gebhart/patrepeval huggingface dataset:
Management of Fibrosis: The Mesenchymal Stromal Cells Breakthrough (2014)

Fibrosis is the endpoint of many chronic inflammatory diseases and is defined by an abnormal accumulation of extracellular matrix components. Despite its slow progression, it leads to organ malfunction. Fibrosis can affect almost any tissue. Due to its high frequency, in particular in the heart, lungs, liver, and kidneys, many studies have been conducted to find satisfactory treatments. Despite these efforts, current fibrosis management therapies either are insufficiently effective or induce severe adverse effects. In the light of these facts, innovative experimental therapies are being investigated. Among these, cell therapy is regarded as one of the best candidates. In particular, mesenchymal stromal cells (MSCs) have great potential in the treatment of inflammatory diseases. The value of their immunomodulatory effects and their ability to act on profibrotic factors such as oxidative stress, hypoxia, and the transforming growth factor-β1 pathway has already been highlighted in preclinical and clinical studies. Furthermore, their propensity to act depending on the microenvironment surrounding them enhances their curative properties. In this paper, we review a large range of studies addressing the use of MSCs in the treatment of fibrotic diseases. The results reported here suggest that MSCs have antifibrotic potential for several organs.
A method for including redundant data in computed tomography (2000)

A method for including redundant data in fan-beam computed tomography (CT) is presented. It is a natural extension of the Parker [Med. Phys. 9, 254-257 (1982)] short-scan approach applied to divergent fan-beam (or cone-beam) data when the data set covers between the minimally complete set of 180 degrees plus fan angle and 360 degrees. A virtual fan angle is introduced whose value is the difference between the angular range of the data collected and 180 degrees. Parker-weights are then applied as if the field-of-view is spanned by the virtual fan angle.
Production and in vivo biologic actions of recombinant mouse interferon alpha 2. (1989)

We have expressed a recombinant mouse interferon alpha (r.Mu-IFN alpha 2) in Escherichia coli under the control of a tryptophan promoter using a synthetic adaptor formed by annealing two partially complementary oligonucleotides which introduced an ATG start codon and re-established the complete coding sequence of the mature IFN alpha 2 protein in the expression vector. Levels of up to 10(7) reference units of Mu-IFN alpha 2 per liter of culture were obtained using this construction. This recombinant mouse interferon alpha 2 exhibited antiviral activity in mice infected with EMC virus and antitumor activity in mice inoculated with Friend leukemia cells in a manner similar to that of natural mouse interferon alpha/beta.
In vitro permeability of round window membrane to transforming dexamethasone with delivery vehicles — a dosage estimation (2007)

The combination of alginate and chitin could be used as vehicle for sustained release of dexamethasone in intratympanic application.
Generation of Specific Deoxynojirimycin-type Inhibitors of the Non-lysosomal Glucosylceramidase (1998)

The existence of a non-lysosomal glucosylceramidase in human cells has been documented (van Weely, S., Brandsma, M., Strijland, A., Tager, J. M., and Aerts, J. M. F. G. (1993) Biochim. Biophys. Acta 1181, 55-62). Hypothetically, the activity of this enzyme, which is localized near the cell surface, may influence ceramide-mediated signaling processes. To obtain insight in the physiological importance of the non-lysosomal glucosylceramidase, the availability of specific inhibitors would be helpful. Here we report on the generation of hydrophobic deoxynojirimycin (DNM) derivatives that potently inhibit the enzyme. The inhibitors were designed on the basis of the known features of the non-lysosomal glucosylceramidase and consist of a DNM moiety, an N-alkyl spacer, and a large hydrophobic group that promotes insertion in membranes. In particular, N-(5-adamantane-1-yl-methoxy)pentyl)-DNM is a very powerful inhibitor of the non-lysosomal glucosylceramidase at nanomolar concentrations. At such concentrations, the lysosomal glucocerebrosidase and alpha-glucosidase, the glucosylceramide synthase, and the N-linked glycan-trimming alpha-glucosidases of the endoplasmic reticulum are not affected.
Site-specific conjugation of a radioiodinated phenethylamine derivative to a monoclonal antibody results in increased radioactivity localization in tumor (1993)

