gebhart/patrepeval huggingface dataset:
Synthetic Oligonucleotides with Particular Base Sequences from the cDNA Encoding Proteins of Mycobacterium bovis BCG Induce Interferons and Activate Natural Killer Cells (1992)

Thirteen kinds of 45-mer single-stranded oligonucleotide, having sequence randomly selected from the known cDNA encoding BCG proteins, were tested for their capability to augment natural killer (NK) cell activity of mouse spleen cells in vitro. Six out of the 13 oligonucleotides showed the activity, while the others did not. In order to know the minimal and essential sequence(s) responsible for the biological activity, 2 kinds of 30-mer and 5 kinds of 15-mer oligonucleotide fragments of an active 45-mer nucleotide were tested for their activity. One of the 30-mer oligonucleotides, designated BCG-A4a, was active, but the other 30-mer was inactive. All of the 15-mer oligonucleotide fragments were inactive. The BCG-A4a also stimulated the spleen cells to produce interferon (IFN)-alpha and -gamma. An experiment using anti-IFN antisera showed that the NK cell activation by the oligonucleotide was ascribed to the IFN-alpha produced. It was noticed that all of the biologically active oligonucleotides possessed one or more palindrome sequence(s), and the inactive ones did not, with an exception of a 45-mer inactive oligonucleotide containing overlapping palindrome sequences (GGGCCCGGG). These findings strongly suggest that certain palindrome sequences, like GACGTC, GGCGCC and TGCGCA, are essential for 30-mer oligonucleotides, like BCG-A4a, to induce IFNs.
Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces (2011)

There is a general need for the engineering of protein-like molecules that organize into geometrically specific superstructures on molecular surfaces, directing further functionalization to create richly textured, multilayered assemblies. Here we describe a computational approach whereby the surface properties and symmetry of a targeted surface define the sequence and superstructure of surface-organizing peptides. Computational design proceeds in a series of steps that encode both surface recognition and favorable intersubunit packing interactions. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes (SWNTs). The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of SWNTs into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the SWNT axis.
Measurement and Estimation of GFR in Children and Adolescents (2009)

GFR is the best indicator of renal function in children and adolescents and is critical for diagnosing acute and chronic kidney impairment, intervening early to prevent end-stage renal failure, prescribing nephrotoxic drugs and drugs cleared by a failing kidney, and monitoring for side effects of medications. Renal inulin clearance was the gold standard for GFR but is compromised by lack of availability, difficult assays, and problems of collecting timed urine samples, especially in children with vesicoureteral reflux or bladder dysfunction. Creatinine clearance-based estimates of GFR are often used in pediatrics. The addition of cimetidine to eliminate creatinine secretion permits accurate measurement of GFR in those who can completely empty their bladders to provide timed urine collections. Radioisotopes are used in plasma disappearance GFR determinations; however, these are not ideal for use in children, especially for repeated studies. The plasma disappearance of iohexol serves as a promising alternative GFR marker, because it is safe and not radioactive, easily measured, not metabolized or transported by the kidney, and excreted primarily by glomerular filtration. GFR estimating equations, based on serum concentrations of creatinine or cystatin C, are popular clinically and in research studies. Efforts are ongoing to improve these estimating equations for children and make the results readily available to clinicians obtaining standard chemistry profiles, as is being done for adults. However, at this time, there is no dependable substitute for an accurately determined GFR, and iohexol plasma disappearance offers the best combination of safety, accuracy, and reproducible precision.
Inhibition of the alternative complement activation pathway in traumatic brain injury by a monoclonal anti-factor B antibody: a randomized placebo-controlled study in mice (2007)

Inhibition of the alternative complement pathway by posttraumatic administration of a neutralizing anti-factor B antibody appears to represent a new promising avenue for pharmacological attenuation of the complement-mediated neuroinflammatory response after head injury.
Compliant leg behaviour explains basic dynamics of walking and running (2006)

