gebhart/patrepeval huggingface dataset:
Structure-related variable responses of calcium sensitive MRI probes (2011)

A new series of Gd3+ complexes based on DO3A (GdL1–GdL4) was synthesized and investigated. They possess side chains with different structures which determine their varying binding properties and response towards endogenous metal ions, measured by changes in the longitudinal relaxivity (r1). GdL4 exhibits the highest selectivity toward Ca2+ in comparison to the other complexes, with up to a 63% increase of the r1. GdL2 and GdL3 also respond to different Ca2+ concentration ranges, however with a lower selectivity since the r1 changes are also observed in the presence of other cations such as Mg2+, Zn2+ or Cu2+. Assessment of the hydration number (q) via luminescence lifetime measurements confirmed that the change in q is responsible for the r1 response for all the complexes.
Interferon Alpha as Adjuvant Postsurgical Treatment of Melanoma: A Meta-Analysis (2004)

High and low doses of IFN-alpha significantly decrease the RR, but the OS does not seem to be improved.
CD74 Is a Member of the Regulated Intramembrane Proteolysis-processed Protein Family (2005)

Quite a few regulatory proteins, including transcription factors, are normally maintained in a dormant state to be activated after internal or environmental cues. Recently, a novel strategy, requiring proteolytic cleavage, was described for the mobilization of dormant transcription factors. These transcription factors are initially synthesized in an inactive form, whereas "nesting" in integral membrane precursor proteins. After a cleavage event, these new active factors are released from the membrane and can migrate into the nucleus to drive regulated gene transcription. This mechanism, regulated intramembrane proteolysis (RIP), controls diverse biological processes in prokaryotes and eukaryotes in response to a variety of signals. The MHC class II chaperone, CD74 (invariant chain, Ii), was previously shown to function as a signaling molecule in several pathways. Recently, we demonstrated that after intramembranal cleavage, the CD74 cytosolic fragment (CD74-ICD) is released and induces activation of transcription mediated by the NF-kappaB p65/RelA homodimer and the B-cell-enriched coactivator, TAF(II)105. Here, we add CD74 to the growing family of RIP-processed proteins. Our studies show that CD74 ectodomain must be processed in the endocytic compartments to allow its intramembrane cleavage that liberates CD74 intracellular domain (CD74-ICD). We demonstrate that CD74-ICD translocates to the nucleus and induces the activation of the p65 member of NF-kappaB in this compartment.
Rotating light with light: Generation of helical modes of light by spin-to-orbital angular momentum conversion in inhomogeneous liquid crystals (2007)

I review recent results on a novel method for generating helical waves of visible light based on inhomogeneous birefringent plates made of a suitably patterned liquid crystal. These devices, dubbed "q-plates", act on the light wave by converting its spin angular momentum into orbital angular momentum, an optical process not envisioned before. The output helical wave can be easily and rapidly switched between opposite wavefront helicities by switching the input polarization with standard electro-optics devices. The process can be cascaded, so that rapid switching can take place among multiple values of the wavefront helicity. More generally, patterned liquid-crystal devices similar to those realized for generating helical beams may be used for shaping the optical wavefront in any prescribed way, with the possibility of dynamical polarization multiplexing between conjugate wavefronts. This is an application of the Pancharatnam-Berry phase principle, allowing the realization of a novel kind of optical elements for wavefront shaping. Potential developments in the fields of optical communication and quantum computation are briefly discussed.
MICs of Mutacin B-Ny266, Nisin A, Vancomycin, and Oxacillin against Bacterial Pathogens (2000)

Peptide antibiotics, particularly lantibiotics, are good candidates for replacing antibiotics to which bacteria have become resistant. In order to compare two such lantibiotics with two antibiotics, the MICs of nisin A, mutacin B-Ny266, vancomycin, and oxacillin against various bacterial pathogens were determined. The results indicate that nisin A and mutacin B-Ny266 are as active as vancomycin and oxacillin against most of the strains tested. Furthermore, mutacin B-Ny266 remains active against strains that are resistant to nisin A, oxacillin, or vancomycin. The wide spectrum of activity of mutacin B-Ny266, its low MICs against bacterial pathogens, and its activity against bacteria resistant to other inhibitors support the development of this substance for therapeutic use.
Invitro Antibodies: Strategies For Production And Application (1992)

