gebhart/patrepeval huggingface dataset:
The nonerythropoietic asialoerythropoietin protects against neonatal hypoxia‐ischemia as potently as erythropoietin (2004)

Recently, erythropoietin (EPO) and the nonerythropoietic derivative asialoEPO have been linked to tissue protection in the nervous system. In this study, we tested their effects in a model of neonatal hypoxia-ischemia (HI) in 7-day-old rats (unilateral carotid ligation and exposure to 7.7% O(2) for 50 min). EPO (10 U/g body weight = 80 ng/g; n = 24), asialoEPO (80 ng/g; n = 23) or vehicle (phosphate-buffered saline with 0.1% human serum albumin; n = 24) was injected intraperitoneally 4 h before HI. Both drugs were protective, as judged by measuring the infarct volumes, neuropathological score and gross morphological score. The infarct volumes were significantly reduced by both EPO (52%) and asialoEPO (55%) treatment, even though the plasma levels of asialoEPO had dropped below the detection limit (1 pm) at the onset of HI, while those of EPO were in the nanomolar range. Thus, a brief trigger by asialoEPO before the insult appears to be sufficient for protection. Proteomics analysis after asialoEPO treatment alone (no HI) revealed at least one differentially up-regulated protein, synaptosome-associated protein of 25 kDa (SNAP-25). Activation (phosphorylation) of ERK was significantly reduced in asialoEPO-treated animals after HI. EPO and the nonerythropoietic asialoEPO both provided significant and equal neuroprotection when administered 4 h prior to HI in 7-day-old rats. The protection might be related to reduced ERK activation and up-regulation of SNAP-25.
Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88 (2010)

Rates of cell proliferation in the vertebrate intestinal epithelium are modulated by intrinsic signaling pathways and extrinsic cues. Here, we report that epithelial cell proliferation in the developing zebrafish intestine is stimulated both by the presence of the resident microbiota and by activation of Wnt signaling. We find that the response to microbial proliferation-promoting signals requires Myd88 but not TNF receptor, implicating host innate immune pathways but not inflammation in the establishment of homeostasis in the developing intestinal epithelium. We show that loss of axin1, a component of the β-catenin destruction complex, results in greater than WT levels of intestinal epithelial cell proliferation. Compared with conventionally reared axin1 mutants, germ-free axin1 mutants exhibit decreased intestinal epithelial cell proliferation, whereas monoassociation with the resident intestinal bacterium Aeromonas veronii results in elevated epithelial cell proliferation. Disruption of β-catenin signaling by deletion of the β-catenin coactivator tcf4 partially decreases the proliferation-promoting capacity of A. veronii. We show that numbers of intestinal epithelial cells with cytoplasmic β-catenin are reduced in the absence of the microbiota in both WT and axin1 mutants and elevated in animals' monoassociated A. veronii. Collectively, these data demonstrate that resident intestinal bacteria enhance the stability of β-catenin in intestinal epithelial cells and promote cell proliferation in the developing vertebrate intestine.
Studying Lactoferrin N-Glycosylation (2017)

Lactoferrin is a multifunctional glycoprotein found in the milk of most mammals. In addition to its well-known role of binding iron, lactoferrin carries many important biological functions, including the promotion of cell proliferation and differentiation, and as an anti-bacterial, anti-viral, and anti-parasitic protein. These functions differ among lactoferrin homologs in mammals. Although considerable attention has been given to the many functions of lactoferrin, its primary nutritional contribution is presumed to be related to its iron-binding characteristics, whereas the role of glycosylation has been neglected. Given the critical role of glycan binding in many biological processes, the glycan moieties in lactoferrin are likely to contribute significantly to the biological roles of lactoferrin. Despite the high amino acid sequence homology in different lactoferrins (up to 99%), each exhibits a unique glycosylation pattern that may be responsible for heterogeneity of the biological properties of lactoferrins. An important task for the production of biotherapeutics and medical foods containing bioactive glycoproteins is the assessment of the contributions of individual glycans to the observed bioactivities. This review examines how the study of lactoferrin glycosylation patterns can increase our understanding of lactoferrin functionality.
Co-inoculation of nitrogen-fixing and phosphate-solubilizing bacteria to promote growth, yield and nutrient uptake in chickpea (2007)