The preparation of a novel radioiodination reagent, the (aminooxy)acetyl derivative of (p-[125]-iodophenyl)ethylamine, is described. Conventional radioiodination of proteins involves the formation of iodotyrosine residues, but for in vivo applications such as thyroid or stomach immunoscintigraphy, the susceptibility of these residues to tissue dehalogenases constitutes a serious disadvantage. Using our new compound, which has a particularly nonreactive aromatic ring, we confirm and extend studies published by other workers indicating the much greater in vivo stability of iodophenyl compounds compared to the more conventional iodophenolic ones. In addition, the aminooxy group of our reagent gives a stable and specific linkage to aldehyde groups formed by periodate oxidation on the sugar moiety of antibody molecules. In vitro, favorable binding activity and high stability was obtained with a (([125I]iodoaryl)amino)oxy labeled monoclonal antibody directed against carcinoembryonic antigen. In vivo, using paired labeling experiments in nude mice bearing colon carcinoma xenografts, the (([125I]iodoaryl)amino)oxy-MAb (MAb = monoclonal antibody) was compared with the same MAb 131I-labeled by conventional chloramine-T method. Tumor 125I concentration of (arylamino)oxy MAb (measured as percent injected dose per gram) was significantly higher as compared to values obtained with a conventionally labeled 131I antibody. Additionally, thyroid uptake, an indicator of iodine release from the antibody, was up to 25 times lower after injection of 125I-MAb obtained by the new method as compared to the conventionally iodinated 131I-MAb.
Radon in groundwater: A tool to assess infiltration from surface waters to aquifers (1989)

We measured the concentrations of natural 222 Rn (half‐life 3.8 days) in groundwater at three sites in Switzerland; here groundwater is recharged mainly by river water. Upon infiltration and movement in the ground, the radon concentration in the water increases by more than two orders of magnitude to reach a steady state. This increase was found at two of the three sites. At the site of main interest, we used the ingrowth of radon between the river and nearby observation wells to estimate groundwater residence times of up to about four half lives. We assumed that the ingrowth of radon can be described by the growth law of radioactivity, that the progenitors of radon ( 226 Ra, 238 U) are homogeneously distributed in the aquifer, and that the freshly infiltrated water is not mixed significantly with older groundwater. A linear regression through the data at the site of main interest yielded an average flow velocity of 4.6 m −1 , which confirms earlier tracer observations. Radon accumulates to higher concentrations, when the top soil layer is frozen or exhibits a high moisture content. During these conditions the radon data cannot be used for dating purposes.
Morning levels of fibrinogen in children with sleep-disordered breathing (2004)

Elevated fibrinogen level is a predictor of cardiovascular disease in adults, and it is associated with sleep-disordered breathing. Levels of fibrinogen in adults are affected by other co-existing cardiovascular risk factors, which are not usually present in children. To investigate the association between fibrinogen and sleep-disordered breathing, a case-control study was carried out in children with and without habitual snoring. All snoring children underwent polysomnography. Morning fibrinogen values in 30 children with snoring and an apnoea-hypopnoea index (AHI) > or =5 episodes x h(-1) (median (interquartile range) 318 mg x dL(-1) (290-374)) were similar to values in 61 children with snoring and an AHI <5 episodes x h(-1) (307 (269-346)). Both groups had higher fibrinogen values than those in 23 controls without snoring (271 mg x dL(-1) (244-294)). There was no correlation between fibrinogen values and AHI, respiratory movement/arousal index or haemoglobin desaturation index. In conclusion, fibrinogen values are higher in children with snoring than in controls, but there is no association between these values and polysomnography indices.
On wavelength translation in all-optical networks (2002)

In this paper we study the benefits of wavelength translation in all-optical networks providing clear channel circuit-switching among users. We first establish approximate analytical models for a static-routing circuit-switched network with an arbitrary topology, both with and without wavelength translation. We then study performance of the non-blocking centralized switch, the mesh-torus network and the ring network, using the analytical models and simulation results. It is shown that the analytical models match the simulation results very well in the case of the centralized switch and the mesh network. The results of our study also show that the benefits of wavelength translation are marginal for the centralized switch and the ring network. On the other hand, the results show that wavelength translation can significantly improve performance of a large mesh network.
Prurigo nodularis in an HIV positive man. (1995)