The basic mechanics of human locomotion are associated with vaulting over stiff legs in walking and rebounding on compliant legs in running. However, while rebounding legs well explain the stance dynamics of running, stiff legs cannot reproduce that of walking. With a simple bipedal spring-mass model, we show that not stiff but compliant legs are essential to obtain the basic walking mechanics; incorporating the double support as an essential part of the walking motion, the model reproduces the characteristic stance dynamics that result in the observed small vertical oscillation of the body and the observed out-of-phase changes in forward kinetic and gravitational potential energies. Exploring the parameter space of this model, we further show that it not only combines the basic dynamics of walking and running in one mechanical system, but also reveals these gaits to be just two out of the many solutions to legged locomotion offered by compliant leg behaviour and accessed by energy or speed.
Inhibition of matrix metalloproteinase 2 maturation and HT1080 invasiveness by a synthetic furin inhibitor (1998)

The close correlation observed between matrix metalloproteinase 2 (MMP-2) activation and metastatic progression in various tumors suggests that MMP-2 is a 'master switch' triggering tumor spread. Recently, membrane type 1 MMP (MT1-MMP) was identified as a potential physiological activator of MMP-2. Like all other MMPs, MT1-MMP possesses a pro-domain which must be removed for the enzyme to acquire its catalytic potential. The presence of a typical recognition motif (RXKR) for the furin-like convertases at the end of its pro-domain suggests a potential role for these proteinases in MT1-MMP processing. In order to evaluate the implication of furin in pro-MT1-MMP processing, we treated HT1080 cells with a synthetic furin inhibitor and monitored their ability to activate pro-MMP-2 as well as their invasive potential. Our results demonstrated that the furin inhibitor decreased pro-MT1-MMP processing as well as pro-MMP-2 activation and cell invasiveness. Therefore, our data bring further evidence that furin is a key factor in the maturation of MMPs associated with the invasive and metastatic potential of tumor cells.
Synergy of IL-12 and IL-18 for IFN-γ Gene Expression: IL-12-Induced STAT4 Contributes to IFN-γ Promoter Activation by Up-Regulating the Binding Activity of IL-18-Induced Activator Protein 1 (2002)

IL-12 and IL-18 synergistically enhance IFN-gamma mRNA transcription by activating STAT4 and AP-1, respectively. However, it is still unknown how STAT4/AP-1 elicit IFN-gamma promoter activation. Using an IL-12/IL-18-responsive T cell clone, we investigated the mechanisms underlying synergistic enhancement of IFN-gamma mRNA expression induced by these two cytokines. Synergy was observed in a reporter gene assay using an IFN-gamma promoter fragment that binds AP-1, but not STAT4. An increase in c-Jun, a component of AP-1, in the nuclear compartment was elicited by stimulation with either IL-12 or IL-18, but accumulation of serine-phosphorylated c-Jun was induced only by IL-18 capable of activating c-Jun N-terminal kinase. The binding of AP-1 to the relevant promoter sequence depended on the presence of STAT4. STAT4 bound with c-Jun, and a phosphorylated c-Jun-STAT4 complex most efficiently interacted with the AP-1-relevant promoter sequence. Enhanced cobinding of STAT4 and c-Jun to the AP-1 sequence was also observed when activated lymph node T cells were exposed to IL-12 plus IL-18. These results show that STAT4 up-regulates AP-1-mediated IFN-gamma promoter activation without directly binding to the promoter sequence, providing a mechanistic explanation for IL-12/IL-18-induced synergistic enhancement of IFN-gamma gene expression.
Surface Learning with Applications to Lipreading (1993)

Most connectionist research has focused on learning mappings from one space to another (eg. classification and regression). This paper introduces the more general task of learning constraint surfaces. It describes a simple but powerful architecture for learning and manipulating nonlinear surfaces from data. We demonstrate the technique on low dimensional synthetic surfaces and compare it to nearest neighbor approaches. We then show its utility in learning the space of lip images in a system for improving speech recognition by lip reading. This learned surface is used to improve the visual tracking performance during recognition. 1 Surface Learning Mappings are an appropriate representation for systems whose variables naturally decompose into &amp;quot;inputs&amp;quot; and &amp;quot;outputs&amp;quot;. To use a learned mapping, the input variables must be known and error-free and a single output value must be estimated for each input. Many tasks in vision, robotics, and control must maintain relationships between variable...
Exciton diffusion and dissociation in conjugated polymer/fullerene blends and heterostructures (1999)

