gebhart/patrepeval huggingface dataset:
Structure of the murine macrophage scavenger receptor gene and evaluation of sequences that regulate expression in the macrophage cell line, P388D. (1995)

The structure of the entire murine scavenger receptor gene was determined; it consists of eleven exons spanning more than 60 kilobases. Primer extension showed that transcription initiates at a cluster of sites unassociated with a TATAA element. DNA sequences adjacent to these transcription start sites are highly conserved in murine, human, and bovine genes. When transcriptional activity was tested using a luciferase reporter gene, a promoter fragment (-124 to +20) stimulated luciferase production in P388D1 macrophage-like cells but not in non-macrophage COS-7 or 3T3 cells. A longer promoter fragment (approximately 5 kb) stimulated luciferase activity a further 10-fold in P388D1 cells. However, using a series of fragments from -67 to -1500 bp, a 127 bp fragment (-67 to +50) was as active as a 1500 bp fragment in these assays. Mutation of a putative AP-1 element in the -67 to +50 promoter fragment reduced luciferase activity by 40%; mutation of a putative GATA factor element to TATA increased luciferase activity nearly 2-fold while mutation to AATA had no effect and deletion of the GATA sequence inhibited activity by about 50%. The results suggest that a scavenger receptor promoter fragment can confer cell-specific transcription and that the activity may be mediated in part by factors that recognize the AP-1 and GATA elements.
Fetal Rat Pancreas: Differentiation of the Islet Cell Component in Vivo and in Vitro (1973)

Fetal rat pancreases, Day 16 through Day 22 postcoitum, were analyzed by immunoassay for insulin to assess islet cell development in vivo. The rise in pancreatic insulin concentration observed during gestation was relatively constant, amounting to 50 to 100 per cent per day, and was accompanied by increases in the total islet mass of the pancreas. A difference was found in the potential of the pancreas for islet differentiation in organ culture which was related to the developmental state of the pancreas at the time of explantation. Highly differentiated islets of twenty-two day fetal pancreas were maintained in organ culture, while large increases in the islet mass occurred following organ culture of relatively undifferentiated eighteen day fetal pancreas. Using the present organ culture system, explants can be produced which are composed of 25 per cent islet cells and contain 17 mU. of insulin activity per milligram.
The Outcomes of Primary Scleral Buckling during Repair of Posterior Segment Open-Globe Injuries (2014)

PSB procedure during posterior segment OGI repair may decrease the risk of subsequent retinal complications and improve final visual outcome.
<i>Lps2</i>and Signal Transduction in Sepsis: At the Intersection of Host Responses to Bacteria and Viruses (2003)

A phenotype-driven approach led to the first understanding of precisely what the Toll-like receptors (TLR) did, when it was determined that the mammalian endotoxin (lipopolysaccharide; LPS) receptor is encoded by TLR4. The TLRs are the primary sensors of the innate immune system, and without them, small inocula of microorganisms pose a major threat to the host, growing unchecked for a long period before they are recognized. Mutations that affect innate immune sensing may account for a substantial fraction of sepsis, and a highly significant excess of mutations in TLR4 has been identified in patients with systemic meningococcal disease. As such, it is important to understand the pathways that are responsible for innate immune sensing, including the signaling intermediates utilized by the TLRs. Random germline mutagenesis identified a locus, Lps2, which is required for normal responses to double-stranded RNA and LPS. Hence, a single transducer was found to serve both the TLR3 and TLR4 response pathways. The Lps2 mutation was found to ablate entirely the MyD88-independent pathway for LPS sensing, indicating that two and only two branches of the LPS sensing pathway exist in macrophages, and homozygotes for the mutation were resistant to LPS, but markedly susceptible to infection with mouse cytomegalovirus. Remarkably, Lps2 mutant mice entirely failed to produce type I interferons in response to a viral infection. It would appear that Lps2 is the most proximal component of a signal integration system required for innate immune responses to both viral and bacterial diseases. Positional cloning revealed that the TIR adapter protein Trif/Ticam-1 is structurally altered by the Lps2 mutation. This adapter is responsible for shared effects of responses to viral and bacterial pathogens.
CO/sub 2/ laser performance with a distributed gold catalyst (1989)

