gebhart/patrepeval huggingface dataset:
Systemic administration of bone morphogenetic proteins (2008)

Apart from the local application, bone morphogenetic proteins (BMPs) have been systemically applied in rats for the following indications: bone formation in a model of osteoporosis [1], kidney regeneration in models of acute and chronic renal failure [2–7], liver regeneration [8], ischemic coronary infarction [6, 9] and stroke [10], and in a nude mouse model of human prostate, breast, brain and melanocyte cancer [11–14]. BMPs induced organ regeneration recapitulating embryonic development without recorded systemic side effects, except transient bone formation at the site of injection around the tail vein. This was not unexpected, since around the blood vessels the existing progenitor cells can differentiate into cartilage and bone in the presence of a recombinant BMP. No ossification of other tissues has been recorded even after a long period of daily BMP injections. The idea of using BMPs systemically for promoting tissue regeneration and repair has existed for years. However, do we have enough information on their pharmacodynamic and pharmacokinetic properties and a reproducible production of pure preparations for clinical use, and on reproducible results of their efficacy? Do BMPs circulate under physiological conditions? These questions are discussed in this chapter in an attempt to support evidence for their systemic use.
Improved Methods for Encoding and Decoding Dialkylamine-Encoded Combinatorial Libraries (1999)

Optimized methods for utilizing and analyzing dialkylamine tags in encoded combinatorial chemistry are reported. A previously described LC/fluorescence method has been shortened from over 1 h to 6 min. A novel ion exchange LC/MS method for decoding has been developed which is both fast and rugged. The use of quantitative encoding schemes is described. These new techniques have allowed a simplified, automated sample preparation scheme, and over 300 encoded bead samples can be read in a day.
Distinct patterns of brain activity in progressive supranuclear palsy and Parkinson's disease (2015)

The basal ganglia-thalamo-cortical and cerebello-thalamo-cortical circuits are important for motor control. Whether their functioning is affected in a similar or different way by progressive supranuclear palsy (PSP) and Parkinson's disease (PD) is not clear. A functional magnetic resonance imaging (fMRI) force production paradigm and voxel-based morphometry were used to assess differences in brain activity and macrostructural volumes between PSP, PD, and healthy age-matched controls. We found that PSP and PD share reduced functional activity of the basal ganglia and cortical motor areas, but this is more pronounced in PSP than in PD. In PSP the frontal regions are underactive, whereas the posterior parietal and occipital regions are overactive as compared with controls and PD. Furthermore, lobules I through IV, V, and VI of the cerebellum are hypoactive in PSP and PD, whereas Crus I and lobule IX are hyperactive in PSP only. Reductions in gray and white matter volume are specific to PSP. Finally, the functional status of the caudate as well as the volume of the superior frontal gyrus predict clinical gait and posture measures in PSP. PSP and PD share hypoactivity of the basal ganglia, motor cortex, and anterior cerebellum. These patients also display a unique pattern, such that anterior regions of the cortex are hypoactive and posterior regions of the cortex and cerebellum are hyperactive. Together, these findings suggest that specific structures within the basal ganglia, cortex, and cerebellum are affected differently in PSP relative to PD.
Classical Nevanlinna-Pick Interpolation with Real Interpolation Points (2000)

We consider a scalar Nevanlinna-Pick interpolation problem with at most countably many interpolation points which lie in ℂ+ ∪ ℝ. Questions about the existence and uniqueness of the solutions are considered. In the case of nonuniqueness a description of all solutions is given which generalizes Potapov’s formula. Our results are obtained in two ways: in Sections 1–5 through the theory of selfadjoint extensions of a symmetric relation in a Hilbert space, including Krein’s formula and the socalled u-resolvent matrix, and in Sections 6 and 7 via the theory of reproducing kernel Hilbert spaces.
Nomenclature of New Biosimilars Will Be Highly Controversial (2011)

Biopharmaceuticals, including products approved as biosimilars, must be clearly defined, identified, and named to ensure accuracy in writing and filling prescriptions (1–4). The US biosimilars law enacted last year enables the Food and Drug Administration (FDA) to approve abbreviated biosimilar biologics license applications (bBLAs) or 351(k) filings based largely on their sponsors proving structural, composition, and clinical similarities with an approved biologic (reference product), much like generic drug approvals (5). The agency has yet to disclose how it will implement biosimilar approvals. Factors to take into consideration include types of clinical trials, required data, and names to be officially designated and allowed for product labeling, inserts, and marketing. The established (also referred to as compendial, nonproprietary, or official) names to be designated by the FDA and used for biosimilars are likely to be highly controversial. The agency will have to make difficult choices such as • whether to assign either unique, similar, or generic (the same as reference product) names to biosimilars • whether and how biosimilarity relationships, structures, product class, and other information should be ref lected in biosimilar names • whether there should be any system and predictability to names. Hardly anyone, even many people within the industry, is yet very knowledgeable concerning biosimilars, a totally new class of products and approvals. Established names will be the first identifier or piece of descriptive information regarding these products that users will encounter (other than registered trademarks, which are often meaningless and convey no information). So the established names to be adopted will profoundly affect the core perceptions of biosimilar products (e.g., whether the products are generic) and so affect their use, branding, and marketing.
Targeted recombination with single-stranded DNA vectors in mammalian cells (1993)