A non-Hodgkin's lymphoma in a patient with Non-Hodgkin's lymphoma is a well known complication in persons with HIV-1 infec- tion. HV-2 is a less pathogenic virus, but HIV-2 infected individuals also may progress to AIDS, clinically indistinguishable from AIDS caused by HIV-1 infection.'So far only four cases of non-Hodgkin's lymphoma in HIV-2 infected individuals have been reported.2We describe a fifth case.A 67 year old bisexual man was diagnosed with HIV-2 infection in 1987.His CD4 lym- phocyte count at that time was 216/mm.3In December 1988 zidovudine treatment was started.In 1989 he developed polyneuropa- thy and minor cognitive disorders.After 1992 he suffered recurrent attacks of angina pec- toris because of severe coronary insufficiency.In December 1993 he was hospitalised because of severe weight loss, fatigue, nausea and abdominal pain, mainly localised in the left part of the abdomen.His CD4 count was 100/mm.3At colonoscopy a tumour was observed at the level of the splenic angle.A biopsy revealed a non-Hodgkin's lymphoma.No other lesions outside the gastro-intestinal track were found.Initially, he was treated with endoxan, adriamycin, vincristine and prednisolone.His abdominal pain disap- peared but he continued to lose weight.Despite chemotherapy he developed a large bowel obstruction and died in September 1994.A post-mortem examination was not performed.HIV-2 infection is mainly prevalent in West Africa.Because in this part of the world the facilities for the diagnosis of lymphoma are often lacking, it is likely that lymphoma remains often undiagnosed in African AIDS patients.With increasing numbers of patients with HIV-2 infection seen in the developed world it is expected that cases of non- Hodgkin's lymphoma associated with HIV-2 infection will also increase.
Enhanced angiogenesis and improvement of neuropathy by cotransfection of human hepatocyte growth factor and prostacyclin synthase gene (2003)

The current therapeutic angiogenesis strategy to treat ischemic disease by using angiogenic growth factors has been limited to use of a single gene. However, as vasodilator substances such as prostacyclin are widely used for the treatment of peripheral arterial disease, it might be useful to combine angiogenesis with vasodilation of new vessels. In a mouse hind limb ischemia model, cotransfection of the hepatocyte growth factor (HGF) gene with the prostacyclin synthase gene demonstrated a further increase in blood flow and capillary density compared with a single gene. Even in the rabbit ischemia model, cotransfection of HGF plasmid with the prostacyclin synthase gene demonstrated a further increase in angiogenic activity compared with HGF alone. Because peripheral neuropathy due to diabetes is common for significant morbidity, we examined the hypothesis that experimental diabetic neuropathy can be reversed by HGF and prostacyclin synthase genes. Severe peripheral neuropathy, characterized by significant slowing of nerve conduction velocity compared with nondiabetic control animals, was ameliorated. Overall, cotransfection of the prostacyclin synthase and HGF genes is more effective than single-gene transfection to stimulate angiogenesis, and it significantly improved neuropathy. These data provide important information relating to the clinical application of therapeutic angiogenesis to treat peripheral arterial disease.
Capecitabine Plus Erlotinib in Gemcitabine-Refractory Advanced Pancreatic Cancer (2007)

The combination of capecitabine and erlotinib is active in patients with gemcitabine-refractory pancreatic cancer. This regimen may represent an acceptable treatment option in patients who experience treatment failure with standard first-line therapy with gemcitabine or for whom gemcitabine may not be an appropriate first-line treatment option.
Systemic Chemotherapy with Epirubicin for Treatment of Advanced or Multifocal Hepatocellular Carcinoma (2001)

Epirubicin appears to be an active therapeutic option for patients with non-resectable HCC. Especially the subgroup of patients with low levels of AFP may benefit from this treatment.
Multiphoton stimulation of neurons (2002)