The performance of a CO/sub 2/ laser was improved by coating the inside wall of the discharge tube with a discontinuous gold film. In the presence of the discharge, the gold acts as an ambient temperature catalyst to reform decomposed CO/sub 2/. The gold coated laser delivered 122 W/m for both sealed-off and flowing operation. CO/sub 2/ decomposition levels are presented as a function of input power, gas pressure, and temperature. Atomic oxygen, generated by the discharge, appears to be required for gold to exhibit any detectable catalytic activity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
iReplayer: in-situ and identical record-and-replay for multithreaded applications (2018)

Reproducing executions of multithreaded programs is very challenging due to many intrinsic and external non-deterministic factors. Existing RnR systems achieve significant progress in terms of performance overhead, but none targets the in-situ setting, in which replay occurs within the same process as the recording process. Also, most existing work cannot achieve identical replay, which may prevent the reproduction of some errors. This paper presents iReplayer, which aims to identically replay multithreaded programs in the original process (under the "in-situ" setting). The novel in-situ and identical replay of iReplayer makes it more likely to reproduce errors, and allows it to directly employ debugging mechanisms (e.g. watchpoints) to aid failure diagnosis. Currently, iReplayer only incurs 3% performance overhead on average, which allows it to be always enabled in the production environment. iReplayer enables a range of possibilities, and this paper presents three examples: two automatic tools for detecting buffer overflows and use-after-free bugs, and one interactive debugging tool that is integrated with GDB.
Evaluation of the Tenax trap in the Sample Analysis at Mars instrument suite on the Curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater (2015)

Abstract The Sample Analysis at Mars (SAM) instrument suite aboard Curiosity has detected chlorinated organic compounds in Martian sediment samples. The chlorine in these molecules is thought to derive from oxychlorine salts in Martian sediments, but the carbon source remains under investigation. To constrain possible carbon sources, we investigated how the composition and concentration of oxychlorine phases in solid samples affect organic molecules released from the Tenax traps on board SAM. We created Mars analogue soils by spiking olivine sand with calcium perchlorate, magnesium perchlorate, or ferric iron chloride and analyzed the volatiles generated during pyrolysis–gas chromatography–mass spectrometry using commercial instruments operated under SAM‐like conditions, with and without a Tenax trap. Benzoic acid, phthalic anhydride, high molecular weight aromatics, and chlorobenzenes are produced from the trap in response to volatiles released during Cl salt pyrolysis. Changes in composition or concentration of oxychlorine phases between samples could thus potentially produce an increase in chlorobenzene, as observed between samples from Rocknest and Cumberland. However, in our experiments benzoic acid, phthalic anhydride, and chlorobenzenes increase in proportion with the amount of HCl sent to the trap, while in Cumberland samples the chlorobenzene increase showed no corresponding increase in HCl. Based on our experiments, the Tenax trap is a possible source of the traces of chlorobenzene observed at Rocknest, John Klein, and Confidence Hills. The order‐of‐magnitude higher chlorobenzene abundances observed at Cumberland cannot be attributed to the Tenax trap. Furthermore, we found no evidence of significant trap degradation after hundreds of experiments with Cl salt‐containing analogue soils.
Validation of an RNA cell cycle progression (CCP) score for predicting prostate cancer death in a conservatively managed needle biopsy cohort. (2014)