The approaches to the production of antibodies (Ab) using the techniques of genetic engineering and expression are reviewed. Genetic engineering facilitates the production of proteins tailormade for an intended use. Bacterial and mammalian expression systems are commonly used for the production of Ab and Ab-like molecules. While genomic or cDNA cloning can be used to obtain the relevant variable regions, PCR-based cloning approaches facilitate the acquisition of additional binding specificities. Large numbers of different chimeric Abs with murine variable regions joined to constant regions from human and other species have been expressed and found to exhibit the expected binding specificities and effector functions. These molecules have been used to study the structural basis of effector functions such as complement activation and Fc receptor binding, and potentially they may be used as therapeutic agents. Carbohydrate has been shown to influence both variable and constant region function. Single-chain Abs and fusion proteins with Ab binding specificities joined to nonimmunoglobulin sequences provide a source of Ab-like molecules with novel properties, and genetically engineered Ab-like molecules provide a source of useful antigens. Combinatorial libraries produced in bacteriophage present an alternative to hybridomas for the production of Abs with desired combining specifities. Issues of the immunogenicity of the recombinant molecules are addressed.
A Unified Theory of Neuro-MRI Data Shows Scale-Free Nature of Connectivity Modes (2017)

A primary goal of many neuroimaging studies that use magnetic resonance imaging (MRI) is to deduce the structure-function relationships in the human brain using data from the three major neuro-MRI modalities: high-resolution anatomical, diffusion tensor imaging, and functional MRI. To date, the general procedure for analyzing these data is to combine the results derived independently from each of these modalities. In this article, we develop a new theoretical and computational approach for combining these different MRI modalities into a powerful and versatile framework that combines our recently developed methods for morphological shape analysis and segmentation, simultaneous local diffusion estimation and global tractography, and nonlinear and nongaussian spatial-temporal activation pattern classification and ranking, as well as our fast and accurate approach for nonlinear registration between modalities. This joint analysis method is capable of extracting new levels of information that is not achievable from any of those single modalities alone. A theoretical probabilistic framework based on a reformulation of prior information and available interdependencies between modalities through a joint coupling matrix and an efficient computational implementation allows construction of quantitative functional, structural, and effective brain connectivity modes and parcellation. This new method provides an overall increase of resolution, accuracy, level of detail, and information content and has the potential to be instrumental in the clinical adaptation of neuro-MRI modalities, which, when jointly analyzed, provide a more comprehensive view of a subject's structure-function relations, while the current standard, wherein single-modality methods are analyzed separately, leaves a critical gap in an integrated view of a subject's neuorphysiological state. As one example of this increased sensitivity, we demonstrate that the jointly estimated structural and functional dependencies of mode power follow the same power law decay with the same exponent.
Disease‐modifying therapies in Alzheimer's disease (2008)

Alzheimer's disease (AD) is a chronic, progressive, neurodegenerative disorder that places a substantial burden on patients, their families, and society. The disease affects approximately 5 million individuals in the United States, with an annual cost of care greater than $100 billion. During the past dozen years, several agents have been approved that enhance cognition and global function of AD patients, and recent advances in understanding AD pathogenesis has led to the development of numerous compounds that might modify the disease process. A wide array of antiamyloid and neuroprotective therapeutic approaches are under investigation on the basis of the hypothesis that amyloid beta (A beta) protein plays a pivotal role in disease onset and progression and that secondary consequences of A beta generation and deposition, including tau hyperphosphorylation and neurofibrillary tangle formation, oxidation, inflammation, and excitotoxicity, contribute to the disease process. Interventions in these processes with agents that reduce amyloid production, limit aggregation, or increase removal might block the cascade of events comprising AD pathogenesis. Reducing tau hyperphosphorylation, limiting oxidation and excitotoxicity, and controlling inflammation might be beneficial disease-modifying strategies. Potentially neuroprotective and restorative treatments such as neurotrophins, neurotrophic factor enhancers, and stem cell-related approaches are also under investigation.
Hypocretins (Orexins) Regulate Serotonin Neurons in the Dorsal Raphe Nucleus by Excitatory Direct and Inhibitory Indirect Actions (2002)

