gebhart/patrepeval huggingface dataset:
A stress response pathway from the endoplasmic reticulum to the nucleus requires a novel bifunctional protein kinase/endoribonuclease (Ire1p) in mammalian cells (1998)

Eukaryotes respond to the presence of unfolded protein in the endoplasmic reticulum (ER) by up-regulating the transcription of genes encoding ER protein chaperones, such as BiP. We have isolated a novel human cDNA encoding a homolog to Saccharomyces cerevisiae Ire1p, a proximal sensor for this signal transduction pathway in yeast. The gene product hIre1p is a type 1 transmembrane protein containing a cytoplasmic domain that is highly conserved to the yeast counterpart having a Ser/Thr protein kinase domain and a domain homologous to RNase L. However, the luminal domain has extensively diverged from the yeast gene product. hIre1p expressed in mammalian cells displayed intrinsic autophosphorylation activity and an endoribonuclease activity that cleaved the 5' splice site of yeast HAC1 mRNA, a substrate for the endoribonuclease activity of yeast Ire1p. Overexpressed hIre1p was localized to the ER with particular concentration around the nuclear envelope and some colocalization with the nuclear pore complex. Expression of Ire1p mRNA was autoregulated through a process that required a functional hIre1p kinase activity. Finally, overexpression of wild-type hIre1p constitutively activated a reporter gene under transcriptional control of the rat BiP promoter, whereas expression of a catalytically inactive hIre1p acted in a trans-dominant-negative manner to prevent transcriptional activation of the BiP promoter in response to ER stress induced by inhibition of N-linked glycosylation. These results demonstrate that hIre1p is an essential proximal sensor of the unfolded protein response pathway in mammalian cells.
Efficient adenoviral gene transfer to kidney cortical vasculature utilizing a fiber modified vector (1999)

We conclude that incorporating a high affinity peptide ligand into the adenoviral fiber protein can preferentially enhance in vitro and in vivo adenoviral transfection efficiency in endothelial cells. Enhancing transfection efficiency will not only broaden the scope of disease processes addressed with adenoviral vectors but also allow the use of lower titer, thereby limiting toxicity. This vector has additional potential to transduce endothelial cells within tumors or ischemic tissue where alpha v integrins are upregulated.
Febuxostat (TMX‐67), a Novel, Non‐Purine, Selective Inhibitor of Xanthine Oxidase, Is Safe and Decreases Serum Urate in Healthy Volunteers (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Inhibition of gene expression by a short sense fragment (1991)

In order to further investigate the mechanism of antisense inhibition of gene expression, a series of plasmids which generate short antisense RNAs deriving from the 5' end of the CAT gene were constructed. When transfected into COS1 cells, these constructions were capable of specifically reducing CAT gene expression. Unexpectedly, transfection with constructions expressing defective RNA in the sense orientation also resulted in reduced levels of both CAT enzyme and mRNA. This was mediated by both short and full-length CAT-gene fragments, and was dependent on the presence of the tested transcriptional promoters, either the herpes simplex virus thymidine kinase (TK) or simian virus 40 late (SVL) promoters. These results, in conjunction with computer aided secondary structure prediction, indicate a possible similarity of regulatory mechanism for both senses of RNA acting within the cell.
Reduced Graphene Oxide Electrically Contacted Graphene Sensor for Highly Sensitive Nitric Oxide Detection (2011)

We develop graphene-based devices fabricated by alternating current dielectrophoresis (ac-DEP) for highly sensitive nitric oxide (NO) gas detection. The novel device comprises the sensitive channels of palladium-decorated reduced graphene oxide (Pd-RGO) and the electrodes covered with chemical vapor deposition (CVD)-grown graphene. The highly sensitive, recoverable, and reliable detection of NO gas ranging from 2 to 420 ppb with response time of several hundred seconds has been achieved at room temperature. The facile and scalable route for high performance suggests a promising application of graphene devices toward the human exhaled NO and environmental pollutant detections.
Intuitive 3D caricature face maker (2010)