We pulsed the activation of neurons using a femtosecond laser. Pyramidal neurons are depolarized and fire action potentials when high intensity mode-locked infrared light irradiates somatic membranes and axon initial segments. This depolarization is reversible, does not occur with CW laser light, and appears to be due to multiphoton excitation. We describe two regimes of multiphoton optical stimulation. Low intensity, long duration laser irradiation produces a sustained depolarization, insensitive to sodium channel blockers yet sensitive to antioxidants. On the other hand, high intensity, short duration irradiation can induce fast depolarizations, which appear due to different mechanism. The combination of multiphoton stimulation and optical probing could enable systematic analysis of circuits.
Analysis of glycosylation of prostate-specific membrane antigen derived from LNCaP cells, prostatic carcinoma tumors, and serum from prostate cancer patients (1996)

Oligosaccharides present on PSMA derived from both tissue culture LNCaP cells and in vivo specimens are primarily N-linked and comprise about 20-25% of the native molecular weight. N-linked glycans of PSMA derived from in vivo sources were found to be complex type, lacking polylactosamine structures. In contrast, LNCaP cells express only high mannose-type structures. These results will be useful in our ongoing efforts to develop monoclonal antibodies which are specific for protein epitopes present in the extracellular domain of the protein.
Reversible Silencing of CFTR Chloride Channels by Glutathionylation (2005)

The cystic fibrosis transmembrane conductance regulator (CFTR) is a phosphorylation- and ATP-dependent chloride channel that modulates salt and water transport across lung and gut epithelia. The relationship between CFTR and oxidized forms of glutathione is of potential interest because reactive glutathione species are produced in inflamed epithelia where they may be modulators or substrates of CFTR. Here we show that CFTR channel activity in excised membrane patches is markedly inhibited by several oxidized forms of glutathione (i.e., GSSG, GSNO, and glutathione treated with diamide, a strong thiol oxidizer). Three lines of evidence indicate that the likely mechanism for this inhibitory effect is glutathionylation of a CFTR cysteine (i.e., formation of a mixed disulfide with glutathione): (a) channels could be protected from inhibition by pretreating the patch with NEM (a thiol alkylating agent) or by lowering the bath pH; (b) inhibited channels could be rescued by reducing agents (e.g., DTT) or by purified glutaredoxins (Grxs; thiol disulfide oxidoreductases) including a mutant Grx that specifically reduces mixed disulfides between glutathione and cysteines within proteins; and (c) reversible glutathionylation of CFTR polypeptides in microsomes could be detected biochemically under the same conditions. At the single channel level, the primary effect of reactive glutathione species was to markedly inhibit the opening rates of individual CFTR channels. CFTR channel inhibition was not obviously dependent on phosphorylation state but was markedly slowed when channels were first "locked open" by a poorly hydrolyzable ATP analogue (AMP-PNP). Consistent with the latter finding, we show that the major site of inhibition is cys-1344, a poorly conserved cysteine that lies proximal to the signature sequence in the second nucleotide binding domain (NBD2) of human CFTR. This region is predicted to participate in ATP-dependent channel opening and to be occluded in the nucleotide-bound state of the channel based on structural comparisons to related ATP binding cassette transporters. Our results demonstrate that human CFTR channels are reversibly inhibited by reactive glutathione species, and support an important role of the region proximal to the NBD2 signature sequence in ATP-dependent channel opening.
CTRL: A Conditional Transformer Language Model for Controllable Generation (2019)

Large-scale language models show promising text generation capabilities, but users cannot easily control particular aspects of the generated text. We release CTRL, a 1.63 billion-parameter conditional transformer language model, trained to condition on control codes that govern style, content, and task-specific behavior. Control codes were derived from structure that naturally co-occurs with raw text, preserving the advantages of unsupervised learning while providing more explicit control over text generation. These codes also allow CTRL to predict which parts of the training data are most likely given a sequence. This provides a potential method for analyzing large amounts of data via model-based source attribution. We have released multiple full-sized, pretrained versions of CTRL at https://github.com/salesforce/ctrl.
Truncated tau expression levels determine life span of a rat model of tauopathy without causing neuronal loss or correlating with terminal neurofibrillary tangle load (2008)

