gebhart/patrepeval huggingface dataset:
Human embryonic stem cell–derived hematopoietic cells are capable of engrafting primary as well as secondary fetal sheep recipients (2005)

The human/sheep xenograft model has proven valuable in assessing the in vivo hematopoietic activity of stem cells from a variety of fetal and postnatal human sources. CD34+/lineage- or CD34+/CD38- cells isolated from human embryonic stem cells (hESCs) differentiated on S17 feeder layer were transplanted by intraperitoneal injections into fetal sheep. Chimerism in primary transplants was established with polymerase chain reaction (PCR) and flow cytometry of bone marrow and peripheral blood samples. Whole bone marrow cells harvested from a primary recipient were transplanted into a secondary recipient. Chimerism was established as described before. This animal was stimulated with human GM-CSF, and an increase in human hematopoietic activity was noted by flow cytometry. Bone marrow aspirations cultured in methylcellulose generated colonies identified by PCR to be of human origin. We therefore conclude that hESCs are capable of generating hematopoietic cells that engraft primary recipients. These cells also fulfill the criteria for long-term engrafting hematopoietic stem cells as demonstrated by engraftment and differentiation in the secondary recipient.
Structural Homology-Based Drug Repurposing Approach for Targeting NSP12 SARS-CoV-2 (2022)

The severe acute respiratory syndrome coronavirus 2, also known as SARS-CoV-2, is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 has a highly conserved non-structural protein 12 (NSP-12) involved in RNA-dependent RNA polymerase (RdRp) activity. For the identification of potential inhibitors for NSP-12, computational approaches such as the identification of homologous proteins that have been previously targeted by FDA-approved antivirals can be employed. Herein, homologous proteins of NSP-12 were retrieved from Protein DataBank (PDB) and the evolutionary conserved sequence and structure similarity of the active site of the RdRp domain of NSP-12 was characterized. The identified homologous structures of NSP-12 belonged to four viral families: <i>Coronaviridae</i>, <i>Flaviviridae</i>, <i>Picornaviridae</i>, and <i>Caliciviridae</i>, and shared evolutionary conserved relationships. The multiple sequences and structural alignment of homologous structures showed highly conserved amino acid residues that were located at the active site of the RdRp domain of NSP-12. The conserved active site of the RdRp domain of NSP-12 was evaluated for binding affinity with the FDA-approved antivirals, i.e., Sofosbuvir and Dasabuvir in a molecular docking study. The molecular docking of Sofosbuvir and Dasabuvir with the active site that contains conserved motifs (motif A-G) of the RdRp domain of NSP-12 revealed significant binding affinity. Furthermore, MD simulation also inferred the potency of Sofosbuvir and Dasabuvir. In conclusion, targeting the active site of the RdRp domain of NSP-12 with Dasabuvir and Sofosbuvir might reduce viral replication and pathogenicity and could be further studied for the treatment of SARS-CoV-2.
Selection of the Truncation Lag in Structural VARs (or VECMs) with Long-Run Restrictions (2021)

authors examine the issue of lag-length selection in the context of a structural vector autoregression (VAR) and a vector error-correction model with long-run restrictions. First, they show that imposing long-run restrictions implies, in general, a moving-average (MA) component in the stationary multivariate representation. Then they examine the sensitivity of estimates of the permanent and transitory components to the selection of the lag length required in a VAR system to approximate this MA component. In summary, they find that using a lag structure that is too short can lead to a significant estimation bias of the permanent and transitory components. In addition, in comparing four different lag-selection criteria, they find that the Schwarz information criterion systematically underperforms relative to the other tests. More generally, as the order of the VAR that best approximates the data-generating process increases, the sequence-based tests (Wald, likelihood ratio) tend to provide more reliable results than the information-based tests (Akaike, Schwarz).
Unidirectional surface-acoustic-wave transducers with a ZnO film on glass substrate (1977)

A unidirectional surface-acoustic-wave transducer with a sputtered ZnO film on a glass substrate is presented, consisting of interdigital electrodes and a plate electrode on both sides of the film. Experiments are in good agreement with the equivalent-network approach, which is similar to Smith&apos;s networks for the normal interdigital transducer.
Computer aided design and analysis of standard IIR architectures — Part II (1982)

For pt.I see ibid., vol.3, no.4, p.2-6 (1981). The static equations are developed and integrated into a design and analysis software system. New state variable formulation for the Gray-Markel and wave filter are presented. Those state-variable forms provide the formulation for comprehensive filter design and analysis software package reported in part III.
Proteomic pipeline to identify age-related compositional and structural changes of the human dentin extracellular matrix (2020)

Abstract Objective Devise a pipeline to investigate the protein composition of the human root dentin extracellular matrix (ECM) from single individuals of different age cohorts. Design Individual cervical root dentin of sound human molars from two age brackets, young (18-25 years old; n=3) and old (75-85 years old; n=3), were cut and pulverized. Protein extraction and fractionation were completed by sequential demineralization with EDTA buffer, chaotropic extraction with guanidine hydrochloride, and urea. The resulting protein extracts of differential solubility were digested into peptides and peptides were analyzed by mass spectrometry. Data generated for this study are available via ProteomeXchange, identifier PXD018320. Results We found that protein extracts of different solubilities present distinct biochemical compositions. We further define the matrisome of young (48 proteins) and old (50 proteins) human root dentin and report the identification of compositional and structural differences in ECM proteins from young and old teeth. Conclusion Our study provides a rigorous pipeline, from sample preparation to data analysis, to investigate the ECM composition – or matrisome – of the dentin. This pipeline has the potential to lead to the discovery of biomarkers of tooth aging and health.
Time-dependency of edema-based assessment of area-at-risk in reperfused acute myocardial infarction (2011)