We has developed an interactive system for generating caricatured 3D face with a single photo by combining the 2D caricature generation methods and 3D morphing methods. Recently there are many studies in capturing the 3D geometry and especially capturing a model of a human face is of special interest in several domains such as for the movies and games. Lim has introduced a 3D Caricature generation system on the mobile devices [Lim et al. 2007], but he has only generated the face geometry. Unlike these methods, our system supports not only creating a 3D caricature face using an exaggerated picture but also can automatically generate a facial texture image for realistic facial rendering through a simple system. We exaggerate the input face image based upon the facial features and make the exaggerated 3D face model using geometrical morphing. After we create a personalized 3D face mesh, a facial texture is automatically extracted from an exaggerated photo by projecting 3D geometry on to a caricatured face for realistic face rendering. The most important components of our system are to create an exaggerated 3D model without any camera calibration and to generate a facial texture automatically. In this way, our system produces real-time 3D caricature faces.
Urokinase receptor mRNA level and gene transcription are strongly and rapidly increased by phorbol myristate acetate in human monocyte-like U937 cells. (1991)

We have studied the effect of the tumor promotor phorbol myristate acetate (PMA) on the level of mRNA for the receptor for urokinase-type plasminogen activator (u-PAR) in the human monocyte-like cell line U937. PMA causes an early increase in the u-PAR mRNA level which reaches a maximal 50-fold enhancement after 24 h of treatment. Half-maximal stimulation occurs at approximately 5 nM PMA. The effect is observed only with phorbol esters that also act as tumor promotors. The protein synthesis inhibitor cycloheximide (10 micrograms/ml) also increases the level of u-PAR mRNA. Nuclear run-on experiments show a time-dependent increase in the u-PAR gene transcription rate after exposure of the cells to PMA. The PMA-induced increase in u-PAR mRNA is paralleled by a time-dependent increase in u-PAR protein as detected by cross-linking studies with radiolabeled ligand. We conclude that PMA stimulates transcription of the u-PAR gene in U937 cells, and this is responsible at least in part for the accumulation of the u-PAR mRNA and for the subsequent increase in urokinase-binding capacity.
Genetic control of hematopoietic stem cell frequency in mice is mostly cell autonomous (2000)

Previously we reported that the size of the stem cell compartment (measured as LTC-IC) is 11-fold greater in DBA/2 than in C57BL/6 mice, and we identified genes that regulate the size of the stem cell pool. To determine whether stem cell intrinsic or extrinsic events account for these differences, we created chimeras by aggregating morulae from the strains C57BL/6 and DBA/2. In these chimeras stem cells of both genotypes are exposed to a common mixed environment. Thus, an equalization of stem cell frequencies is expected if stem cell extrinsic effects dominate. Conversely, the parental ratio of LTC-IC should be preserved if the regulation is stem cell autonomous. For each chimera, individual LTC-IC were genotyped on the clonal levels by analyzing their progeny. We found that most of the difference that regulates the size of the stem cell compartment was intrinsic.
Transcription yield of fully 2′-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants (2015)

On average, mutations are deleterious to proteins. Mutations conferring new function to a protein often come at the expense of protein folding or stability, reducing overall activity. Over the years, a panel of T7 RNA polymerases have been designed or evolved to accept nucleotides with modified ribose moieties. These modified RNAs have proven useful, especially in vivo, but the transcriptional yields tend to be quite low. Here we show that mutations previously shown to increase the thermal tolerance of T7 RNA polymerase can increase the activity of mutants with expanded substrate range. The resulting polymerase mutants can be used to generate 2'-O-methyl modified RNA with yields much higher than enzymes currently employed.
Structuring of conductive silver line by electrohydrodynamic jet printing and its electrical characterization (2008)

A set of silver lines with a few hundred nanometers in thickness and with a few hundred micrometers in width were obtained using the electrohydrodynamic jet printing. The lines exhibited about three times higher resistivity (4.8 μΩcm) than that of bulk silver after thermal sintering process. The characteristic impedance of the silver line was about 18 Ω while the value calculated was 20 Ω. This paper demonstrated the possibility of using electrohydrodynamic jet printing of silver nanoparticles to obtain conductive line onto circuit boards.
Neutrophil cell surface receptors and their intracellular signal transduction pathways (2013)