We studied the ability of single-stranded DNA (ssDNA) to participate in targeted recombination in mammalian cells. A 5' end-deleted adenine phosphoribosyltransferase (aprt) gene was subcloned into M13 vector, and the resulting ssDNA and its double-stranded DNA (dsDNA) were transfected to APRT-Chinese hamster ovary cells with a deleted aprt gene. APRT+ recombinants with the ssDNA was obtained at a frequency of 3 x 10(-7) per survivor, which was almost equal to that with the double-stranded equivalent. Analysis of the genome in recombinant clones produced by ssDNA revealed that 12 of 14 clones resulted from correction of the deletion in the aprt locus. On the other hand, the locus of the remaining 2 was not corrected; instead, the 5' deletion of the vector was corrected by end extension, followed by integration into random sites of the genome. To exclude the possibility that input ssDNA was converted into its duplex form before participating in a recombination reaction, we compared the frequency of extrachromosomal recombination between noncomplementary ssDNAs, and between one ssDNA and one dsDNA, of two phage vectors. The frequency with the ssDNAs was 0.4 x 10(-5), being 10-fold lower than that observed with the ssDNA and the dsDNA, suggesting that as little as 10% of the transfected ssDNA was converted into duplex forms before the recombination event, hence 90% remained unchanged as single-stranded molecules. Nevertheless, the above finding that ssDNA was as efficient as dsDNA in targeted recombination suggests that ssDNA itself is able to participate directly in targeted recombination reactions in mammalian cells.
Formulas and tables to facilitate the calculation of recombination values in heredity (1956)

This study provides the following aids for using the method of maximum likelihood to estimate recombination values and examine heterogeneity when complex genetic data are available: Estimation equations for a variety of backcross, F2, and F3 situations, including equations for estimating linkage intensities between a member of a complementary or duplicate pair, or a gene pair producing a 13:3 ratio, and a third gene pair; Tables of scores to facilitate the numerical solution of these equations; Tables to facilitate the calculation of the standard error of the recombination value. Since advance planning is important in linkage investigations, the use of the tables for this purpose is also described.
Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form (2014)

Forskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13R)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13R)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals.
Camera on a chip (2002)

Recent advances in video compression and digital networking technology, combined with the ever increasing power of PCs and workstations, are creating enormous opportunities to develop new multimedia products and services built upon sophisticated voice, data, image and video processing. This will create a significant demand for compact, low-cost, low-power electronic cameras for video and still image capture. These cameras will be a standard peripheral on all PCs bundled for multimedia applications. Given that in excess of 60M PCs will be sold this year, a sizable new market for electronic cameras is being created.
Efficacy of Herbicide Active Ingredients Against Aquatic Weeds (2006)

SS-AGR-44, a 4-page fact sheet by K. Langeland, M. Netherland, W. Haller, and T. Koschnick, provides a table for quick reference to the effectiveness of herbicide active ingredients for controlling common aquatic weeds, and outlines the regulatory conditions and resources for further assistance. Published by the UF Department of Agronomy, September 2006. SS-AGR-44/AG262: Efficacy of Herbicide Active Ingredients Against Aquatic Weeds (ufl.edu)
Transport Layer Security (TLS) Protocol Compression Using Lempel-Ziv-Stac (LZS) (2004)

The Transport Layer Security (TLS) protocol (RFC 2246) includes features to negotiate selection of a lossless data compression method as part of the TLS Handshake Protocol and then to apply the algorithm associated with the selected method as part of the TLS Record Protocol. TLS defines one standard compression method, which specifies that data exchanged via the record protocol will not be compressed. This document describes an additional compression method associated with the Lempel-Ziv-Stac (LZS) lossless data compression algorithm for use with TLS. This document also defines the application of the LZS algorithm to the TLS Record Protocol.
Macroporous materials: microfluidic fabrication, functionalization and applications (2017)

This article provides an up-to-date highly comprehensive overview (594 references) on the state of the art of the synthesis and design of macroporous materials using microfluidics and their applications in different fields.
The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain. (1993)

