thus, our findings support the idea that mPFC gates impulse transmission from the BLA to Ce, perhaps through GABAergic intercalated cells, thereby gating the expression of conditioned fear.
Cyclopamine: inhibiting hedgehog in the treatment of psoriasis. (2006)

The steroidal alkaloid cyclopamine, a direct inhibitor of the hedgehog (Hh) intracellular signaling pathway, has demonstrated promising initial results in the treatment of psoriasis. Cyclopamine initially was shown to be effective in the induction of the differentiation and apoptosis of basal cell carcinomas (BCCs). This brief review explains both the details of Hh signaling and the role of cyclopamine in interrupting it. Most importantly, this article discusses the implications of recent findings on the treatment of psoriasis. Although considerable research and clinical trials lie ahead, cyclopamine-induced Hh inhibition may represent the latest mechanistic pathway to combat psoriasis.
Telomere length measurement by a novel monochrome multiplex quantitative PCR method (2009)

The current quantitative polymerase chain reaction (QPCR) assay of telomere length measures telomere (T) signals in experimental DNA samples in one set of reaction wells, and single copy gene (S) signals in separate wells, in comparison to a reference DNA, to yield relative T/S ratios that are proportional to average telomere length. Multiplexing this assay is desirable, because variation in the amount of DNA pipetted would no longer contribute to variation in T/S, since T and S would be collected within each reaction, from the same input DNA. Multiplexing also increases throughput and lowers costs, since half as many reactions are needed. Here, we present the first multiplexed QPCR method for telomere length measurement. Remarkably, a single fluorescent DNA-intercalating dye is sufficient in this system, because T signals can be collected in early cycles, before S signals rise above baseline, and S signals can be collected at a temperature that fully melts the telomere product, sending its signal to baseline. The correlation of T/S ratios with Terminal Restriction Fragment (TRF) lengths measured by Southern blot was stronger with this monochrome multiplex QPCR method (R(2) = 0.844) than with our original singleplex method (R(2) = 0.677). Multiplex T/S results from independent runs on different days were highly reproducible (R(2) = 0.91).
Safflower germplasm: past, present, and future. (2008)

Germplasm collections are a critical resource for development and improving safflower (Carthamus tinctorius L.) cultivars and germplasm. Our objective here is to describe the safflower germplasm collection at the Western Regional Plant Introduction Station (WRPIS), Pullman WA, USA, in light of past, present, and future safflower germplasm uses and needs. The WRPIS maintains 2477 C. tinctorius accessions of which 90% are available for distribution. As many as 300 safflower accessions are regenerated each year under screen cages to prevent genetic contamination by insect cross pollination. The active collection is maintained at 4°C and 24% r.h. to facilitate management and distribution, while long-term, security back-up of accessions is at -18°C. Over the last ten years 11485 seed packets have been distributed from the WRPIS with 77% to scientists outside the US. The GRIN database contains 61982 data entries for safflower accessions including information on growth and development, disease resistance, oil content, and fatty acid profiles. Recent innovations in safflower germplasm using WRPIS germplasm include high vitamin E types, high saturated fatty acid types, the first mapped safflower genes, and winter adapted safflower. Current acquisition needs for the WRPIS include collections in southwest and central Asia and wild Carthamus species. Future uses of safflower are expected to include expanded use of hybrids, biofuels, new fatty acid combinations, and transgenic safflower for producing pharmaceuticals. In all these efforts, the WRPIS and other genebanks will play a central role by providing the needed genetic resources.
High-frequency steering maneuvers mediated by tactile cues: antennal wall-following in the cockroach (1999)

Cockroaches (Periplaneta americana) use their antennae to detect a wall and to maintain a constant distance from it as they walk or run along it. The faster they run, the closer they position themselves to the wall. They also use their antennae to detect and follow multiple accordion-like projections in the wall. They can make up to 25 body turns s-1 for short periods during rapid running to follow such wall projections. Each turn apparently involves a change in stepping direction. These turns help to avoid collisions with the outward projections, while keeping the body close to the wall. Sensory inputs from the flagellum of the antenna, and not from its base, appear to evoke the turns in response to wall projections. These flagellar inputs appear to report the position along the antenna of its contact with the wall and/or the position of the consequent antennal bend. This flagellar information constitutes a one-dimensional sensory map, with location along the map indicating the distance to the wall.
A Toll-like Receptor That Prevents Infection by Uropathogenic Bacteria (2004)

Toll-like receptors (TLRs) recognize molecular patterns displayed by microorganisms, and their subsequent activation leads to the transcription of appropriate host-defense genes. Here we report the cloning and characterization of a member of the mammalian TLR family, TLR11, that displays a distinct pattern of expression in macrophages and liver, kidney, and bladder epithelial cells. Cells expressing TLR11 fail to respond to known TLR ligands but instead respond specifically to uropathogenic bacteria. Mice lacking TLR11 are highly susceptible to infection of the kidneys by uropathogenic bacteria, indicating a potentially important role for TLR11 in preventing infection of internal organs of the urogenital system.
Human monoclonal antibodies to nuclear antigens (1990)

