gebhart/patrepeval huggingface dataset:
Hypoxia-inducible factor–2 (HIF-2) regulates hepatic erythropoietin in vivo (2007)

Erythropoiesis is critically dependent on erythropoietin (EPO), a glycoprotein hormone that is regulated by hypoxia-inducible factor (HIF). Hepatocytes are the primary source of extrarenal EPO in the adult and express HIF-1 and HIF-2, whose roles in the hypoxic induction of EPO remain controversial. In order to define the role of HIF-1 and HIF-2 in the regulation of hepatic EPO expression, we have generated mice with conditional inactivation of Hif-1alpha and/or Hif-2alpha (Epas1) in hepatocytes. We have previously shown that inactivation of the von Hippel-Lindau tumor suppressor pVHL, which targets both HIFs for proteasomal degradation, results in increased hepatic Epo production and polycythemia independent of Hif-1alpha. Here we show that conditional inactivation of Hif-2alpha in pVHL-deficient mice suppressed hepatic Epo and the development of polycythemia. Furthermore, we found that physiological Epo expression in infant livers required Hif-2alpha but not Hif-1alpha and that the hypoxic induction of liver Epo in anemic adults was Hif-2alpha dependent. Since other Hif target genes such phosphoglycerate kinase 1 (Pgk) were Hif-1alpha dependent, we provide genetic evidence that HIF-1 and HIF-2 have distinct roles in the regulation of hypoxia-inducible genes and that EPO is preferentially regulated by HIF-2 in the liver.
A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells (2012)

We have developed a new technique for proximity-dependent labeling of proteins in eukaryotic cells. Named BioID for proximity-dependent biotin identification, this approach is based on fusion of a promiscuous Escherichia coli biotin protein ligase to a targeting protein. BioID features proximity-dependent biotinylation of proteins that are near-neighbors of the fusion protein. Biotinylated proteins may be isolated by affinity capture and identified by mass spectrometry. We apply BioID to lamin-A (LaA), a well-characterized intermediate filament protein that is a constituent of the nuclear lamina, an important structural element of the nuclear envelope (NE). We identify multiple proteins that associate with and/or are proximate to LaA in vivo. The most abundant of these include known interactors of LaA that are localized to the NE, as well as a new NE-associated protein named SLAP75. Our results suggest BioID is a useful and generally applicable method to screen for both interacting and neighboring proteins in their native cellular environment.
Neurotrophin 3 stimulates the differentiation of motoneurons from avian neural tube progenitor cells. (1994)

Neurotrophin 3 (NT-3) promotes differentiation of neural tube progenitors into motoneurons expressing the BEN/SC1 and islet-1 epitopes. A 1.75- to 6.7-fold increase in BEN-positive motoneurons was obtained when quail neural tube cells were cultured with NT-3 at 0.1-10 ng/ml, respectively. In contrast, the overall number of cells, as well as the proportion of motoneurons that developed from cycling precursors, did not change. Addition of NT-3 at 1 ng/ml to cells obtained from ventral half-neural tubes promoted a 2.5-fold stimulation in motoneuron number, confirming the specificity of the effect. Moreover, NT-3 had no significant effect on survival of differentiated avian motoneurons. The distribution of trkC mRNA, which encodes the high-affinity receptor for NT-3, is consistent with these findings. trkC expression is homogeneous in the embryonic day 2 (E2) neural tube, becomes restricted to the mantle layer on E3, where differentiation occurs, and disappears from the ventral third of the E4-E5 spinal cord right before the onset of normal motoneuron death. These results suggest that NT-3 and trkC regulate early neurogenesis in the avian central nervous system.
Hepatocyte Organoid Culture in Elliptic Hollow Fibers to Develop a Hybrid Artificial Liver (2004)