We investigate the exciton dynamics in composite systems of conjugated polymers and fullerene molecules by photoluminescence (PL) and femtosecond transient absorption experiments. In solid mixtures (blends) we find a strong concentration-dependent quenching of the polymer PL. This is attributed to an efficient electron transfer (ET) from the photoexcited conjugated polymer to the fullerene. The ET dynamics is directly monitored by measuring the transient stimulated emission of the conjugated polymer. The transfer rate depends linearly on the ${\mathrm{C}}_{60}$ concentration and ranges between $(66\mathrm{ps}{)}^{\ensuremath{-}1}$ and $(5\mathrm{ps}{)}^{\ensuremath{-}1}$ for concentrations from 0.5% to 5%. This dependence is in accordance with an exciton diffusion process occurring prior to the ET. The exciton diffusion length in the conjugated polymer is directly determined by measuring the PL quenching in well-defined heterostructures comprising a self-assembled fullerene monolayer and a thin spin-coated polymer layer of variable thickness. From these measurements we infer a value of 14 nm for the exciton diffusion length in ladder-type poly (p-phenylene). Our results are of direct relevance for further optimization of polymer photovoltaic devices.
Development of a propidium iodide fluorescence assay for proliferation and cytotoxicity assays (1995)

A propidium iodide fluorescence assay (PIA) was developed to characterize the in vitro growth of human tumor cell lines as well as to test the cytotoxic activity of standard compounds. Propidium iodide (PI) was used as a dye which penetrates only damaged cellular membranes. Intercalation complexes are formed by PI with double-stranded DNA which effect an amplification of the fluorescence. Incubation of the total cell population with PI and subsequent fluorescence detection allowed assessment of the number of non-vital cells (first measurement). After freezing the cells at -20 degrees C for 24 h PI had access to total DNA leading to total cell population counts (second measurement). The number of viable cells was calculated by the difference between these two measurements. In the proliferation and cytotoxicity assays 5 x 10(3) cells per well were plated in 96 multiwells and finally stained with 50 micrograms/ml PI in 25 microliters for 10 min. A correlation between the log of cell number and the log of fluorescence units could be demonstrated over a 2.5-3 log range (r = 0.97). The lower limit of cell detection was 150-500 cells/wells. In cytotoxicity assays eight clinically used cytostatics were tested which effected a clear dose-response relationship (r = 0.93-0.98) and high reproducibility (r = 0.92). In conclusion, this assay is a simple and rapid test system, the main advantages are the absence of any washing steps and the small number of tumor cells necessary for drug testing. The PIA can easily be used for cell number determinations in biological and pharmacological studies.
Milatuzumab: a promising new agent for the treatment of lymphoid malignancies (2008)

Milatuzumab is cytotoxic to lymphoma and multiple myeloma cell lines and mouse-human xenografts. The efficacy dramatically increases when milatuzumab is attached to a toxin or a radioactive agent. Phase I trials of milatuzumab are now underway in human subjects with lymphoma and multiple myeloma.
Learning to Label Aerial Images from Noisy Data (2012)

When training a system to label images, the amount of labeled training data tends to be a limiting factor. We consider the task of learning to label aerial images from existing maps. These provide abundant labels, but the labels are often incomplete and sometimes poorly registered. We propose two robust loss functions for dealing with these kinds of label noise and use the loss functions to train a deep neural network on two challenging aerial image datasets. The robust loss functions lead to big improvements in performance and our best system substantially outperforms the best published results on the task we consider. 1.
Jesuitas de principio a fin. Algunas consideraciones historiográficas sobre la Compañía de Jesús. (A resultas del Quinto Centenario del nacimiento del cofundador Alfonso Salmerón, 1515) (2016)