Neutrophils play a critical role in the host defense against bacterial and fungal infections, but their inappropriate activation also contributes to tissue damage during autoimmune and inflammatory diseases. Neutrophils express a large number of cell surface receptors for the recognition of pathogen invasion and the inflammatory environment. Those include G-protein-coupled chemokine and chemoattractant receptors, Fc-receptors, adhesion receptors such as selectins/selectin ligands and integrins, various cytokine receptors, as well as innate immune receptors such as Toll-like receptors and C-type lectins. The various cell surface receptors trigger very diverse signal transduction pathways including activation of heterotrimeric and monomeric G-proteins, receptor-induced and store-operated Ca(2+) signals, protein and lipid kinases, adapter proteins and cytoskeletal rearrangement. Here we provide an overview of the receptors involved in neutrophil activation and the intracellular signal transduction processes they trigger. This knowledge is crucial for understanding how neutrophils participate in antimicrobial host defense and inflammatory tissue damage and may also point to possible future targets of the pharmacological therapy of neutrophil-mediated autoimmune or inflammatory diseases.
Highly Branched Poly(l-lysine) (2003)

This paper describes the synthesis of several novel water-soluble highly branched polypeptides. The synthesis starts with the ring-opening polymerization of epsilon-benzyloxycarbonyl-l-lysine N-carboxyanhydride (Z-Lys NCA) or epsilon-trifluoroacetyl-l-lysine N-carboxyanhydride (TFA-Lys NCA), followed by end functionalization of the peptide chain with N(alpha),N(epsilon)-di(9-fluorenylmethoxycarbonyl)-l-lysine (N(alpha),N(epsilon)-diFmoc Lys). Deprotection of the N(alpha),N(epsilon)-diFmoc Lys end group affords two new primary amine groups that can initiate the polymerization of a second generation of branches. Repetition of this ring-opening polymerization-end functionalization sequence affords highly branched poly(epsilon-benzyloxycarbonyl-l-lysine) (poly(Z-Lys)) and poly(epsilon-trifluoroacetyl-l-lysine) (poly(TFA-Lys)) in a small number of straightforward synthetic steps. Removal of the side-chain protective groups yields water-soluble and highly branched poly(l-lysine)s, which may be of potential interest for a variety of medical applications.
Gentoo package dependencies over time (2014)

Open source distributions such as Gentoo need to accurately track dependency relations between software packages in order to install working systems. To do this, Gentoo has a carefully authored database containing those relations. In this paper, we extract the Gentoo package dependency graph and its changes over time. The final dependency graph spans 15 thousand open source projects and 80 thousand dependency relations. Furthermore, the development of this graph is tracked over time from the beginning of the Gentoo project in 2000 to the first quarter of 2012, with monthly resolution. The resulting dataset provides many opportunities for research. In this paper we explore cluster analysis to reveals meaningful relations between packages and in a separate paper we analyze changes in the dependencies over time to get insights in the innovation dynamics of open source software.
A high power K/Ka-band monolithic T/R switch (2002)

A high-power K/Ka-band MESFET switch monolithic microwave integrated circuit (MMIC) has been developed for use in transmit/receive (T/R) modules. The switch demonstrates 0.2 dB insertion loss compression with 30 dBm input power, 12 dB higher than previously reported for K/Ka-band MESFET switches. Also, no isolation degradation was apparent with up to 28 dBm input power, a 13 dB improvement over the same previously demonstrated switches. A combination of techniques was used to yield higher power handling while preserving low loss and high isolation. These circuit techniques include the use of stacked MESFETs with large peripheries to improve power handling and transmission line transformers to minimize loss and maintain high isolation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effects of S-Nitrosation and Cross-Linking of Hemoglobin on Hypoxic Pulmonary Vasoconstriction in Isolated Rat Lungs (2002)

