gebhart/patrepeval huggingface dataset:
Generation of varicella-zoster virus (VZV) and viral mutants from cosmid DNAs: VZV thymidylate synthetase is not essential for replication in vitro. (1993)

Four overlapping cosmid clones were constructed that contain the complete genome of the attenuated Oka strain of VZV. Transfection of human melanoma cells with the four cosmids resulted in production of infectious VZV. A double-stranded oligonucleotide, encoding a stop codon in all three open reading frames, was inserted into one of the cosmids at the 5' end of the viral thymidylate synthetase gene. Transfection of melanoma cells with the mutant cosmid, along with the other three cosmids, resulted in VZV that does not express the viral thymidylate synthetase protein. The mutant virus grew at a rate similar to that of the parental Oka strain virus. Production of recombinant VZV using cosmid DNAs will be useful for studying the function of viral genes in VZV replication and establishment of latency. Furthermore, manipulation of the Oka strain of VZV might allow one to produce a vaccine virus that does not establish latency in the central nervous system or a virus that encodes foreign antigens for use as a polyvalent live virus vaccine.
SOAP, a novel malaria ookinete protein involved in mosquito midgut invasion and oocyst development (2003)

An essential, but poorly understood part of malaria transmission by mosquitoes is the development of the ookinetes into the sporozoite-producing oocysts on the mosquito midgut wall. For successful oocyst formation newly formed ookinetes in the midgut lumen must enter, traverse, and exit the midgut epithelium to reach the midgut basal lamina, processes collectively known as midgut invasion. After invasion ookinete-to-oocyst transition must occur, a process believed to require ookinete interactions with basal lamina components. Here, we report on a novel extracellular malaria protein expressed in ookinetes and young oocysts, named secreted ookinete adhesive protein (SOAP). The SOAP gene is highly conserved amongst Plasmodium species and appears to be unique to this genus. It encodes a predicted secreted and soluble protein with a modular structure composed of two unique cysteine-rich domains. Using the rodent malaria parasite Plasmodium berghei we show that SOAP is targeted to the micronemes and forms high molecular mass complexes via disulphide bonds. Moreover, SOAP interacts strongly with mosquito laminin in yeast-two-hybrid assays. Targeted disruption of the SOAP gene gives rise to ookinetes that are markedly impaired in their ability to invade the mosquito midgut and form oocysts. These results identify SOAP as a key molecule for ookinete-to-oocyst differentiation in mosquitoes.
The link between neurosteroids and syndromic/syndromal components of the mood spectrum disorders in women during the premenstrual phase (2008)

Levels of allopregnanolone and progesterone do not correlate with the association of the depressive and manic syndromes, but rather with mixed symptomatological aspects, and in particular with cognitive manic and depressive (with suicidal thoughts) dimensions. Further studies should be carried out to confirm these findings.
Analogs of capsaicin with agonist activity as novel analgesic agents; structure-activity studies. 1. The aromatic "A-region" (1993)

A series of compounds incorporating replacements for the amide bond "B-region" moiety of capsaicin have been synthesized, including vanillylamides and esters, homovanillic acid amides and esters, ureas, and thioureas. These have been tested in an in vitro assay for agonism (45Ca2+ influx into dorsal root ganglia neurones), which is predictive of analgesic activity, to investigate the requirements in this region of capsaicin for activity. N-(4-Hydroxy-3-methoxybenzyl)-N'-octylthiourea (14a) emerged as the most potent analogue (EC50 = 0.06 microM). An operational model based on multiple hydrogen-bonding interactions is proposed to explain the structure-activity profile observed. In combination with studies on the other regions of the capsaicin molecule these results describe a picture of the molecular interactions of capsaicin with its putative receptor.
Biological performance of boron-modified bioactive glass particles implanted in rat tibia bone marrow (2006)