The hypocretins (hcrt1 and hcrt2) are expressed by a discrete population of hypothalamic neurons projecting to many regions of the CNS, including the dorsal raphe nucleus (DRN), where serotonin (5-HT) neurons are concentrated. In this study, we investigated responses to hcrts in 216 physiologically identified 5-HT and non-5-HT neurons of the DRN using intracellular and whole-cell recording in rat brain slices. Hcrt1 and hcrt2 induced similar amplitude and dose-dependent inward currents in most 5-HT neurons tested (EC50, approximately 250 nm). This inward current was not blocked by the fast Na+ channel blocker TTX or in a Ca2+-free solution, indicating a direct postsynaptic action. The hcrt-induced inward current reversed near -18 mV and was primarily dependent on external Na+ but not on external or internal Ca2+, features typical of Na+/K+ nonselective cation channels. At higher concentrations, hcrts also increased spontaneous postsynaptic currents in 5-HT neurons (EC50, approximately 450-600 nm), which were TTX-sensitive and mostly blocked by the GABA(A) antagonist bicuculline, indicating increased impulse flow in local GABA interneurons. Accordingly, hcrts were found to increase the basal firing of presumptive GABA interneurons. Immunolabeling showed that hcrt fibers projected to both 5-HT and GABA neurons in the DRN. We conclude that hcrts act directly to excite 5-HT neurons primarily via a TTX-insensitive, Na+/K+ nonselective cation current, and indirectly to activate local inhibitory GABA inputs to 5-HT cells. The greater potency of hcrts in direct excitation compared with indirect inhibition suggests a negative feedback function for the latter at higher levels of hcrt activity.
Reg gene family and human diseases (2003)

Regenerating gene (Reg or REG) family, within the superfamily of C-type lectin, is mainly involved in the liver, pancreatic, gastric and intestinal cell proliferation or differentiation. Considerable attention has focused on Reg family and its structurally related molecules. Over the last 15 years, 17 members of the Reg family have been cloned and sequenced. They have been considered as members of a conserved protein family sharing structural and some functional properties being involved in injury, inflammation, diabetes and carcinogenesis. We previously identified Reg IV as a strong candidate for a gene that was highly expressed in colorectal adenoma when compared to normal mucosa based on suppression subtractive hybridization (SSH), reverse Northern blot, semi-quantitative reverse transcriptase PCR (RT-PCR) and Northern blot. In situ hybridization results further support that overexpression of Reg IV may be an early event in colorectal carcinogenesis. We suggest that detection of Reg IV overexpression might be useful in the early diagnosis of carcinomatous transformation of adenoma. This review summarizes the roles of Reg family in diseases in the literature as well as our recent results of Reg IV in colorectal cancer. The biological properties of Reg family and its possible roles in human diseases are discussed. We particularly focus on the roles of Reg family as sensitive reactants of tissue injury, prognostic indicators of tumor survival and early biomarkers of carcinogenesis. In addition to our current understanding of Reg gene functions, we postulate that there might be relationships between Reg family and microsatellite instability, apoptosis and cancer with a poor prognosis. Investigation of the correlation between tumor Reg expression and survival rate, and analysis of the Reg gene status in human malignancies, are required to elucidate the biologic consequences of Reg gene expression, the implications for Reg gene regulation of cell growth, tumorigenesis, and the progression of cancer. It needs to be further attested whether Reg gene family is applicable in early detection of cancer and whether Reg and Reg-related molecules can offer novel molecular targets for anticancer therapeutics. This has implications with regard to prognosis, such as in monitoring cancer initiation, progression and recurrence, as well as the design of chemotherapeutic drugs.
The activity of two immunotoxins composed of monoclonal antibody MoAb-16 and A-chain of ricin (MoAb-16-RTA) or A-chain of mistletoe lectin I (MoAb-16-MLIA). (1992)