Free hemoglobin (Hb) and red blood cells augment hypoxic pulmonary vasoconstriction (HPV) by scavenging nitric oxide (NO). S-nitrosation of Hb (SNO-Hb) may confer vasodilatory properties by allowing release of NO during deoxygenation and/or by interaction with small-molecular weight thiols. Likewise, cross-linking of free Hb may limit its vasoconstrictive effect by preventing abluminal movement of the molecule. We compared the effects of free SNO-Hb and Hb intramolecularly cross-linked at the β-cysteine 93 residue [Bis(maleidophenyl)-polyethylene glycol2000HbA (Bis-Mal-PEGHb)] to those of free oxyHb on pulmonary artery pressure (PAP), HPV, and exhaled NO (eNO) in isolated, perfused rat lungs. Ventilation of lungs with anoxic gas for 5 minutes reduced perfusate P o 2 to 11±1.0 Torr. Addition of SNO-Hb or Bis-Mal-PEGHb (100 μmol/L) to buffer perfusate increased normoxic PAP and augmented HPV in similar magnitude as free oxyHb, but had no effect on eNO. Addition of the allosteric modulator inositol hexaphosphate to increase Hb P50 and the thiol glutathione (GSH) to allow removal of NO from Hb via transnitrosation to the perfusate did not reduce augmentation of HPV by SNO-Hb or increase eNO. GSH resulted in an ≈50% reduction in perfusate [ S -nitrosothiol], in association with an increase in perfusate [metHb]. Free SNO-Hb is a net NO scavenger and pulmonary vasoconstrictor in this model, although thiol-mediated release of NO from SNO-Hb does occur. However, release of NO from SNO-Hb was not influenced by deoxygenation-mediated allosteric changes in Hb across a broad range of oxyHb saturation. Cross-linking of Hb does not limit its pulmonary vasoconstrictor effects.
A critical review of cyclosporine therapy in inflammatory bowel disease (1995)

Cyclosporine A (CsA) is a potent inhibitor of cell-mediated immunity. Controlled trials in Crohn's disease with low-dose CsA (≤5 mg/kg/day) did not show efficacy for either chronically active inflammatory disease or for maintenance of remission. Uncontrolled trials of high-dose CsA (≥ 5 mg/kg/day oral or 4 mg/kg/day i.v.) suggest efficacy for both inflammatory and fistulous Crohn's disease. Both uncontrolled trials and one controlled study suggest that high-dose CsA is efficacious for severe ulcerative colitis (UC). A controlled trial of low-dose CsA enemas for left-sided UC did not show efficacy. There is a significant theoretical risk of irreversible CsA-associated nephropathy following treatment of inflammatory bowel disease (IBD) with high-dose CsA. Severe infectious complications may also occur rarely. It appears that CsA must be used at relatively high (and potentially toxic) dosages to achieve efficacy in IBD. Future studies should evaluate the efficacy and safety of the short-term use of high-dose CsA as “rescue therapy” in severe inflammatory Crohn's disease and UC, as well as in fistulous Crohn's disease.
Overview of the CHORUS ® Distributed Operating Systems (1991)

The CHORUS technology has been designed for building new generations of open, distributed, scalable operating systems. CHORUS has the following main characteristics: # a communication-based architecture, relying on a minimal Nucleus which integrates distributed processing and communication at the lowest level, and which implements generic services used by a set of subsystem servers to extend standard operating system interfaces. A UNIX subsystem has been developed; other subsystems such as objectoriented systems are planned; # a real-time Nucleus providing real-time services which are accessible to system programmers; # a modular architecture providing scalability, and allowing, in particular, dynamic configuration of the system and its applications over a wide range of hardware and network configurations, including parallel and multiprocessor systems. CHORUS-V3 is the current version of the CHORUS Distributed Operating System, developed by Chorus systemes. Earlier versions were st...
Contrast Microsphere Destruction by a Continuous Flow Ventricular Assist Device: An In Vitro Evaluation Using a Mock Circulation Loop (2017)

Contrast microsphere transit through a CF-VAD within a MCL resulted in significant reduction in signal intensity, consistent with destruction within the pump. This was evident at all CF-VAD pump speeds but relative signal drop was inversely proportional to pump speed.
Anthocyanin Carrying Structures in Specific Genotypes of Matthiola incana R. Br. (1981)

Abstract Several lines of the genetically well defined Matthiola incana (Brassicaceae) concerning the anthocyanin biosynthesis (line 02, 06, 10, and 14) store the anthocyanin pigment as crystals (line 06) or in anthocyanoblasts (“balls”) in the epidermal cells (line 02, 10, and 14) of the flower petals. The genetic constitution of these genotypes is in addition to the basic factors f + , g + , and e + , b + b + or bb (cyanidin or pelargonidin type), ll, u + u + , and v + v + or vv, demonstrating that the ll, u + u + constitution is responsible for precipitation of anthocyanins in a certain structure indepen­ dent of the other modificationally acting genes b and v. The ll, u + u + types accumulate preferentially acylated 3-biosides.
Human papillomavirus oncogenic expression in the dysplastic portio; an investigation of biopsies from 190 cervical cones (2004)