The aim of the present study was to characterize the neoformed bone tissue around boron-modified bioactive glass particles implanted in rat tibia bone marrow by histologic, histomorphometric and microchemical evaluation. Melt-derived glasses were prepared from a base 45S5 bioactive glass of nominal composition (45% SiO(2), 24.5% CaO, 24.5% Na(2)O and 6% P(2)O(5) in wt%). The glass composition was modified by adding 2% wt of boron oxide (45S5.2B). Histological and histomorphometric analyses using undecalcified sections showed that at 15 days post-implantation the area of neoformed bone tissue around the 45S5.2B particles was significantly higher than control 45S5 glass. No statistically significant differences were observed at 30 days post-implantation. The thickness of osseointegrated tissue on 45S5.2B BG particles was significantly greater than on the control at all experimental time-points evaluated. A statistically significant increase in the Ca:P ratio was observed in the neoformed bone around 45S5.2B particles 15 days post-implantation. The results of the present study provide evidence that particles of boron-modified 45S5 BG (45S5.2B) enhance bone formation more than 45S5 glass when implanted into the intramedullary canal of rat tibiae.
ALK5 and Smad4 are involved in TGF‐β1‐induced pulmonary endothelial permeability (2005)

The ability of inflammatory cytokine TGF-beta1 to alter endothelial cell phenotype suggests its role in the regulation of vascular endothelial cell permeability. We demonstrate that depletion of TGF-beta1 receptor ALK5 and regulatory protein Smad4, but not ALK1 receptor attenuates TGF-beta1-induced permeability increase and significantly inhibits TGF-beta1-induced EC contraction manifested by actin stress fiber formation and increased MLC and MYPT1 phosphorylation. Consistent with these results, EC treatment with SB 431542, an inhibitor of ALK5 but not ALK1 receptor, significantly attenuates TGF-beta1-induced permeability. Thus, our data demonstrate for the first time direct link between TGF-beta1-mediated activation of ALK5/Smad and EC barrier dysfunction.
Drugs Used to Treat Parkinsons Disease, Present Status and Future Directions (2008)

Parkinson's disease (PD) is the second most common neurodegenerative disorder, after Alzheimer's disease. In PD, motor symptoms result from the degeneration and loss of pigmented dopaminergic neurons of the substantia nigra pars compacta of the basal ganglia. Other neuronal fields and neurotransmitter systems are also involved, including non-adrenergic, serotonergic and cholinergic neurons. Since the early 1960s the treatment of PD has been based on the pharmacologic replacement of dopamine accomplished with the precursor of dopamine, 3, 4-dihydroxy-L-phenylalanine (L-dopa). The addition of carbidopa, an inhibitor of the decarboxylase represented a tremendous improvement in therapy and is still a mainstay of the treatment of PD. Dopamine agonists may also be used, as well as inhibitors of monoamine oxidase-B or catechol-O-methyltransferase. Other medications include anticholinergics and amantadine. These therapies are only symptomatic and none halt or lessen dopaminergic neuron degeneration and the progression of the disease. This has prompted the search for novel and alternative pharmacological targets and neuroprotective therapies. In this context, there are data to suggest a benefit from glial cell line-derived neurotrophic factor, neuroimmumophilin ligands, minocycline, Coenzyme Q10, creatine, reduced glutathione, adenosine A2A receptor antagonists as well as glutamate release inhibitors. Restorative techniques to compensate for cell loss include tissue transplantation and gene transfer therapy. Due to the paucity of data regarding non-pharmacological approaches such as diet therapy or antioxidant therapy, these await more studies. There are also few studies on medicinal plants. Other areas of increasing importance would thus include the investigation of active constituents of plants and phytomedicines with a view to the discovery of new compounds. Finally, stem cell therapy may offer the promise of restoring functionality.
The Unified Butterfly Effect: Efficient Security Credential Management System for Vehicular Communications (2018)

With the increasing demand for intelligent transportation systems (ITS), security and privacy requirements are paramount. This led to many proposals aimed at creating a Vehicular Public Key Infrastructure (VPKI) able to address such prerequisites. Among them, the Security Credential Management System (SCMS) is particularly promising, providing data authentication in a privacy-preserving manner and also supporting revocation of misbehaving vehicles. Despite SCMS's appealing design, in this paper we show that its certificate issuing process can be further improved. Namely, one of the main benefits of SCMS is its so-called butterfly key expansion process, which issues arbitrarily large batches of pseudonym certificates by means of a single request. Although this protocol requires the vehicle to provide two separate public/private key pairs to registration authorities, we hereby propose an improved approach that unifies them into a single key. As a result, the processing and bandwidth utilization for certificate provisioning are reduced from 10% to 50% for all entities involved in the protocol. We also show that such performance gains come with no negative impact in terms of security, flexibility or scalability when compared to the original SCMS.
[An experimental study on the implantation of a biomaterial with electro-activity for replacement of hard tissue in bone]. (2001)