A total of 32 bacterial isolates including Mesorhizobium (N=10), Azotobacter (N=12) and phosphate-solubilizing bacteria (N=10) were isolated and tested for siderophore, HCN, ammonia, indole acetic acid production and phosphate solubilization in vitro . The bacterial cultures were positive for siderophore, HCN and ammonia. Among the isolates, M. ciceri RC3 and A. chrococcum A4 displayed 35 and 14 μg ml −1 of IAA, respectively, whereas Bacillus produced 19 ( Bacillus PSB1) and 17 μg ml −1 ( Bacillus PSB10) of IAA in Luria Bertani broth. The diameter of the P solubilization zone varied between 4 ( Bacillus PSB1) and 5 mm ( Bacillus PSB10) and a considerable amount of tricalcium phosphate (7 and 8 μg ml −1 by Bacillus PSB1 and Bacillus PSB10, respectively) was released in liquid medium, with a concomitant drop in pH. The effects of N 2 -fixing and PS bacteria on the growth, chlorophyll content, seed yield, grain protein and N uptake of chickpea plants in field trials varied considerably between the treatments. Nodule number and biomass were significantly greater at 90 days after sowing (DAS), decreasing by 145 DAS. Seed yield increased by 250% due to inoculation with M. ciceri RC3 + A. chroococcum A4 + Bacillus PSB10, relative to the control treatment. Grain protein content ranged from 180 ( Bacillus PSB1) to 309 ng g −1 ( M. ciceri RC3 + A. chroococcum A4 + Bacillus PSB10) in inoculated chickpea. The N contents in roots and shoots differed considerably among the treatments.
[Expression and purification of tissue factor pathway inhibitor in Pichia pastoris]. (2007)

Introduction of the silent mutation at the specific site of TFPI cDNA can increase the recombinant protein expression in Pichia pastoris, which is much higher than that in insect cells or saccharomyces cerevisiae.
Document‐centric XML workflows with fragment digital signatures (2010)

Abstract The use of digital document management and processing is increasing. Traditional workflows of paper forms are being replaced by electronic workflows of digital documents. These workflows often require multiple signatures to be added to the documents for authorization and/or integrity. We describe examples of digital workflows that illustrate problems with digital signatures: i.e. the use of digital signatures across entire documents results in signatures that can be unnecessarily invalidated by subsequent modification of the document. We propose the use of fragment signatures, which reduce unnecessary invalidation of signatures and enable greater concurrency in workflows. Our approach is document‐centric and does not use a centralized database. We report on an implementation that allows fragment signatures over document fragments as well as the attachment (or embedding) of other documents. This allows collaborative or cooperative editing to occur on parts of a document without disturbing unrelated signatures. We describe the lessons learned from our deployments and offer further ways to embed such signatures into other document types. Copyright © 2010 John Wiley & Sons, Ltd.
Guided harmonic sinusoid estimation in a multi-pitch environment (2009)

We describe an algorithm to accurately estimate the fundamental frequency of harmonic sinusoids in a mixed voice recording environment using an aligned electronic score as a guide. Taking the pitch tracking results on individual voices prior to mixing as ground truth, we are able estimate the pitch of individual voices in a 4-part piece to within 50 cents of the correct pitch more than 90% of the time.
Single‐Cell Analysis Using Droplet Microfluidics (2019)