A novel organoid culture was developed in which hepatocytes maintain high liver functions for more than several weeks in vitro. The main disadvantage of tissue-engineered organoids is the lack of a blood vessel structure between the aggregated cells. Because of depletion of oxygen, the thickness from the surface of an organoid at which hepatocytes can survive is limited. This study showed that a rat hepatocyte organoid that forms by using centrifugal force in a hollow fiber (HF) had a survival limit thickness of about 80 - 100 microm from the surface of the organoid. Based on the value, we designed an elliptic HF having less than 150 microm minor diameter by using a simple annealing method. All hepatocytes were supplied with oxygen and formed an organoid without a dead cell layer in this HF A hepatocyte organoid in an elliptic HF maintained ammonia removal activity twice as high as in the original HF for at least one month during culture. Albumin secretion activity of an organoid in an elliptic HF was also maintained for at least one month and was the same level as that of liver in a living body. In conclusion, organoid culture by using an elliptic HF seems to be a promising technique to develop a hybrid artificial liver.
IL-10 in HIV infection: increasing serum IL-10 levels with disease progression—down-regulatory effect of potent anti-retroviral therapy (1999)

To examine the potential pathogenic role of IL-10 in HIV infection, we measured serum IL-10 levels in 51 HIV-infected patients and 23 healthy controls both on cross-sectional and longitudinal testing. All clinical groups (Centers for Disease Control (CDC) categories) of HIV-infected patients had significantly higher circulating IL-10 levels than controls, with the highest levels among the AIDS patients, particularly in patients with ongoing Mycobacterium avium complex (MAC) infection. Among 32 HIV-infected patients followed with longitudinal testing (median observation time 39 months), patients with disease progression had increasing IL-10 levels in serum, in contrast to non-progressing patients where levels were stable. While both IL-10 and tumour necrosis factor-alpha (TNF-alpha) increased in patients with disease progression, the IL-10/TNF-alpha ratio decreased in these patients, suggesting imbalance between these two cytokines. Finally, we found that highly active anti-retroviral therapy (HAART) induced a significant, gradual decrease in IL-10 levels but without normalization. These findings suggest a pathogenic role for IL-10 in HIV infection, and may suggest a possible role for immunomodulating therapy which down-regulates IL-10 activity in addition to concomitant potent anti-retroviral therapy in HIV-infected patients.
Functional Analyses of the Superficial Stratum Corneum in Atopic Xerosis (1991)

Dermatologists universally recognize that the unaffected skin of patients with atopic dermatitis tends to be dry and slightly scaly. To characterize the functional properties of the superficial stratum corneum in atopic xerosis, we studied the forearms of 28 patients with atopic dermatitis, aged 14 to 30 years, and 18 age-matched controls, with the use of mainly noninvasive methods. Patients with atopic xerosis showed markedly higher transepidermal water loss and markedly lower skin surface hydration levels than did the controls. The corneocytes in atopic xerosis tended to desquamate in clumps of cell aggregates instead of as individual cells. They contained a substantially lower amount of water-soluble amino acids, which play a role in the water-retaining capacity of stratum corneum, than did those of controls. Although the number of stratum corneum cell layers in atopic xerosis (21 +/- 4) was substantially larger than that in controls (15 +/- 1), its turnover time (7 +/- 2 days) was appreciably shorter than that for controls (14 +/- 2 days). Like those noted in the skin with increased epidermal proliferation, the size of superficial corneocytes in patients with atopic xerosis was substantially smaller than in controls. Histopathologic examination revealed acanthotic epidermis, mild perivascular mononuclear cell infiltrate, and pigment incontinence. Atopic xerosis, the dry skin of patients with atopic dermatitis, shows various stratum corneum functional impairments, probably reflecting increased epidermal proliferation due to a low-level ongoing dermatitis.
Conductivity in transparent oxide semiconductors (2011)