HABTs could promote osteogenesis.
Overexpression of Urokinase by Macrophages or Deficiency of Plasminogen Activator Inhibitor Type 1 Causes Cardiac Fibrosis in Mice (2004)

Several studies implicate elevated matrix metalloproteinase activity as a cause of cardiac fibrosis. However, it is unknown whether other proteases can also initiate cardiac fibrosis. Because absence of urokinase plasminogen activator (uPA) prevents development of cardiac fibrosis after experimental myocardial infarction in mice, we hypothesized that elevated activity of uPA or deficiency of the uPA inhibitor plasminogen activator inhibitor-1 (PAI-1) might cause cardiac fibrosis. We used mice with scavenger-receptor (SR)-directed, macrophage-targeted uPA overexpression (SR-uPA+/0 mice) and PAI-1 null mice to test these hypotheses. Our studies revealed that SR-uPA+/0 mice developed cardiac fibrosis beginning between 5 and 10 weeks of age. Fibrosis was preceded by cardiac macrophage accumulation, implicating uPA-secreting macrophages as important contributors to development of fibrosis. A key role for uPA-secreting macrophages in development of cardiac fibrosis was supported by experiments in which recipients of bone marrow transplants from SR-uPA+/0 donors but not nontransgenic donors developed cardiac macrophage accumulation and fibrosis. SR-uPA+/0 mice and recipients of SR-uPA+/0 bone marrow had neither macrophage accumulation nor fibrosis in other major organs despite the presence of higher levels of uPA in these organs than in hearts. PAI-1 null mice but not congenic, age-matched controls also developed macrophage accumulation and fibrosis in hearts but not in other organs. We conclude: (1) either elevated macrophage uPA expression or PAI-1 deficiency is sufficient to cause cardiac macrophage accumulation and fibrosis; (2) macrophages are important contributors to the development of cardiac fibrosis; and (3) the heart is particularly sensitive to the effects of excess uPA activity.
Reducing cellular autofluorescence in flow cytometry: an in situ method. (1997)

Cellular autofluorescence affects the sensitivity of flow cytometric assays by interfering with detection of low level specific fluorescence. These detection limits increase with use of protocols, such as thermocycling and fluorescent in-situ hybridization (FISH), that can increase intrinsic cellular fluorescence to 5,000-20,000 fluorescein isothiocyanate (FITC) equivalents. In order to improve signal to noise ratios when using FITC labeled probes in these procedures, we employed a method using the polyanionic azo dye, trypan blue, to reduce intracellular autofluorescence. Dyes such as these are commonly used in immunofluorescent microscopy to reduce background fluorescence. By using this method, we realized an approximately 5-fold increase in signal to noise ratio (S/N) in the direct detection of RNA target probes using flow cytometry. Trypan blue aided in the resolution of dim surface antibodies, internal markers and probes, and functions to reduce background autofluorescence after thermocycling and hybridization. This technique is rapid and easily applicable for reducing intracellular autofluorescence, and can be used in single and dual color applications.
Camera-IMU-based localization: Observability analysis and consistency improvement (2013)

This work investigates the relationship between system observability properties and estimator inconsistency for a Vision-aided Inertial Navigation System (VINS). In particular, first we introduce a new methodology for determining the unobservable directions of nonlinear systems by factorizing the observability matrix according to the observable and unobservable modes. Subsequently, we apply this method to the VINS nonlinear model and determine its unobservable directions analytically. We leverage our analysis to improve the accuracy and consistency of linearized estimators applied to VINS. Our key findings are evaluated through extensive simulations and experimental validation on real-world data, demonstrating the superior accuracy and consistency of the proposed VINS framework compared to standard approaches.
On-fiber plasmonic interferometer for multi-parameter sensing (2015)