Human lymph node lymphocytes from cancer patients were fused with either the UC 729-6 or SHFP-1 human fusion partners. Resulting human-human hybridomas were tetraploid, expressed markers from both parent cells, and secreted approximately 1 microgram Ig/10(6) cells/ml/day. Immunofluorescence analysis of some of the human MAbs with a panel of normal and malignant cell lines revealed a staining pattern of only the nuclear region. One IgM secreting hybridoma, TLN1F4, derived from a teratocarcinoma lymph node, predominantly stained the nuclear regions of adherent tumor cell lines and no hematopoietic cell lines or normal fibroblasts. PLN3C8, an IgG1 secreting hybridoma, derived from a prostate carcinoma lymph node, predominantly stained the nucleolus of LnCap, a a carcinoma of the prostate cell line. CLN2E5, an IgM secreting human hybridoma, derived from a carcinoma of the cervix lymph node, predominantly stained both cytoplasmic and nuclear components to tumor cell lines and not normal fibroblasts or hematopoietic cell lines. These data suggest that the immune response occurring within regional draining lymph nodes is capable of recognizing nuclear-associated antigens.
Conditional expression of human TNF‐α: A system for inducible cytotoxicity (1994)

Tumour necrosis factor-alpha (TNF-alpha) is currently being used in clinical trials for cancer treatment, but toxic side effects, due to systemic administration and high doses, are observed. Inducible expression of TNF may permit selective killing of tumour cells in gene therapy protocols without need for prolonged and/or high-level TNF expression. A conditional TNF expression vector has been constructed in which the coding sequences of human TNF have been placed under the transcriptional control of the glucocorticoid-regulated murine mammary tumour virus long terminal repeat (MMTV-LTR). Negligible levels of TNF expression, associated with no phenotypic alterations, are observed in cells transfected with MMTV-TNF vectors in the absence of glucocorticoid. Expression levels could be stimulated by the addition of the synthetic glucocorticoid dexamethasone. Increasing expression levels of TNF were associated with enhanced cytotoxicity. Our results suggest the potential use of inducible TNF systems for the treatment of tumours in gene therapy protocols.
Temporal and Spatial Expression Patterns of Transgenes Containing Increasing Amounts of theDrosophilaClock Geneperiodand alacZReporter: Mapping Elements of the PER Protein Involved in Circadian Cycling (1997)

Rhythmic oscillations of the PER protein, the product of the Drosophila period ( per ) gene, in brain neurons of the adult fly are strongly involved in the control of circadian rhythms. We analyzed temporal and spatial expression patterns of three per–reporter fusion genes, which share the same 4 kb regulatory upstream region but contain increasing amounts of per ’s coding region fused in frame to the bacterial lacZ gene. The fusion proteins contained either the N-terminal half (SG), the N-terminal two-thirds (BG), or nearly all (XLG) of the PER protein. All constructs led to reporter signals only in the known per -expressing cell types within the anterior CNS and PNS. Whereas the staining intensity of SG flies was constantly high at different Zeitgeber times, the in situ signals in BG and XLG flies cycled with ∼24 hr periodicity in the PER-expressing brain cells in wild-type and per 01 loss of function flies. Despite the rhythmic fusion-gene expression within the relevant neurons of per 01 BG flies, their locomotor activity in light/dark cycling conditions and in constant darkness was identical to that of per 01 controls, uncoupling protein cycling from rhythmic behavior. The XLG construct restored weak behavioral rhythmicity to (otherwise) per 01 flies, indicating that the C-terminal third of PER (missing in BG) is necessary to fulfill the biological function of this clock protein.
Cytotoxicity of a recombinant ricin‐A‐chain fusion protein containing a proteolytically‐cleavable spacer sequence (1990)

Chimeric proteins composed of ricin toxin A chain (RTA) and staphylococcal protein A (PA) have been produced in E. coli. Constructs consisting of N-terminal RTA and C-terminal PA (RTA-PA) or N-terminal PA and C-terminal (PA-RTA) were capable of binding to immunoglobulin G (via PA) and of specifically depurinating 28 S ribosomal RNA (via RTA). However, neither fusion protein was cytotoxic to antigen-bearing target cells in the presence of an appropriate monoclonal antibody presumably because the RTA could not be released from the PA within the cytosol where the ribosomal substrate of RTA is located. The overcome this, a short amino acid sequence from diphtheria toxin was engineered between the RTA and PA to produce a disulfide-linked loop containing a trypsin sensitive cleavage site. Cleavage of this fusion protein with trypsin converted the RTA-DT-PA to the two chain form consisting of RTA linked by a disulfide bond to PA. The cleaved fusion protein was highly toxic to Daudi cells coated with anti-immunoglobulin antibody suggesting that the RTA could be released from the PA by reduction within the cytosol.
Time Integrating Optical Signal Processing (1980)

Time integrating acousto-optic processors realize flexible, multipurpose complex signal processing architectures based on correlation algorithms. One- and two-dimensional techniques are presented including examples of spectral analysis and ambiguity function processing. Noncoherent optical processor implementation using interferometric detection with electronic reference is described and experimental results are given.
Expression, purification, and MALDI analysis of RPE65. (2001)

RPE65 is expressed in two forms, one of which is membrane associated and contains significant posttranslational modifications, similar to the native membrane-associated form.