Despite an extensive research effort for over 60 years, an understanding of the origins of conductivity in wide band gap transparent conducting oxide (TCO) semiconductors remains elusive. While TCOs have already found widespread use in device applications requiring a transparent contact, there are currently enormous efforts to (i) increase the conductivity of existing materials, (ii) identify suitable alternatives, and (iii) attempt to gain semiconductor-engineering levels of control over their carrier density, essential for the incorporation of TCOs into a new generation of multifunctional transparent electronic devices. These efforts, however, are dependent on a microscopic identification of the defects and impurities leading to the high unintentional carrier densities present in these materials. Here, we review recent developments towards such an understanding. While oxygen vacancies are commonly assumed to be the source of the conductivity, there is increasing evidence that this is not a sufficient mechanism to explain the total measured carrier concentrations. In fact, many studies suggest that oxygen vacancies are deep, rather than shallow, donors, and their abundance in as-grown material is also debated. We discuss other potential contributions to the conductivity in TCOs, including other native defects, their complexes, and in particular hydrogen impurities. Convincing theoretical and experimental evidence is presented for the donor nature of hydrogen across a range of TCO materials, and while its stability and the role of interstitial versus substitutional species are still somewhat open questions, it is one of the leading contenders for yielding unintentional conductivity in TCOs. We also review recent work indicating that the surfaces of TCOs can support very high carrier densities, opposite to the case for conventional semiconductors. In thin-film materials/devices and, in particular, nanostructures, the surface can have a large impact on the total conductivity in TCOs. We discuss models that attempt to explain both the bulk and surface conductivity on the basis of bulk band structure features common across the TCOs, and compare these materials to other semiconductors. Finally, we briefly consider transparency in these materials, and its interplay with conductivity. Understanding this interplay, as well as the microscopic contenders for providing the conductivity of these materials, will prove essential to the future design and control of TCO semiconductors, and their implementation into novel multifunctional devices.
Synthesis of Retigabine Analogues for the Treatment of Tinnitus and Progress Towards a Concise Route to XJB-5-131 (2015)

The first part of this thesis describes the synthesis of retigabine analogues for the treatment of tinnitus. Retigabine is a clinically proven anticonvulsant that modulates potassium ion channel activity and has been shown to stop the onset of tinnitus when administered shortly after exposure to extreme levels of sound. Alteration of the fluorophenyl and carbamate functionalities present in the parent compound resulted in the synthesis of a small library of compounds with the goal of improving potency and selectivity for the Kv7.2/3 potassium ion channels. In vivo and in vitro testing is underway to determine efficacy. The second part of this thesis describes efforts to develop and improved route to XJB-5-131, a truncated Gramicidin S-derived peptide designed to control reactive oxygen species (ROS) production in mitochondria. A new route to XJB-5-131 was explored utilizing a stereoselective α-alkenylation protocol and starting from vinyl boronic acids.
A polymorphism of the complement regulatory protein MCP (membrane cofactor protein or gp45-70). (1987)

Membrane cofactor protein (MCP or gp45-70) is a recently described regulatory glycoprotein of the complement system which binds iC3 or C3b and is present on human platelets, T cells, B cells, monocytes, and mononuclear-derived cell lines. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, MCP migrates as a doublet with an Mr of the upper band of 63,000 and the lower band of 58,000. The same pattern was found on all cell populations in a given individual and was stable over time. In order to further characterize the two band pattern on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, MCP was isolated by affinity chromatography or immunoprecipitation from 72 healthy unrelated donors. All individuals expressed both bands and, based on the densitometric scanning of gels, three patterns were noted: upper band predominant in 65%, approximately equal distribution of upper and lower bands in 29%, and lower band predominant in 6%. These observed phenotypic frequencies fit with expectations based on Hardy-Weinberg equilibrium for a two-allele system. Family studies also support this model as none of the 26 offspring had a phenotype that deviated from the expected, assuming an autosomal codominant model of inheritance. These results are consistent with a simple two-allele system that controls the expression of the two bands of MCP.
A 5.6-GHz UWB Position Measurement System (2012)

This paper describes the design and realization of a 5.6-GHz ultrawide-bandwidth-based position measurement system. The system was entirely made using off-the-shelf components and achieves centimeter-level accuracy in an indoor environment. It is based on asynchronous modulated pulse round-trip time measurements. Both system level and realization details are described along with experimental results including estimates of measurement uncertainties.
APPENDIX 4 On-line C. elegans Resources (1997)