The hflA (high frequency of lysogenization) locus of Escherichia coli governs the lysis-lysogeny decision of bacteriophage lambda by controlling stability of the phage cII protein. hflA contains three genes, hflX, hflK, and hflC, encoding polypeptides of 50, 46, and 37 kDa, respectively. We have determined the nucleotide sequence of 3843 base pairs containing hflA and have found three large open reading frames corresponding to hflX, hflK, and hflC. HflX contains the three sequence motifs typical of GTP-binding proteins and appears to be a member of a distinct family of putative GTPases. HflC and HflK appear to be integral membrane proteins which show some similarity to each other and to a human membrane protein. The C-terminal region of HflC contains a domain resembling the catalytic domain of ClpP, a bacterial ATP-dependent protease. We hypothesize that HflK and HflC constitute a distinct membrane-bound protease whose activity may be modulated by HflX GTPase.
Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS (2009)

The RpoS sigma factor protein of Escherichia coli RNA polymerase is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense of scavenging for scarce resources, causing a trade-off between stress tolerance and nutrient acquisition. This trade-off favors non-functional rpoS alleles in nutrient-poor environments. We used experimental evolution to explore how natural selection modifies the regulatory network of strains lacking RpoS when they evolve in an osmotically stressful environment. We found that strains lacking RpoS adapt less variably, in terms of both fitness increase and changes in patterns of transcription, than strains with functional RpoS. This phenotypic uniformity was caused by the same adaptive mutation in every independent population: the insertion of IS10 into the promoter of the otsBA operon. OtsA and OtsB are required to synthesize the osmoprotectant trehalose, and transcription of otsBA requires RpoS in the wild-type genetic background. The evolved IS10 insertion rewires expression of otsBA from RpoS-dependent to RpoS-independent, allowing for partial restoration of wild-type response to osmotic stress. Our results show that the regulatory networks of bacteria can evolve new structures in ways that are both rapid and repeatable.
Biodistribution of NX211, liposomal lurtotecan, in tumor-bearing mice (2001)

Prolonging tumor exposure to topoisomerase I inhibitors has been correlated to enhance the efficacy of those agents. Lurtotecan, a water-soluble camptothecin analog, was formulated as a liposomal drug, NX211, to enhance the delivery of drug to tumors. Tumor-bearing mice were treated with either [14C]NX211 containing [14C]lurtotecan, [3H]NX211 containing [3H]phosphatidylcholine or [14C]lurtotecan, euthanized at selected times post-injection, and tissues, plasma, urine and feces were collected. These studies demonstrated that KB tumors of [14C]NX211-treated mice had approximately 70-fold greater concentrations of [14C]lurtotecan at 24 h, respectively, compared to concentrations of [14C]lurtotecan of the KB tumors of [14C]lurtotecan-treated mice. The area under curve (AUC) from 0 to 48 h of [14C]lurtotecan for the KB tumors of [14C]NX211-treated animals was over 17-fold greater than the AUC of [14C]lurtotecan for the tumors of [14C]lurtotecan-treated animals. Treatment with [3H]NX211 demonstrated that the lipid component continually accumulated over 24 h in the tissues. HPLC analysis of extracted material from tumors of [14C]NX211-treated mice showed that more than 95% of the radioactive material was intact [14C]lurtotecan. These findings are one of the keys justifying the development of a liposomal formulation of lurtotecan, which has the intent to increase tumor exposure and increase antitumor efficacy.
Angiopoietin-Like Protein 2 Is a Potent Hemangiogenic and Lymphangiogenic Factor in Corneal Inflammation (2013)

Our findings demonstrated Angptl2 to be upregulated in corneal inflammation, and highlight that corneal hemangiogenesis and lymphangiogenesis may be driven by Angptk2 overexpression via macrophage infiltration and IL-1β expression. Angptl2 may be a novel therapeutic target for preventing blindness.
Arbitrarily high focal depth with a quasioptimum real and positive transmittance apodizer (1989)

Focal depth is assessed by the average value of the square modulus of the slope associated with the complex amplitude along the optical axis. Then, the calculus of variations is used for identifying the optimum apodizer, characterized by a Strehl ratio vs defocus with high focal depth, for a specified light throughput. We show that a certain Lorentzian profile is a quasioptimum solution for the above requirements. This apodizer has real and positive transmittance, and it can be modified to achieve arbitrarily high focal depth. A closed formula relates focal depth to light throughput.
Development of an in vitro pancreatic tissue model to study regulation of islet neogenesis associated protein expression (2006)