Droplet microfluidics has revolutionized the study of single cells. The ability to compartmentalize cells within picoliter droplets in microfluidic devices has opened up a wide range of strategies to extract information at the genomic, transcriptomic, proteomic, or metabolomic level from large numbers of individual cells. Studying the different molecular landscapes at single-cell resolution has provided the authors with a detailed picture of intracellular heterogeneity and the resulting changes in cellular phenotypes. In addition, these technologies have aided in the discovery of rare cells in tumors or in the immune system, and left the authors with a deeper understanding of the fundamental biological processes that determine cell fate. This review aims to provide a detailed overview of the various droplet microfluidic strategies reported in the literature, taking into account the sometimes subtle differences in workflow or reagents that enable or improve certain protocols. Specifically, approaches to targeted- and whole-genome analysis, as well as whole-transcriptome profiling techniques, are reviewed. In addition, an up-to-date overview of new methods to characterize and quantify single-cell protein levels, and of developments to screen secreted molecules such as antibodies, cytokines, or metabolites at the single-cell level, is provided.
Verification of security policy filtering rules by Model Checking (2011)

One of the very important tasks, a computer network (or security) administrator has to fulfill under constructing a (distributed) firewall security policy, is to guarantee the absence of inconsistencies (or anomalies) and possibility to implement the policy in the given network configuration. The paper outlines an approach to verification of filtering rules of firewalls. The approach is intended for detection and resolution of filtering anomalies in the specification of security policy of computer networks. It is based on Model Checking technique. The paper proposes the models of computer networks, the models of firewalls and filtering anomalies, as well as an algorithm of detection of such anomalies. We suggest also a method for verification of filtering rules based on the mentioned models. The main peculiarities of the approach consist in using Model Checking exactly to detect the anomalies of filtering rules and in ability to specify temporal parameters in filtering rules.
Where Does Combination Therapy With an SGLT2 Inhibitor Plus a DPP-4 Inhibitor Fit in the Management of Type 2 Diabetes? (2015)

Hyperglycemia is the critical risk factor for diabetic microvascular complications. Several landmark studies, e.g., UK Prospective Diabetes Study (UKPDS) and Diabetes Control and Complications Trial (DCCT), have demonstrated that lowering the HbA1c by 1% decreases microvascular complications by approximately 35% (1,2). Despite the unequivocal evidence for the importance of achieving good glycemic control in patients with type 2 diabetes mellitus (T2DM), approximately half of individuals with T2DM fail to achieve the American Diabetes Association (ADA) goal of glycemic control (HbA1c <7.0%) (3). Thus, novel therapeutic agents and strategies are required to improve glycemic control in T2DM patients.

Two novel classes of antihyperglycemic drugs have been developed during the last decade for the treatment of T2DM: dipeptidyl peptidase-4 inhibitors (DPP-4i) (4) and sodium–glucose cotransporter 2 (SGLT2) inhibitors (SGLT2i) (5).

DPP-4i have been in clinical use for the treatment of T2DM for more than a decade. DPP-4i inhibit the enzyme that degrades the incretin hormones, GLP-1 and glucose-dependent insulinotropic polypeptide (GIP), and result in elevated plasma GLP-1 and GIP concentrations. The increase in plasma GLP-1 and GIP concentrations stimulates insulin secretion from the β-cell and inhibits glucagon secretion from the α-cell, leading to inhibition of endogenous glucose production (EGP) and reduction in plasma glucose concentration (6).

SGLT2i are a novel class of antidiabetes drugs that recently have been approved for the treatment of T2DM. Members of this class reduce the plasma glucose concentration by inhibiting renal glucose reabsorption and producing glucosuria. Urinary glucose loss results in negative energy balance and because SGLT2i also block sodium absorption in the proximal tubule, they cause weight loss (∼2–3 kg) and decrease in blood pressure (4–6/1–2 mmHg systolic/diastolic) (5).