The A-chains of ricin obtained from Ricinus communis or mistletoe lectin I from Viscum album were coupled to the monoclonal, anti-L1210V antibody MoAb-16, using SPDP as a cross linking agent. The cytotoxic activity in vitro of these immunotoxins was compared. Each of two immunotoxins tested, applied in vitro for 1 h in appropriate doses, caused irreversible inhibition of leukemic L1210 cells proliferation. Unexpectedly, MoAb-16-MLIA immunotoxin appeared to be cytotoxic to normal bone marrow progenitor cells, as observed in NCFUS tests. Moreover, this immunotoxin revealed cytotoxic effect to the P388 leukemia cells which do not share the antigen, common within L1210 leukemia cells, detected by MoAb-16 antibody.
The effect of anionic, cationic and neutral surfactants on the photophysics and isomerization of 3,3′-diethylthiacarbocyanine (2001)

The photophysical properties and isomerization of 3,3′-diethylthiacarbocyanine (DTC) were studied in isooctane/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/water reverse micelles and in aqueous solutions containing sodium dodecylsulfate (SDS), cetyltrimethylammonium bromide (CTAB) and chloride (CTAC) and Triton X-100 (TX100) at concentrations below and above the critical micelle concentrations (c.m.c.). The absorption and fluorescence spectra of DTC in AOT reverse micelles are red-shifted and the nonradiative deactivation rate constant decreases strongly relative to that in water, leading to higher fluorescence quantum yields (Φf) and lifetimes. The DTC fluorescence decay in AOT reverse micelles and TX100 normal micelles is biexponential. SDS induces aggregation of DTC in water at concentrations well below the c.m.c. (10−5–10−3 mol l−1). Addition of SDS and TX100 at concentrations just above the c.m.c. increases Φf steeply, while CTAB (or CTAC) exerts such an effect only at concentrations much higher than the c.m.c. A rise in the isomerization activation energy and the pre-exponent is observed in the reverse micelles with small w0 (w0 = [water]/[AOT]); the isomerization rate constant decreases in SDS, TX100 and CTAC micelles.
Observations on the Effects of Infusion of Prostnglnndin E in Man (1959)

Abstract. Chemically pure prostaglandin E was infused in doses of 0.2–4.7 μglkglrnin in two healthy male subjects over periods of 4–10 min. Tachycardia, reddening of the faoe, headache and an oppressive feeling in the chest were noted. Systemic arterial blood pressure and cardiac output fell moderately.
Platelet-derived Growth Factor C (PDGF-C), a Novel Growth Factor That Binds to PDGF α and β Receptor (2001)

We have characterized platelet-derived growth factor (PDGF) C, a novel growth factor belonging to the PDGF family. PDGF-C is a multidomain protein with the N-terminal region homologous to the extracellular CUB domain of neuropilin-1, and the C-terminal region consists of a growth factor domain (GFD) with homology to vascular endothelial growth factor (25%) and PDGF A-chain (23%). A serum-sensitive cleavage site between the two domains allows release of the GFD from the CUB domain. Competition binding and immunoprecipitation studies on cells bearing both PDGF alpha and beta receptors reveal a high affinity binding of recombinant GFD (PDGF-CC) to PDGF receptor-alpha homodimers and PDGF receptor-alpha/beta heterodimers. PDGF-CC exhibits greater mitogenic potency than PDGF-AA and comparable or greater mitogenic activity than PDGF-AB and PDGF-BB on several mesenchymal cell types. Analysis of PDGF-CC in vivo in a diabetic mouse model of delayed wound healing showed that PDGF-CC significantly enhanced repair of a full-thickness skin excision. Together, these studies describe a third member of the PDGF family (PDGF-C) as a potent mitogen for cells of mesenchymal origin in in vitro and in vivo systems with a binding pattern similar to PDGF-AB.
An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice (2013)

Modulation of the gut microbiota (by an increase in the Akkermansia spp. population) may contribute to the antidiabetic effects of metformin, thereby providing a new mechanism for the therapeutic effect of metformin in patients with T2D. This suggests that pharmacological manipulation of the gut microbiota in favour of Akkermansia may be a potential treatment for T2D.
Transmembrane cytoskeletal modulation in preterminal growing axons: I. Arrest of bulk and organelle transport in goldfish retinal ganglion cell axons regenerating in vitro by lectins binding to sialoglycoconjugates (1990)