5059 Background: The natural history of prostate cancer is highly variable and difficult to predict accurately. Better markers are needed to guide management and avoid unnecessary treatment. To validate the predictive value of a cell cycle progression (CCP) score and a pre-specified linear combination of the CCP score with standard clinical variables (CAPRA) to form a combined clinical cell cycle risk (CCR) score for predicting prostate cancer death in a cohort of conservatively managed patients diagnosed by needle biopsy. Methods: A retrospective cohort study of 585 men diagnosed by needle biopsy in the UK from 1990-2003 using UK cancer registry data - supplemented by hospital records and histopathology review of diagnostic needle biopsies. The primary endpoint was prostate cancer death. Clinical variables consisted of centrally reviewed Gleason score, baseline PSA, age, clinical stage, and extent of disease. These were combined into a single predefined risk assessment (CAPRA) score. Results: In univariate analysis, the CCP score hazard ratio (HR) was 2.08 (95% CI (1.76, 2.46), P < 10-13) for a one unit change of the score and in a bivariate analysis including CAPRA, the CCP score HR was only marginally decreased (HR=1.76, 95% CI (1.44, 2.14)), and remained highly significant (P < 10-6). The predefined CCR score combining CCP and CAPRA was highly predictive (HR = 2.17; 95% CI (1.8, 2.6), χ ² = 89.0, P < 10-20) and captured all available prognostic information. The predictive value of the CCP score was maintained for 10 years, and there was no significant interaction with other prognostic factors. CAPRA identified 80 men (13.7%) in the low risk group (0-2) and they had a 10y prostate cancer mortality of 4.3%. CCR indicated 19 (3.2%) of these men had a higher risk, but identified a further 31 (5.3%) men with CAPRA > 2, but with a risk < 4.3% using the combined score. Conclusions: The CCP score provides substantially more significant pre-treatment prognostic information than available from clinical variables and is useful for determining which patients can be safely managed by a conservative policy avoiding radical treatment.
Ion-Exchange Properties of Li Ion Conductor, LiTixZr2−x(PO4)3 (1992)

Abstract The NASICON-type compounds, HTixZr2−x(PO4)3 [0 ≤ x ≤ 2] were prepared by acid treatments of Li+-introduced titanium-zirconium triphosphates. Their ion-exchange properties were investigated by measuring metal ion adsorption from buffer solution of pH 8.1. The materials, HTixZr2−x(PO4)3 with x = 1.5 and x = 2 showed extremely high selectivity for Na+, as compared to Li+.
OC12.04: Cortical development is correlated with neurodevelopmental outcome at 6 months in fetuses with isolated non‐severe ventriculomegaly (2017)

Differences in cortical development have been described in fetuses with isolated non-severe ventriculomegaly (INSVM). However, correlation with altered neurodevelopment has poorly evaluated. The objective of this study was to analyse whether cortical development in fetuses with INSVM was correlated with poorer neurodevelopment. We prospectively included 32 controls and 37 fetuses with INSVM defined as atrial width between 10.0 and 14.9mm. Fetuses with associated malformation, infection or abnormal microarray were excluded. Cortical development was assessed by neurosonography at 30w applying a scale of maturation from 0 (not visible) and 5 (maximally developed). Neurobehavioral outcome was assessed at 6 months using the Ages and Stages Questionnaire (ASQ). Mean gestational age at US was 30.4±0.6w. Mean ventricular width in INSVM group was 10.7±1.1mm. Overall INSVM have less developed sulci, especially bilateral cases (see table 1). ASQ showed significant differences in INSVM group with worse performance in all areas with significance in problem solving (54.8±6.9 vs. 50.0±9.8, p:0.02). This weaker performance was significantly correlated with right frontal (R=0.52, p=0.04) and right parietal (R=0.40, p=0.05) area grading. Supporting information can be found in the online version of this abstract Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Use of bromovirus RNA3 hybrids to study template specificity in viral RNA amplification (1991)

Brome mosaic virus (BMV) and cowpea chlorotic mottle virus (CCMV) are related positive-strand RNA viruses with genomes divided among RNAs 1, 2, and 3. RNAs 1 and 2 encode the viral RNA replication factors, which share extensive conservation with proteins encoded by the animal alphaviruses and diverse plant viruses. In barley protoplasts, CCMV RNAs 1 and 2 support high but distinguishable amplification of either BMV RNA3 (B3) or CCMV RNA3 (C3), while BMV RNAs 1 and 2 show even greater discrimination, amplifying C3 poorly relative to B3. To identify the cis-acting determinants of these template-specific and virus-specific differences in RNA3 accumulation, we constructed and tested a series of B3/C3 hybrids that exchange in turn the 5',3', and intercistronic noncoding regions, which contain all sequences required in cis for efficient B3 and C3 amplification. Despite suggestive prior in vitro results, the 3' noncoding regions were not the major determinant of the differences in amplification of B3 and C3 in vivo. Rather, 3' exchanges had relatively modest effects and did not transfer the distinctive asymmetry of amplification between B3 and C3. Intercistronic exchanges produced larger effects on RNA3 accumulation and transferred some of the polarized characteristics of the wild-type B3 and C3 behaviors. 5' exchanges revealed context-specific effects showing that the contribution of the B3 5' region to RNA3 amplification is dependent on some other B3 segment or segments. Together with previous results implicating the BMV and CCMV 1a genes in trans-acting discrimination between B3 and C3 (P. Traynor and P. Ahlquist, J. Virol. 64:69-77, 1990), these observations should help to guide studies of protein-RNA interactions governing template specificity in bromovirus RNA replication.
Memory-centric motion estimator (2005)