Estamos acostumbrados a contemplar y estudiar a la Compania de Jesus desde perspectivas distorsionadas, especialmente desde el gran trauma que supuso su primera expulsion y posterior extincion en 1767-1773. Pero el contra-jesuitismo no fue una moda del siglo XVIII, como tampoco logro difuminarse en los siglos  contemporaneos. En primer termino, se intenta vincular el agrio combate entre la orden de los Jesuitas y el Estado regalista borbonico en la larga historia de la Compania desde su constitucion en 1540. Posteriormente se hace un repaso de los puntos de interes y facetas en los que se ha centrado la historiografia jesuitica desde el siglo XIX hasta el XXI; para, por ultimo, proponer algunas direcciones que deben ser reforzadas en la investigacion futura, que ya no parece estar ligada a los profesos de la Compania en exclusividad. Todo para explicar por que es pertinente dedicarle importantes esfuerzos al estudio de la figura del cofundador Alfonso Salmeron.
Rapid peptide mapping by high-performance liquid chromatography (1988)

Short columns, packed with pellicular sorbents made of 2-micron fluid-impervious silica microspheres, were used at elevated column temperatures for rapid peptide mapping by high-performance liquid chromatography (HPLC). Enzymic digests of various proteins were chromatographed by gradient elution. In many cases the time of analysis was 10 min or less. In order to increase the retention particularly, that of short, polar peptides under such conditions, 1 mM octyl sodium sulfate or 5 mM hexyl sodium sulfate were added to the starting eluent. The length of the 4.6 mm I.D. columns was 30 or 75 mm, the sample load was in the range of 10-1000 pmoles. Highest analytical sensitivity was obtained at a flow-rate of 0.5 ml/min and room temperature, whereas for rapid analysis flow-rates of up to 2 ml/min were used at 80 degrees C. This temperature allowed the use of relatively high flow velocities of the mobile phase without significant loss in efficiency. The method was highly reproducible, as shown by the results obtained by automated analysis of cyanogen bromide fragments of lysozyme at high speed. The quality of the rapid peptide maps compares favorably with that of maps obtained by standard reversed-phase HPLC methods, which require much longer analysis times.
One‐Pot Conversion of Carbohydrates into Furan Derivatives via Furfural and 5‐Hydroxylmethylfurfural as Intermediates (2016)

Recently, there has been growing interest in the transformation of renewable biomass into value-added fuels and chemicals. The catalytic conversion of naturally abundant carbohydrates can generate two-important furan chemicals: 5-hydroxymethylfurfural (HMF) from C6 carbohydrates and furfural from C5 carbohydrates. Both HMF and furfural have received great interest as precursors in the synthesis of commodity chemicals and liquid fuels. In recent years, a trend has emerged to integrate sequential catalytic processes involving multistep reactions for the direct one-pot transformation of carbohydrates into the aimed fuels and chemicals. One-pot reactions have remarkably unique and environmentally friendly benefits, including the fact that isolation and purification of intermediate compounds can be avoided. Herein, the present article aims to review recent advances in the one-pot conversion of carbohydrates into furan derivatives via furfural and HMF as intermediates. Special attention will be paid to the catalytic systems, mechanistic insight, reaction pathways, and catalyst stability. It is expected that this review will guide researchers to develop effective catalytic systems for the one-pot transformation of carbohydrates into furan derivatives.
Functional Expression of Hi-Histaminergic Receptors in Xenopus Laevis Oocytes Injected with Bovine Adrenal Medullary mRNA (1991)

We prepared poly (A)+ mRNA from bovine adrenal medulla and electrophysiologically examined the expression of H,-histaminergic receptors in Xenopus laevis oocytes. Histamine dose-dependently induced inward currents in oocytes injected with the mRNA, but not in those injected with water or the non-injected oocytes. This response was also induced by H1-agonists and antagonized by Η1-antagomsts, while both an H2-agonist and an antagonist had no effect. These results clearly demonstrate that H1-histaminergic receptors are functionally expressed in oocytes injected with exogenous mRNA.
Complementary Roles for Exonuclease 1 and Flap Endonuclease 1 in Maintenance of Triplet Repeats (2010)