The wide use of the Internet and World Wide Web (WWW) in the scientific community and the corresponding rapid development of hypertext browser programs have made a bewildering array of on-line resources available for biological researchers. The tables and text on the following pages give brief descriptions and electronic addresses of several major Web sites providing access to information on C. elegans, categorized by general type of data. The sites listed here constitute a basic set of the major electronic C. elegans resources on the Web. Each site, customized by its keepers, may contain links to many other more specific resources such as specialized programs written by C. elegans researchers, data search engines, electronic versions of standard print materials (e.g., the Worm Breeder’s Gazette ), photographic images of worms, the Bionet C. elegans discussion group, and many others. Discovering the wealth of information that is now literally at one’s fingertips requires only standard computer hardware, a graphical link to the Internet, and a bit of time. ACeDB (a C. e legans database) has become the standard electronic mechanism for collection, linking, and display of data on C. elegans, as well as other organisms. The programmers make available by anonymous ftp the program source code; executable binaries for several common Unix, Macintosh, and Windows platforms; and raw data files. Updates to the data and program are published at these sites several times a year. The source code can be used to compile an executable system on computers for which precompiled binaries are not...
Measurement of endotoxin activity in critically ill patients using whole blood neutrophil dependent chemiluminescence (2002)

Endotoxaemia is associated with Gram-negative infection from any source, and with a diagnosis of sepsis and leukocytosis. These correlations were not apparent using the LAL method. The EAA may be a useful diagnostic tool for the investigation of invasive Gram-negative infection and incipient sepsis.
Windowed cross-correlation and peak picking for the analysis of variability in the association between behavioral time series. (2002)

Cross-correlation and most other longitudinal analyses assume that the association between 2 variables is stationary. Thus, a sample of occasions of measurement is expected to be representative of the association between variables regardless of the time of onset or number of occasions in the sample. The authors propose a method to analyze the association between 2 variables when the assumption of stationarity may not be warranted. The method results in estimates of both the strength of peak association and the time lag when the peak association occurred for a range of starting values of elapsed time from the beginning of an experiment.
Energy-Aware High-Performance Computing: Survey of State-of-the-Art Tools, Techniques, and Environments (2019)

The paper presents state of the art of energy-aware high-performance computing (HPC), in particular identification and classification of approaches by system and device types, optimization metrics, and energy/power control methods. System types include single device, clusters, grids, and clouds while considered device types include CPUs, GPUs, multiprocessor, and hybrid systems. Optimization goals include various combinations of metrics such as execution time, energy consumption, and temperature with consideration of imposed power limits. Control methods include scheduling, DVFS/DFS/DCT, power capping with programmatic APIs such as Intel RAPL, NVIDIA NVML, as well as application optimizations, and hybrid methods. We discuss tools and APIs for energy/power management as well as tools and environments for prediction and/or simulation of energy/power consumption in modern HPC systems. Finally, programming examples, i.e., applications and benchmarks used in particular works are discussed. Based on our review, we identified a set of open areas and important up-to-date problems concerning methods and tools for modern HPC systems allowing energy-aware processing.
Glycosylation of type?II collagen is of major importance for T cell tolerance and pathology in collagen-induced arthritis (2002)

Type II collagen (CII) is a candidate cartilage-specific autoantigen, which can become post-translationally modified by hydroxylation and glycosylation. T cell recognition of CII is essential for the development of murine collagen-induced arthritis (CIA) and also occurs in rheumatoid arthritis (RA). The common denominator of murine CIA and human RA is the presentation of an immunodominant CII-derived glycosylated peptide on murine Aq and human DR4 molecules, respectively. To investigate the importance of T cell recognition of glycosylated CII in CIA development after immunization with heterologous CII, we treated neonatal mice with different heterologous CII-peptides (non-modified, hydroxylated and galactosylated). Treatment with the galactosylated peptide (galactose at position 264) was superior in protecting mice from CIA. Protection was accompanied by a reduced antibody response to CII and by an impaired T cell response to the glycopeptide. To investigate the importance of glycopeptide recognition in an autologous CIA model, we treated MMC-transgenic mice, which express the heterologous CII epitope with a glutamic acid in position 266 in cartilage, with CII-peptides. Again, a strong vaccination potential of the glycopeptide was seen. Hence CII-glycopeptides may be the optimal choice of vaccination target in RA, since humans share the same epitope as the MMC mouse.
Induced static magnetic field by a cellular phone (2011)