We demonstrate a novel miniature multi-parameter sensing device based on a plasmonic interferometer fabricated on a fiber facet in the optical communication wavelength range. This device enables the coupling between surface plasmon resonance and plasmonic interference in the structure, which are the two essential mechanisms for multi-parameter sensing. We experimentally show that these two mechanisms have distinctive responses to temperature and refractive index, rendering the device the capability of simultaneous temperature and refractive index measurement on an ultra-miniature form factor. A high refractive index sensitivity of 220 nm per refractive index unit (RIU) and a high temperature sensitivity of -60 pm/ °C is achieved with our device.
Rapid generation of inducible mouse mutants (2003)

We have generated an optimized inducible recombination system for conditional gene targeting based on a Cre recombinase-steroid receptor fusion. This configuration allows efficient Cre-mediated recombination in most organs of the mouse upon induction, without detectable background activity. An ES cell line, was established that carries the inducible recombinase and a loxP-flanked lacZ reporter gene. Out of this line, completely ES cell-derived mice were efficiently produced through tetraploid blastocyst complementation, without the requirement of mouse breeding. Our findings provide a new concept allowing the generation of inducible mouse mutants within 6 months, as compared to 14 months using the current protocol.
Neighborhood Behavior:  A Useful Concept for Validation of “Molecular Diversity” Descriptors (1996)

When searching for new leads, testing molecules that are too "similar" is wasteful, but when investigating a lead, testing molecules that are "similar" to the lead is efficient. Two questions then arise. Which are the molecular descriptors that should be "similar"? How much "similarity" is enough? These questions are answered by demonstrating that, if a molecular descriptor is to be a valid and useful measure of "similarity" in drug discovery, a plot of differences in its values vs differences in biological activities for a set of related molecules will exhibit a characteristic trapezoidal distribution enhancement, revealing a "neighborhood behavior" for the descriptor. Applying this finding to 20 datasets allows 11 molecular diversity descriptors to be ranked by their validity for compound library design. In order of increasing frequency of usefulness, these are random numbers = log P = MR = strain energy < connectivity indices < 2D fingerprints (whole molecule) = atom pairs = autocorrelation indices < steric CoMFA fields = 2D fingerprints (side chain only) = H-bonding CoMFA fields.
Span-disjoint paths for physical diversity in networks (2002)

Diversity has been widely recognized as a critical factor for robustness in networks. In order to resist isolations due to link and node failures, we need to route along paths which are both span-disjoint (physically disjoint) and node-disjoint. In this way we can design the network for fault tolerance or graceful degradation. We demonstrate the procedure to obtain span-disjoint paths. This procedure may be applied to an arbitrary network topology, without restrictions on the span sharing configurations. In those cases where two completely disjoint paths do not exist, the procedure still tries to find a pair of paths which are as diverse as possible. The solution path pair we obtain is not guaranteed to be optimal, but gives us an optimal or near-optimal design, relatively quickly. The algorithm also accepts parameters which can be used to specify the cost-robustness tradeoffs.
Variable Patterns of Septal Activation in Patients with Left Bundle Branch Block and Heart Failure (2003)

The two types of left septal activation observed in patients with LBBB-HF may have consequences for biventricular hemodynamic performance. Conduction slowing along the LV, regionally or globally, suggests a contribution outside the specific conduction system in the ECG pattern of LBBB.
Phase II Trial of Cetuximab in Combination With Fluorouracil, Leucovorin, and Oxaliplatin in the First-Line Treatment of Metastatic Colorectal Cancer (2007)

Cetuximab in combination with FOLFOX-4 is a highly active first-line treatment for mCRC, showing encouraging RR, mPFS, and mOS values. The treatment resulted in a high resectability rate, which could potentially result in an improved cure rate. This combination is under phase III development.
Novel Peptide Linkers for Highly Potent Antibody−Auristatin Conjugate (2008)