In the streaming video processing domain, the only way to meet strict performance and quality requirements and yet to provide the area- and power-wise optimal platform is to apply buffering of the pixel data. Hence, the importance of careful design of the memory subsystem of streaming video SoC is significant. This paper presents the design of a memory subsystem of the high-performance motion estimation processor. The motion estimator is a VLIW-based application specific instruction-set processor (ASIP). Through the reorganization of the pixels within the buffer and taking into account physical features of the instantiated memory banks, the buffer performance is improved by a factor of four compared to earlier designs. We further improve the buffer performance by a factor of two through algorithmic modification. The algorithmic modification does not impair the quality which we demonstrate through evaluation on a set of video sequences.
Low-loss broadband multimode corrugated waveguide performance (1990)

A 30-m-long waveguide run using circular corrugated waveguide (i.d.=6.35 cm) with a corrugated period and depth of 254 μm (0.01 in.) has been fabricated and installed on TFTR (Tokamak Fusion Test Reactor) for use in electron cyclotron emission measurements, and is the first large scale application of this type of waveguide. It is designed for low-loss (&lt;0.01 dB/m) multimode operation between 75 and 575 GHz, and includes three E-plane and four H-plane miter bends. Single-mode measurements at 140 GHz and multimode measurements at 250 GHz indicate that both ohmic losses as well as loss due to mode conversion are negligible with this type of transmission line.
Reversible wafer bonding for reliable compound semiconductor processing (2003)

Reversible wafer bonding is a process enabling reliable compound semiconductor wafer handling for multi-step processes including photolithography, thinning, etching or coating. Two processes using wax and dry film adhesives are presented in this paper.
Sliding Wear and Corrosion Resistance of Copper-based Overhead Catenary for Traction Systems (2010)

In the present study, the electrical sliding wear and corrosion resistance of pure copper (Cu) and six age-hardened copper alloys (CuCr, CuZr, CuCrZr, CuNiSiCr, CuBe and CuBeNi) were investigated by a pin-on-disc tribometer and electrochemical measurement. Various copper-based alloys in the form of cylindrical pin were forced to slide against a counterface stainless steel disc in air under unlubricated condition at a sliding velocity of 31 km/h under normal load up to 20 N with and without electric current. The worn surface of and wear debris from the specimens were studied by scanning electron microscopy. Both mechanical wear and electrical arc erosion were the wear mechanisms for the alloys worn at 50 A. Owing to its good electrical conductivity, high wear and corrosion resistance, CuCrZr is a promising candidate as the overhead catenary material for electric traction systems.
ChemInform Abstract: Synthesis of Thiooxamates from t‐Butyl Sulfinamoylacetates. Occurence of a New Rearrangement Involving a Thione S‐Imide Intermediate. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Therapeutic Potential of AICAR in Attenuating Obesity‐Induced Metabolic, Liver and Kidney Disease (2016)