Recent claims regarding the safety of cellular phones suggest that weak static magnetic fields are induced around the phone, and this field and its gradients may pose a health risk to the user. An experiment was conducted to measure the induced static magnetic field around a cellular phone. 65 μT variations and 18 μT/cm gradients were measured in the magnetic field at 6 cm from the phone. An analytical model is derived to explain the results. The influence that the measured magnetic fields may have on the user is beyond the scope of this research.
시론 : 성인 제1형 당뇨병 환자 관리 실태와 개선 방향 (2014)

Because of the low incidence of type 1 diabetes in Korea, some Korean patients with type 1 diabetes are still being treated like type 2 diabetes patients. In 2011, the national health insurance launched a reimbursement program for the use of blood glucose test strips in type 1 diabetes. The initiation of the reimbursement program could provide an opportunity to assess the national status of type 1 diabetes management. In this context, we will discuss the lessons from the studies involving major national type 1 diabetes registries and the results of recent studies on multiple daily in jection of insulin, continuous glucose monitoring, continuous subcutaneous insulin infusion, use of sensor-augmented insulin pumps, and the structure education program for patients with type 1 diabetes. (J Korean Diabetes 2014;15:1-6)
Ultra wide band pass filters (UWBPF) based on complementary split rings resonators (2005)

Abstract In this work, a new strategy for the design of microstrip filters with ultra‐wide bandwidths is proposed. This is based on the combination of square‐shaped complementary split‐ring resonators (CSRRs) etched in the ground plane and grounded stubs. Coupling between adjacent resonators is achieved by means of λ/4 lines, acting as impedance inverters. To illustrate the potentiality of the approach, a prototype device with 90% fractional bandwidth has been designed for operation at C‐band. The measured fractional bandwidth (87%), in‐band losses (<1.3 dB), and out‐of‐band rejection (>30 dB), obtained on a device scaled down in frequency, point out the high performance achievable with this design methodology. Moreover, the first frequency parasitic (spurious) does not appear up to three times the central filter frequency. Due to the small dimensions, wide bandwidths, and compatibility with planar circuit technology, it is believed that the approach presented in this work can be of actual interest to the design of filters for ultra‐wideband applications. © 2005 Wiley Periodicals, Inc. Microwave Opt Technol Lett 46: 283–286, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20966
A Survey of Soft-Error Mitigation Techniques for Non-Volatile Memories (2017)

Non-volatile memories (NVMs) offer superior density and energy characteristics compared to the conventional memories; however, NVMs suffer from severe reliability issues that can easily eclipse their energy efficiency advantages. In this paper, we survey architectural techniques for improving the soft-error reliability of NVMs, specifically PCM (phase change memory) and STT-RAM (spin transfer torque RAM). We focus on soft-errors, such as resistance drift and write disturbance, in PCM and read disturbance and write failures in STT-RAM. By classifying the research works based on key parameters, we highlight their similarities and distinctions. We hope that this survey will underline the crucial importance of addressing NVM reliability for ensuring their system integration and will be useful for researchers, computer architects and processor designers.
[Effect of L-DOPA administration on brain bioelectrical activity in hypothalamo-hypophyseal diseases]. (1978)

The influence of the L-DOPA preparation on the bioelectrical activity of the brain was studied in 15 patients with Itsenko-Cushing's disease and in 12 patients with diencephalic obesity. L-DOPA administration caused an increase of the theta-rhythm index in the anterior leads in comparison with the initial recording, although the periods of detection of this elevation differed in various patients. No changes of the character of the EEG recording during the test with L-DOPA in comparison with the background recording was revealed in the patients with Itsenko-Cushings disease.