Auristatins are highly potent antimitotic agents that have received considerable attention because of their activities when targeted to tumor cells in the form of antibody-drug conjugates (ADCs). Our lead agent, SGN-35, consists of the cAC10 antibody linked to the N-terminal amino acid of monomethylauristatin E (MMAE) via a valine-citrulline p-aminobenzylcarbamate (val-cit-PABC) linker that is cleaved by intracellular proteases such as cathepsin B. More recently, we developed an auristatin F (AF) derivative monomethylauristatin F (MMAF), which unlike MMAE contains the amino acid phenylalanine at the C-terminal position. Because of the negatively charged C-terminal residue, the potency of AF and MMAF is impaired. However, their ability to kill target cells is greatly enhanced through facilitated cellular uptake by internalizing mAbs. Here, we explore the effects of linker technology on AF-based ADC potency, activity, and tolerability by generating a diverse set of dipeptide linkers between the C-terminal residue and the mAb carrier. The resulting ADCs differed widely in activity, with some having significantly improved therapeutic indices compared to the original mAb-Val-Cit-PABC-MMAF conjugate. The therapeutic index was increased yet further by generating dipeptide-based ADCs utilizing new auristatins with methionine or tryptophan as the C-terminal drug residue. These results demonstrate that manipulation of the C-terminal peptide sequence used to attach auristatins to the mAb carrier can lead to highly potent and specific conjugates with greatly improved therapeutic windows.
Substrate determinants for cleavage in cis and in trans by the hepatitis C virus NS3 proteinase (1995)

Processing of the hepatitis C virus polyprotein is accomplished by a series of cotranslational and posttranslational cleavages mediated by host cell signalases and two virally encoded proteinases. Of these the NS3 proteinase is essential for processing at the NS3/4A, NS4A/4B, NS4B/5A, and NS5A/5B junctions. Processing between NS3 and NS4A occurs in cis, implying an intramolecular reaction mechanism, whereas cleavage at the other sites can also be mediated in trans. Sequence analysis of the amino termini of mature cleavage products and comparisons of amino acid residues around the scissile bonds of various hepatitis C virus isolates identified amino acid residues which might contribute to substrate specificity and processing efficiency: an acidic amino acid at the P6 position, a Thr or Cys at the P1 position, and a Ser or Ala at the P1' position. To study the importance of these residues for NS3-mediated cleavage we have undertaken a mutational analysis using an NS3'-5B polyprotein expressed by recombinant vaccinia viruses in mammalian cells. For all NS3-dependent cleavage sites P1 substitutions had the most drastic effects on cleavage efficiency, showing that amino acid residues at this position are the most critical substrate determinants. Since less drastic effects were found for substitutions at the P1' position, these residues appear to be less important for proper cleavage. For all cleavage sites the P6 acidic residue was dispensable, suggesting that it is not essential for substrate recognition and subsequent cleavage. Analysis of a series of mutations at the NS3/4A site revealed great flexibility for substitutions compared with more stringent requirements at the trans cleavage sites. On the basis of these results we propose a model in which processing in cis is determined primarily by polyprotein folding, whereas cleavage in trans is governed not only by the structure of the polyprotein but also by specific interactions between the proteinase and the polyprotein substrate at or around the scissile bond.
How and Where Does Acute Pancreatitis Begin? (1992)

Circumstantial evidence suggests that gallstone-induced pancreatitis is triggered by obstruction of the pancreatic duct. In this report I will review the results of studies conducted during the last decade that have employed the diet-induced, secretagogue-induced, and duct obstruction-induced models of experimental pancreatitis to investigate the early events that lead to the development of acute pancreatitis. In each of these models, digestive enzyme zymogens and the lysosomal hydrolase cathepsin B were found to become colocalized. These observations have led to the hypothesis that intra-acinar cell activation of digestive enzyme zymogens by lysosomal hydrolases may be an important critical event in the development of acute pancreatitis. Recent morphologic studies evaluating the initial 24 hours after ligation of the opossum pancreatic duct indicate that the earliest lesions in this model of hemorrhagic pancreatitis occur in acinar cells.
Linear scaffolds for multivalent targeting of melanocortin receptors (2015)

Molecules bearing one, two, three, or four copies of the tetrapeptide His-dPhe-Arg-Trp were attached to scaffolds based on ethylene glycol, glycerol, and d-mannitol by means of the copper-assisted azide-alkyne cyclization. The abilities of these compounds to block binding of a probe at the melanocortin 4 receptor were evaluated using a competitive binding assay. All of the multivalent molecules studied exhibited 30- to 40-fold higher apparent affinites when compared to a monovalent control. These results are consistent with divalent binding to receptor dimers. No evidence for tri- or tetravalent binding was obtained. Differences in the interligand spacing required for divalent binding, as opposed to tri- or tetravalent binding, may be responsible for these results.