Study Objective Obesity is a risk factor for organ inflammation, diabetes, and kidney disease. Here we evaluated the therapeutic potential of AICAR (an AMPK activator) in obesity‐induced metabolic, kidney and liver disease with High‐Fat‐Diet (HFD) in wild type and adiponectin‐deficient mice. We also correlate our findings to human pathophysiology, by examining human tissue responses to AICAR ex vivo in a proof of concept study. Method Male C57BL/6 or Adiponectin−/− mice were fed a standard (10% fat) or HFD (60% fat) diet for 12 wks. HFD induced obesity and CKD, as evident by increased albuminuria. Vehicle or AICAR (500 mg/g) was given intraperitoneal as interventional therapeutics 3 times weekly, between wk 5–12. Furthermore, omental adipose tissue biopsies were isolated from obese (BMI 35–50), non‐diabetic female bariatric surgery patients (n=4). The adipose explants were incubated ex vivo with vehicle or AICAR (1 mM) for 6 hours at 37 °C, after which leukocytes were characterized by flow cytometry. Results Interventional AICAR treatment protected against obesity‐induced kidney disease, liver steatosis and improved insulin sensitivity in mice. Adipose inflammation is a key driver of obesity‐induced pathophysiology. AICAR attenuated adipose inflammation, by shifting MΦ phenotype from pro‐inflammatory M1 (CD11c + ) to anti‐inflammatory M2 (CD206 + ), while reducing the percentage of CD8 + T‐cells, which correlated with reduced TNF‐α production and increasing adipose pAMPK levels. Interestingly, AICAR reduced interstitial adipose fibrosis, but enhanced omental capsular fibrosis. AICAR‐mediated protection was adiponectin independent, as protection was observed in both obese wild‐type and adiponectin −/− mice. In omental adipose tissue explants isolated from obese patients, AICAR promoted a ‘pro‐inflammatory’ to ‘anti‐inflammatory’ MΦ phenotype switch, which correlated with a reduction in TNF‐α. Conclusion In conclusion, these data support a novel therapeutic paradigm for using AICAR to promote metabolic health and protect against obesity‐induced systemic pathophysiology, e.g. liver and kidney disease. Support or Funding Information Financial support was obtained from the National Institute of Health and Science Foundation Ireland, and EB is a recipient of grants from the Marie Curie International Outgoing fellowship (IOF‐GA‐2011‐301803) and the Swedish Research Council.
Dach2-Hdac9 signaling regulates reinnervation of muscle endplates (2015)

Muscle denervation resulting from injury, disease or aging results in impaired motor function. Restoring neuromuscular communication requires axonal regrowth and endplate reinnervation. Muscle activity inhibits the reinnervation of denervated muscle. The mechanism by which muscle activity regulates muscle reinnervation is poorly understood. Dach2 and Hdac9 are activity-regulated transcriptional co-repressors that are highly expressed in innervated muscle and suppressed following muscle denervation. Dach2 and Hdac9 control the expression of endplate-associated genes such as those encoding nicotinic acetylcholine receptors (nAChRs). Here we tested the idea that Dach2 and Hdac9 mediate the effects of muscle activity on muscle reinnervation. Dach2 and Hdac9 were found to act in a collaborative fashion to inhibit reinnervation of denervated mouse skeletal muscle and appear to act, at least in part, by inhibiting denervation-dependent induction of Myog and Gdf5 gene expression. Although Dach2 and Hdac9 inhibit Myog and Gdf5 mRNA expression, Myog does not regulate Gdf5 transcription. Thus, Myog and Gdf5 appear to stimulate muscle reinnervation through parallel pathways. These studies suggest that manipulating the Dach2-Hdac9 signaling system, and Gdf5 in particular, might be a good approach for enhancing motor function in instances where neuromuscular communication has been disrupted.
BioMEMS and Micro-/Nano-Processing of Polymers- An Overview (2003)

The miniaturization of biomedical and biochemical devices for micro-electromechanical systems (BioMEMS) has gained a great deal of attention in recent years. Products include biochips/biosensors, drug delivery devices, tissue scaffolds, and bioreactors, In the past MEMS devices have been fabricated almost exclusively in silicon, glass or quartz because of the similar technology available in the microelectronics industry. For applications in the biochemistry and biomedical field, polymeric material are a desirable choice because of their lower cost, good processibility, and biocompatibility. Polymer micro-/nanofabrication techniques, however, are still not well developed. In this paper, we briefly introduce various BioMEMS applications, basic microfluidic principles and functions, and processing techniques for micro-/nano-scale structures.