Goldfish retinal ganglion cell (RGC) axons regenerating in vitro exhibit a novel mode of axoplasmic transport that entails a rapid bidirectional bulk redistribution of axoplasm, "packaged" as protruding varicosities and non-protruding phase-dense inclusions (Koenig et al.: J. Neurosci. 5:715-729, 1985; Edmonds and Koenig Brain Res. 406:288-293, 1987). We have used phase-contrast video microscopy to study transmembrane effects of surface-binding lectins on bulk transport and transport of single visible organelles in RGC axons. Our findings show that certain lectins which crosslink sialoglycoconjugates, such as wheat germ agglutinin (WGA) and the more specific sialic acid-binding lectin Limax flavus agglutinin (LFA), induce a rapid inhibition of transport activity. The LFA-induced inhibition of transport can be reversed by appropriate simple sugar haptens, and can also be antagonized by pretreatment with cytochalasin D. One of the consequences of LFA binding is an increase in RITC-conjugated phalloidin fluorescence staining of preterminal axons. The latter observation in conjunction with the antagonistic action of cytochalasin D suggests that one possible explanation for the transmembrane arrest of transport induced by crosslinking of surface sialoglycoconjugates may involve a polymerization and/or reorganization of the actin filament network which hinders translocation of mobile axoplasmic components.
An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus (2020)

Abstract Coronaviruses (CoVs) traffic frequently between species resulting in novel disease outbreaks, most recently exemplified by the newly emerged SARS-CoV-2. Herein, we show that the ribonucleoside analog β-D-N 4 -hydroxycytidine (NHC, EIDD-1931) has broad spectrum antiviral activity against SARS-CoV 2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c Bat-CoVs, as well as increased potency against a coronavirus bearing resistance mutations to another nucleoside analog inhibitor. In mice infected with SARS-CoV or MERS-CoV, both prophylactic and therapeutic administration of EIDD-2801, an orally bioavailable NHC-prodrug (b-D-N 4 -hydroxycytidine-5’-isopropyl ester), improved pulmonary function, and reduced virus titer and body weight loss. Decreased MERS-CoV yields in vitro and in vivo were associated with increased transition mutation frequency in viral but not host cell RNA, supporting a mechanism of lethal mutagenesis. The potency of NHC/EIDD-2801 against multiple coronaviruses, its therapeutic efficacy, and oral bioavailability in vivo , all highlight its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses.
Induction of cancer cell apoptosis by α‐tocopheryl succinate: molecular pathways and structural requirements (2001)

The vitamin E analog alpha-tocopheryl succinate (alpha-TOS) can induce apoptosis. We show that the proapoptotic activity of alpha-TOS in hematopoietic and cancer cell lines involves inhibition of protein kinase C (PKC), since phorbol myristyl acetate prevented alpha-TOS-triggered apoptosis. More selective effectors indicated that alpha-TOS reduced PKCalpha isotype activity by increasing protein phosphatase 2A (PP2A) activity. The role of PKCalpha inhibition in alpha-TOS-induced apoptosis was confirmed using antisense oligonucleotides or PKCalpha overexpression. Gain- or loss-of-function bcl-2 mutants implied modulation of bcl-2 activity by PKC/PP2A as a mitochondrial target of alpha-TOS-induced proapoptotic signals. Structural analogs revealed that alpha-tocopheryl and succinyl moieties are both required for maximizing these effects. In mice with colon cancer xenografts, alpha-TOS suppressed tumor growth by 80%. This epitomizes cancer cell killing by a pharmacologically relevant compound without known side effects.
A fast algorithm for image restoration using a recurrent neural network with bound-constrained quadratic optimization (2001)

This paper presents a fast algorithm for a recurrent neural network that can restore a degraded image with fewer iterations and shorter processing time by using bound-constrained quadratic optimization (BCQO) and a weighted mask. The BCQO technique has already been used in signal restoration, however implementation of this method in image restoration requires considerable memory and it is computationally expensive. The proposed algorithm replaces the weight matrix of the network with a much smaller mask, thus reducing the processing time and requiring much less memory space. This algorithm produces better results than those obtained by Wiener filter, and achieves image restoration with less iterations compared to a modified Hopfield neural network.
Charge sharing concept for power efficiency and EME improvement of boosted charge pumps in NVMs (2003)

A new power saving concept for boosted charge pumps is introduced, which combines two-step charging, charge sharing and a simplified clocking scheme to double the power efficiency. Simultaneously, the peak value of the charging current is reduced by a factor of 3, improving the EME behaviour significantly.