Trinucleotide repeats can form stable secondary structures that promote genomic instability. To determine how such structures are resolved, we have defined biochemical activities of the related RAD2 family nucleases, FEN1 (Flap endonuclease 1) and EXO1 (exonuclease 1), on substrates that recapitulate intermediates in DNA replication. Here, we show that, consistent with its function in lagging strand replication, human (h) FEN1 could cleave 5'-flaps bearing structures formed by CTG or CGG repeats, although less efficiently than unstructured flaps. hEXO1 did not exhibit endonuclease activity on 5'-flaps bearing structures formed by CTG or CGG repeats, although it could excise these substrates. Neither hFEN1 nor hEXO1 was affected by the stem-loops formed by CTG repeats interrupting duplex regions adjacent to 5'-flaps, but both enzymes were inhibited by G4 structures formed by CGG repeats in analogous positions. Hydroxyl radical footprinting showed that hFEN1 binding caused hypersensitivity near the flap/duplex junction, whereas hEXO1 binding caused hypersensitivity very close to the 5'-end, correlating with the predominance of hFEN1 endonucleolytic activity versus hEXO1 exonucleolytic activity on 5'-flap substrates. These results show that FEN1 and EXO1 can eliminate structures formed by trinucleotide repeats in the course of replication, relying on endonucleolytic and exonucleolytic activities, respectively. These results also suggest that unresolved G4 DNA may prevent key steps in normal post-replicative DNA processing.
The Clinical Potential of Senolytic Drugs (2017)

Senolytic drugs are agents that selectively induce apoptosis of senescent cells. These cells accumulate in many tissues with aging and at sites of pathology in multiple chronic diseases. In studies in animals, targeting senescent cells using genetic or pharmacological approaches delays, prevents, or alleviates multiple age-related phenotypes, chronic diseases, geriatric syndromes, and loss of physiological resilience. Among the chronic conditions successfully treated by depleting senescent cells in preclinical studies are frailty, cardiac dysfunction, vascular hyporeactivity and calcification, diabetes mellitus, liver steatosis, osteoporosis, vertebral disk degeneration, pulmonary fibrosis, and radiation-induced damage. Senolytic agents are being tested in proof-of-concept clinical trials. To do so, new clinical trial paradigms for testing senolytics and other agents that target fundamental aging mechanisms are being developed, because use of long-term endpoints such as lifespan or healthspan is not feasible. These strategies include testing effects on multimorbidity, accelerated aging-like conditions, diseases with localized accumulation of senescent cells, potentially fatal diseases associated with senescent cell accumulation, age-related loss of physiological resilience, and frailty. If senolytics or other interventions that target fundamental aging processes prove to be effective and safe in clinical trials, they could transform geriatric medicine by enabling prevention or treatment of multiple diseases and functional deficits in parallel, instead of one at a time.
Dose titration and patient selection increases the efficacy of GH replacement in severely GH deficient adults (1999)

The observed improvement in quality of life in GH deficient adults is proportional to the degree of impairment before commencing therapy. The use of low-dose titration and selection of a population with greater morbidity reduces the occurrence of over-replacement and increases the efficacy of treatment. This allows direction of resources to those in greatest need.
Synthesized Classifiers for Zero-Shot Learning (2016)

Given semantic descriptions of object classes, zero-shot learning aims to accurately recognize objects of the unseen classes, from which no examples are available at the training stage, by associating them to the seen classes, from which labeled examples are provided. We propose to tackle this problem from the perspective of manifold learning. Our main idea is to align the semantic space that is derived from external information to the model space that concerns itself with recognizing visual features. To this end, we introduce a set of "phantom" object classes whose coordinates live in both the semantic space and the model space. Serving as bases in a dictionary, they can be optimized from labeled data such that the synthesized real object classifiers achieve optimal discriminative performance. We demonstrate superior accuracy of our approach over the state of the art on four benchmark datasets for zero-shot learning, including the full ImageNet Fall 2011 dataset with more than 20,000 unseen classes.
Are impurities the cause of ’’self’’-compensation in large-band-gap semiconductors? (1980)

A possible role of impurities in the well-known difficulty of obtaining well-conducting large-band-gap material is investigated. Specifically, the limitations imposed on carrier concentrations by chemical equilibrium considerations are analyzed for a (model) system of a single amphoteric impurity. It is also shown that energies of formation of at least some Group-I interstitials in a typical II–VI semiconductor, ZnSe, are expected to be low compared to those of native donor defects. Since Group-I impurities act as acceptors on a metal substitutional site, but as donors when on a interstitial site, a stable interstitial form results in amphoteric behavior and thus in constraints on achievable carrier concentrations if such impurities are present either deliberately or accidentally.