Because the pathogenesis of T2DM is complex and involves multiple metabolic defects (7), the …
Environmental Concerns in Antimicrobial Finishing of Textiles (2014)

A variety of antimicrobial chemical finishes recently received significant interest in the development of antimicrobial fibrous products. However, an antimicrobial inhibiting the growth or leading the death of microorganism may be harmful to other living species including human being. An increasing consumption of antimicrobial finished fibrous products, and the existing regulations for the registration and control of such products provided strong reasons to appreciate the environment concerns associated with the finished textiles. The published literature in antimicrobial finishing of fibers mainly addressed the development of finish composition, its application, and subsequent evaluation using appropriate methods. Environmental risks that may be associated with the antimicrobial; and its undesired effect during the product service life were the obvious concerns demanding investigations. State of the art development in antimicrobial finishing of textiles emphasized the need for assessing the environment-friendly character of antimicrobial finishes, and the development of antimicrobial effects using natural antimicrobials of plant and animal origin obtainable from the waste materials. Sustainable finish composition and finished fibrous product were apparently found desirable.
Diffuse Traumatic Axonal Injury in the Mouse Induces Atrophy, c-Jun Activation, and Axonal Outgrowth in the Axotomized Neuronal Population (2011)

Traumatic axonal injury (TAI) is a consistent component of traumatic brain injury (TBI) and is associated with much of its morbidity. Little is known regarding the long-term retrograde neuronal consequences of TAI and/or the potential that TAI could lead to anterograde axonal reorganization and repair. To investigate the repertoire of anterograde and retrograde responses triggered by TIA, Thy1-YFP-H mice were subjected to mild central fluid percussion injury and killed at various times between 15 min and 28 d post-injury. Based upon confocal assessment of the endogenous neuronal fluorescence, such injury was found to result in diffuse TAI throughout layer V of the neocortex within yellow fluorescent protein (YFP)-positive axons. When these fluorescent approaches were coupled with various quantitative and immunohistochemical approaches, we found that this TAI did not result in neuronal death over the 28 d period assessed. Rather, it elicited neuronal atrophy. Within these same axotomized neuronal populations, TAI was also found to induce an early and sustained activation of the transcription factors c-Jun and ATF-3 (activating transcription factor 3), known regulators of axon regeneration. Parallel ultrastructural studies confirmed that these reactive changes are consistent with atrophy in the absence of neuronal death. Concurrent with those events ongoing in the neuronal cell bodies, their downstream axonal segments revealed, as early as 1 d post-injury, morphological changes consistent with reactive sprouting that was accompanied by significant axonal elongation over time. Collectively, these TAI-linked events are consistent with sustained neuronal recovery, an activation of a regenerative genetic program, and subsequent axonal reorganization suggestive of some form of regenerative response.
Dynamic Mission Planning for Communication Control in Multiple Unmanned Aircraft Teams (2013)

A multi-UAV system relies on communications to operate. Failure to communicate remotely sensed mission data to the base may render the system ineffective, and the inability to exchange command and control messages can lead to system failures. This paper describes a unique method to control network communications through distributed task allocation to engage under-utilized UAVs to serve as communication relays and to ensure that the network supports mission tasks. This work builds upon a distributed algorithm previously developed by the authors, CBBA with Relays, which uses task assignment information, including task location and proposed execution time, to predict the network topology and plan support using relays. By explicitly coupling task assignment and relay creation processes, the team is able to optimize the use of agents to address the needs of dynamic complex missions. In this work, the algorithm is extended to explicitly consider realistic network communication dynamics, including path loss, stochastic fading, and information routing. Simulation and flight test results validate the proposed approach, demonstrating that the algorithm ensures both data-rate and interconnectivity bit-error-rate requirements during task execution.
Inhibition of TGF‐<i>β</i> signaling by an ALK5 inhibitor protects rats from dimethylnitrosamine‐induced liver fibrosis (2005)