In this study, we investigated the presence of E6/E7 transcripts of seven common high-risk human papillomavirus (HPV) types in 190 cervical biopsies. The RNA-based real-time nucleic acid sequence-based amplification assay (NASBA) and type-specific PCR, both detecting HPV 16, 18, 31, 33, 45, 52, and 58, as well as consensus PCR, were performed on all 190 biopsies. High accordance between type-specific and consensus PCR confirms that the HPV types included in this study are the most common types present in cervical dysplasia. Furthermore, we see a clear increase in the incidence of HPV, both DNA and RNA, along with the histological severity of dysplasia. HPV RNA was detected in all but two PCR-positive cases, confirming that the virus exerts E6/E7 mRNA expression in cases of high-grade dysplasia. Out of 19 women given a normal or borderline diagnosis at conisation, only four were found HPV positive, which may suggest that unnecessary conisations can possibly be reduced by introducing HPV testing into the preoperative routine assessment.
A droplet microfluidics platform for rapid microalgal growth and oil production analysis (2016)

Microalgae have emerged as a promising source for producing future renewable biofuels. Developing better microalgal strains with faster growth and higher oil production rates is one of the major routes towards economically viable microalgal biofuel production. In this work, we present a droplet microfluidics-based microalgae analysis platform capable of measuring growth and oil content of various microalgal strains with single-cell resolution in a high-throughput manner. The platform allows for encapsulating a single microalgal cell into a water-in-oil emulsion droplet and tracking the growth and division of the encapsulated cell over time, followed by on-chip oil quantification. The key feature of the developed platform is its capability to fluorescently stain microalgae within microdroplets for oil content quantification. The performance of the developed platform was characterized using the unicellular microalga Chlamydomonas reinhardtii and the colonial microalga Botryococcus braunii. The application of the platform in quantifying growth and oil accumulation was successfully confirmed using C. reinhardtii under different culture conditions, namely nitrogen-replete and nitrogen-limited conditions. These results demonstrate the capability of this platform as a rapid screening tool that can be applied to a wide range of microalgal strains for analyzing growth and oil accumulation characteristics relevant to biofuel strain selection and development. Biotechnol. Bioeng. 2016;113: 1691-1701. © 2016 Wiley Periodicals, Inc.
Designing Mobile Money Services Lessons from M-PESA (2009)

M-PESA, the Kenyan mobile money service, has seen exceptional growth since its introduction in March 2007.Six million customers have registered with the service (see Figure 1), which represents nearly half the customer base of Safaricom, the mobile operator that launched M-PESA.This is a level of penetration in the mobile base that no other mobile phone-based service has achieved, outside of voice and text messaging.The figures for person-to-person (P2P) transfers are equally impressive: over USD 1.6 billion (120 billion Kenyan Shillings [KSh]) worth of such transfers have been made through the M-PESA system.Its agent network has grown in parallel with the customer base, and the service can be accessed at nearly nine thousand retail outlets nationwide, in both urban and rural areas.M-PESA facilitates a variety of financial transactions through the mobile phone.To access its services, individuals must register at an authorized M-PESA retail agent outlet.They then get an individual electronic money account that is managed by Safaricom, which in turn deposits the full value its customers store in M-PESA accounts at a pooled account in a regulated bank.Thus, the issuer of M-PESA accounts is Safaricom, but the value in the accounts is entirely backed by highly liquid deposits at a commercial bank.Customers can use their mobile phones to transfer money to both registered and non-registered users, check their account balance, pay bills, purchase mobile phone credit, and transfer such credit to other users.They can also make deposits and withdraw cash from their M-PESA account by visiting an authorized M-PESA agent.M-PESA is not the only mobile money service to be launched in Africa, but it is the most successful.For example, South Africa's WIZZIT has managed to attract 250,000 customers in more than four years of operation.Neighboring Tanzania launched its own version of M-PESA in April 2008, but it has only recently crossed the 100,000 customer mark.So why has this service grown so rapidly within the Kenyan context?
The Effect of Endogenous Pyrogen on the Plasma Zinc Concentration of the Rat (1970)

SummaryPlasma zinc concentration was depressed in rats following the injection of endogenous pyrogen. The endogenous pyrogen, obtained from peritoneal leukocytes, was active in endotoxin-tolerant animals and repeated injections of this protein did not produce tolerance.