We have previously demonstrated in a transgenic rat model of tauopathy that human misfolded truncated tau derived from Alzheimer's disease suffices to drive neurofibrillary degeneration in vivo. We employed this model to investigate the impact of truncated tau expression levels on life span, neuronal loss and the final load of neurofibrillary tangles (NFTs) in transgenic rats. Two independent transgenic lines (SHR72, SHR318), that display different expression levels of truncated tau, were utilized in this study. We found that transgene expression levels in the brain of SHR72 rats were 44% higher than in SHR318 rats and that truncated tau protein levels determined the survival rate of transgenic rats. The line with higher expression levels of truncated tau (SHR72) showed decreased median survival (222.5 days) when compared with the line with lower expression (SHR318; 294.5 days). Interestingly, NFT loads (total NFT/total neurons) were very similar in terminal stages of disease in both transgenic lines (SHR72 - 10.9%; SHR318 - 11.6%), despite significantly different expression levels of truncated tau. Moreover, mean neuron numbers in the hippocampus (CA1-3) and brain stem (gigantocellular reticular nucleus) in the two transgenic rat strains in the terminal stages of disease were similar, and did not differ significantly from those observed in age-matched non-transgenic controls. These findings suggest that the expression levels of misfolded truncated tau determine the life span in a transgenic rat model of tauopathy without causing neuronal loss or correlating with terminal NFT load.
Magnetism in Polymers with Embedded Gold Nanoparticles (2007)

Magnetism can be induced in polymers by embedding thiol-capped Au nanoparticles (NPs). The capped NPs (see figure) induce an alteration in the electronic properties of Au, giving rise to ferromagnetic behavior despite the diamagnetic character of bulk Au. When the capped NPs are embedded into a polymeric matrix the magnetic properties are preserved, opening up the possibility of developing Au-based macroscopic magnetic materials.
Self-Formed Hybrid Interphase Layer on Lithium Metal for High-Performance Lithium–Sulfur Batteries (2018)

Lithium-sulfur (Li-S) batteries are promising candidates for high-energy storage devices due to high theoretical capacities of both the sulfur cathode and lithium (Li) metal anode. Considerable efforts have been devoted to improving sulfur cathodes. However, issues associated with Li anodes, such as low Coulombic efficiency (CE) and growth of Li dendrites, remain unsolved due to unstable solid-electrolyte interphase (SEI) and lead to poor capacity retention and a short cycling life of Li-S batteries. In this work, we demonstrate a facile and effective approach to fabricate a flexible and robust hybrid SEI layer through co-deposition of aromatic-based organosulfides and inorganic Li salts using poly(sulfur-random-1,3-diisopropenylbenzene) as an additive in an electrolyte. The aromatic-based organic components with planar backbone conformation and π-π interaction in the SEI layers can improve the toughness and flexibility to promote stable and high efficient Li deposition/dissolution. The as-formed durable SEI layer can inhibit dendritic Li growth, enhance Li deposition/dissolution CE (99.1% over 420 cycles), and in turn enable Li-S batteries with good cycling stability (1000 cycles) and slow capacity decay. This work demonstrates a route to address the issues associated with Li metal anodes and promote the development of high-energy rechargeable Li metal batteries.
Topological dimensionality determination and dimensionality reduction based on minimum spanning trees (2002)

In the design of multidimensional systems for the analysis of complex data, an intelligent reduction of the data dimensionality is needed to enable its efficient and accurate processing without much loss of information. The underlying data transformation process can be implemented by nonlinearly mapping the high-dimensional data space onto a low-dimensional feature space where the mapping preserves the topological structure of the transformed data in the feature space as much as possible. This method is often referred to as Multidimensional Scaling (MDS). This paper describes a new MDS approach for feature extraction purposes. It consists of a fast hierachical Minimal-Spanning-Tree-based method which minimizes the Sammon's criteria with a genetic algorithm. Results presented show that this new approach is promising for several applications.
Characterization of Notch1 Antibodies That Inhibit Signaling of Both Normal and Mutated Notch1 Receptors (2010)

Antibodies that compete with Notch1 ligand binding or that bind to the negative regulatory region can act as potent inhibitors of Notch1 signaling. These antibodies may have clinical utility for conditions in which inhibition of signaling by wild-type Notch1 is desired, but are likely to be of limited value for treatment of T-ALLs associated with aberrant Notch1 activation.