1 Chronic liver disease is characterized by an exacerbated accumulation of matrix, causing progressive fibrosis, which may lead to cirrhosis. Transforming growth factor beta (TGF-beta), a well-known profibrotic cytokine, transduces its signal through the ALK5 ser/thr kinase receptor, and increases transcription of different genes including PAI-1 and collagens. The identification of GW6604 (2-phenyl-4-(3-pyridin-2-yl-1H-pyrazol-4-yl)pyridine), an ALK5 inhibitor, allowed us to evaluate the therapeutic potential of inhibiting TGF-beta pathway in different models of liver disease. 2 A cellular assay was used to identify GW6604 as a TGF-beta signaling pathway inhibitor. This ALK5 inhibitor was then tested in a model of liver hepatectomy in TGF-beta-overexpressing transgenic mice, in an acute model of liver disease and in a chronic model of dimethylnitrosamine (DMN)-induced liver fibrosis. 3 In vitro, GW6604 inhibited autophosphorylation of ALK5 with an IC(50) of 140 nM and in a cellular assay inhibited TGF-beta-induced transcription of PAI-1 (IC(50): 500 nM). In vivo, GW6604 (40 mg kg(-1) p.o.) increased liver regeneration in TGF-beta-overexpressing mice, which had undergone partial hepatectomy. In an acute model of liver disease, GW6604 reduced by 80% the expression of collagen IA1. In a chronic model of DMN-induced fibrosis where DMN was administered for 6 weeks and GW6604 dosed for the last 3 weeks (80 mg kg(-1) p.o., b.i.d.), mortality was prevented and DMN-induced elevations of mRNA encoding for collagen IA1, IA2, III, TIMP-1 and TGF-beta were reduced by 50-75%. Inhibition of matrix genes overexpression was accompanied by reduced matrix deposition and reduction in liver function deterioration, as assessed by bilirubin and liver enzyme levels. 4 Our results suggest that inhibition of ALK5 could be an attractive new approach to treatment of liver fibrotic diseases by both preventing matrix deposition and promoting hepatocyte regeneration.
The Crossed Claisen Ester Condensation Mediated by Titanium(IV) Bistriflate (1986)

Abstract The crossed Claisen ester condensation between methoxymethyl ester and methyl ester promoted by the combined use of titanium(IV) bistriflate and tertiary amine has been established.
Common management architecture for third generation wireless networks (2002)

The wireless market can be divided into mobile/cellular and fixed wireless. The mobile/cellular world is progressively transitioning from 2G (e.g. GSM, 2G-CDMA) to 2.5G (e.g. GPRS, 2.G-CDMA) to 3G (e.g. CDMA-2000, UMTS) technologies. The broadband fixed wireless technology is targeted as one of the "last mile" services available to residents and businesses. It typically requires a licensed frequency with a specific frequency range. A typical broadband fixed wireless system consists of a hub system servicing multiple subscriber end systems over a wireless radio frequency (RF). Examples of fixed wireless solutions include the Multi-channel Multi-point Distribution System (MMDS) and the Local Multi-point Distribution System (LMDS). This paper defines the OSS architecture, based on the Telecom Operation Map framework of the TeleManagement Forum, for mobile and fixed wireless networks. This include the FCAPS five functional areas: fault configuration management, accounting performance management, and management, management, management as well as service restoration, engineering, data collection, service activation, and network planning. The proposed architecture will give service providers the capability to manage their next generation networks in a way that gives them FCAPS in a way that best suits the technology and their business processes.
Multiplex Picoliter-Droplet Digital PCR for Quantitative Assessment of DNA Integrity in Clinical Samples (2013)

The development of DNA-quality assays will enable researchers to downselect samples or process more DNA to achieve reliable genome sequencing with the highest possible efficiency of cost and effort, as well as minimize the waste of precious samples.
Saving power by synthesizing gated clocks for sequential circuits (1994)

Portable devices demand low power consumption to prolong battery life. Gating the clock is one strategy for saving power. The authors' technique identifies self-loops in an FSM and uses the function described by the self-loops to gate the clock. Applying these techniques to standard benchmarks achieved an average 25% less power dissipation at a cost of only 5% more area.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>