Restoration of a functional beta-cell mass in a patient with diabetes may hold the key for curing the disease. In recent years, there has been increasing interest in the development of new strategies to induce beta-cell regeneration and new islet formation in situ and a role for Reg proteins has been suggested. One such protein, islet neogenesis associated protein (INGAP), is a member of the Reg3 family of proteins and has been shown to induce islet neogenesis. Elucidation of the mechanisms and factors involved in the regulation of expression of INGAP and related proteins is, therefore, of great importance. Here, we report the establishment of the first in vitro tissue model of INGAP expression that consists of epithelial cystic structures derived from hamster pancreatic acinar tissue cultured in collagen matrix. The objective of this study was to characterize INGAP expression in this model and to investigate the role of pro-inflammatory cytokines and growth factors. Using quantitative reverse transcriptase PCR, we show that INGAP expression correlates with cyst formation and size suggesting the involvement of intra-luminal pressure associated with cyst growth. We also demonstrate for the first time that INGAP gene expression was significantly induced by treatment with interleukin (IL)-6 and further enhanced by a combination of IL-6 with dexamethazone and nicotinamide. Additionally, our data suggest that the effect of IL-6 on INGAP expression is mediated via the JAK/STAT3 signaling pathway. In summary, the in vitro model of INGAP expression described here represents an important step in the development of strategies for the use of INGAP and related proteins as islet neogenic agents in the pharmacotherapy of both type-1 and type-2 diabetes.
Bone marrow stromal cells protect oligodendrocytes from oxygen‐glucose deprivation injury (2008)

Oligodendrocyte (OLG) damage leads to demyelination, which is frequently observed in ischemic cerebrovascular diseases. In this study, we investigated the effect of bone marrow stromal cells (BMSCs) on OLGs subjected to oxygen-glucose deprivation (OGD). N20.1 cells (mouse OLG cell line) were transferred into an anaerobic chamber for 3 hr in glucose-free and serum-free medium. After OGD incubation, OLG cultures were divided into the following groups: 1) OGD alone, 2) OLG cocultured with BMSCs, 3) treatment with the phosphoinostide 3-kinase (PI3k) inhibitor LY294002, 4) LY294002-treated OLGs with BMSC cocultured, and 5) anti-p75 antibody-treated OLGs. After an additional 3 hr of reoxygenation incubation, OLG viability and apoptosis were measured. The mRNA expression in the BMSCs and OLGs was analyzed using quantitative real-time PCR (RT-PCR). Serine/threonine-specific protein kinase (Akt), phosphorylated Akt (p-Akt), p75, and caspase 3 protein expressions in OLGs were measured by Western blot. Our results suggest that BMSCs produce growth factors, activate the Akt pathway, and increase the survival of OLGs. BMSCs also reduce p75 and caspase 3 expressions in the OGD-OLGs, which leads to decreased OLG apoptosis. BMSCs participate in OLG protection that may occur with promoting growth factors/PI3K/Akt and inhibiting the p75/caspase pathways. Our study provides insight into white matter damage and the therapeutic benefits of BMSC-based remyelinating therapy after stroke and demyelinating diseases.
PON Roadmap [Invited] (2016)

With the recent conclusion of the XGS-PON and NG-PON2 standards in the ITU-T, the fiber access industry is now considering where to go next. This paper reviews the passive optical network (PON) systems market and the services that will drive the take-up of these next-generation PON technologies. The drivers for future PON evolution are discussed, and some technology options for the evolution of PON systems are highlighted.
TRAIN - a Computer Model for the Simulation of Longitudinal Dynamics in Trains (1998)

Since 1980 at the Institute of Transport, Railway Construction and Operation (IVE) a computer model called DYNAMIS has been developed to calculate the exact running times of train configurations. Additionally it is possible to calculate the energy-consumption and the temperature of the locomotive-engine. To calculate signal positions, safety sections behind signals and other safety installations an algorithm has been included to carry out emergency braking or interactive braking at a signal. Based upon this module a much more detailed program concerning the longitudinal dynamics has been further developed to calculate the longitudinal forces accruing in trains. This program has been called TRAIN. Immediate object of the research was the simulation of longitudinal forces and dynamics arising at the buffers and the draw gears of long (freight) trains. The model of the train is implemented by dedicated differential equations for the movements of the vehicles, the main brake pipe and the brake equipment of each wagon. It is possible to set up any variations of simple and coupled trains.
Definition of a quantitative measurement method for acetabular version in a plain radiograph in the healthy adult hip (2015)

By this quantitative method, acetabular morphology may be measured less invasively, easily, quickly and reliably in plain radiograph in transverse plane.
The RAMESSES experiment-III. Controlled-source electromagnetic sounding of the Reykjanes Ridge at 57°45′N (1998)

A controlled-source electromagnetic sounding survey centred on an axial volcanic ridge (AVR) segment of the Reykjanes Ridge at 5745N was performed as part of the RAMESSES experiment. Low-frequency (0.35-11 Hz) electromagnetic signals were transmitted through the crust to an array of horizontal electric field recorders at the seafloor to ranges of 15 km from the source, which was a 100 m long horizontal electric dipole towed at heights of 50-80 m from the seafloor. Coincident seismic and magnetotelluric studies were conducted during the rest of the RAMESSES experiment.