Methods Cardiac MR was used to investigate the development and persistence of edema volume increases in the acute postinfarct period using both T2-weighted STIR imaging and T2 maps. LAD instrumented canines (n=9) underwent three hours of no-flow ischemia followed by reperfusion and were studied [using Siemens 1.5 T Espree scanner] at five time points (before and during ischemia and 2, 5, 7 and 56 days post-reperfusion). Scan parameters for T2-STIR acquisitions were: TE=64ms, TR=2-3 R-R intervals, resolution=0.9x0.9x8.0mm 3 .T 2 maps were computed from multiple T2-prepared acquisitions with different preparation times (0, 24, and 55 ms) with spatial-resolution of 1.0x1.0x8.0mm 3 . Late-enhancement imaging confirmed LAD infarction. Areas of interest were determined as follows: For T2 maps - region with T2 values greater than 2SD from remote territories; and for T2-STIR images- regions exceeding 2SD of the signal intensity of the remote regions. Edema volume was computed as highlighted areas multiplied by imaging slice thickness. Percent volume of edema was computed relative to total myocardial volume. Results are reported as mean ± SEM for each time point. Results Percent volume of edema (Area-At-Risk) - T2 Maps: Pre-ischemia: 0.8±0.4%; Ischemia: 2.5±1.4%; Day 2: 18.3
Electromagnetic Thermography Nondestructive Evaluation: Physics-based Modeling and Pattern Mining (2016)

Electromagnetic mechanism of Joule heating and thermal conduction on conductive material characterization broadens their scope for implementation in real thermography based Nondestructive testing and evaluation (NDT&E) systems by imparting sensitivity, conformability and allowing fast and imaging detection, which is necessary for efficiency. The issue of automatic material evaluation has not been fully addressed by researchers and it marks a crucial first step to analyzing the structural health of the material, which in turn sheds light on understanding the production of the defects mechanisms. In this study, we bridge the gap between the physics world and mathematical modeling world. We generate physics-mathematical modeling and mining route in the spatial-, time-, frequency-, and sparse-pattern domains. This is a significant step towards realizing the deeper insight in electromagnetic thermography (EMT) and automatic defect identification. This renders the EMT a promising candidate for the highly efficient and yet flexible NDT&E.
Corticotectal Projections From the Premotor or Primary Motor Cortex After Cortical Lesion or Parkinsonian Symptoms in Adult Macaque Monkeys: A Pilot Tracing Study (2019)

The corticotectal projections, together with the corticobulbar (corticoreticular) projections, work in parallel with the corticospinal tract (CST) to influence motoneurons in the spinal cord both directly and indirectly <i>via</i> the brainstem descending pathways. The tectospinal tract (TST) originates in the deep layers of the superior colliculus. In the present study, we analyzed the corticotectal projections from two motor cortical areas, namely the premotor cortex (PM) and the primary motor cortex (M1) in eight macaque monkeys subjected to either a cortical lesion of the hand area in M1 (<i>n</i> = 4) or Parkinson's disease-like symptoms PD (<i>n</i> = 4). A subgroup of monkeys with cortical lesion was subjected to anti-Nogo-A antibody treatment whereas all PD monkeys were transplanted with Autologous Neural Cell Ecosystems (ANCEs). The anterograde tracer BDA was used to label the axonal boutons both <i>en passant</i> and <i>terminaux</i> in the ipsilateral superior colliculus. Individual axonal boutons were charted in the different layers of the superior colliculus. In intact animals, we previously observed that corticotectal projections were denser when originating from PM than from M1. In the present M1 lesioned monkeys, as compared to intact ones the corticotectal projection originating from PM was decreased when treated with anti-Nogo-A antibody but not in untreated monkeys. In PD-like symptoms' monkeys, on the other hand, there was no consistent change affecting the corticotectal projection as compared to intact monkeys. The present pilot study overall suggests that the corticotectal projection is less affected by M1 lesion or PD symptoms than the corticoreticular projection previously reported in the same animals.
Analysis on Threshold Energy of Particle Removal in Spray Cleaning Technology (2011)

In the manufacturing of semiconductor devices, the reduction in the physical strength of device structures due to scaling has caused the problem of pattern collapse by the physical force required for removing particles. A novel advanced spray technology has been developed to accurately and tightly control the droplet size and velocity. The influence of droplet characteristics on particle removal was quantitatively investigated using this technology. It was observed that the amount of removed particles was linked to the droplet energy density on the wafer. The threshold energy to remove particles was analyzed and the relationship between particle removal and pattern damage generation was determined. Finally the process window, which is a particle removable area without pattern collapse, was clearly revealed by the gap between the particle removal and the damage threshold curves.
PPARγ agonists attenuate PGE2 via 15-PGDH induction in human non-small cell lung cancer (2005)

4958 Lung cancer cells elaborate immunosuppressive and anti-apoptotic mediators such as Prostaglandin E 2 (PGE2). COX-2 is the rate-limiting enzyme for the production PGE2. In humans, peroxisome proliferator-activated receptor gamma (PPARγ) is expressed in multiple tissues, including the breast, colon, lung, ovary, and placenta. PPARγ ligands such as thiazolidinediones (TZDs) have been recently shown to inhibit lung cancer cell growth. Here we examined the effect of thiazolidinediones (pioglitazone and rosiglitazone) on PGE2 levels in non-small cell cancer cell lines (NSCLC) such as A427 and A549 lines. 24-hour treatment with either pioglitatzone (10uM) or rosiglitazone (10uM) in serum free medium inhibits PGE2 release in both A427 and A549 lung adenocarcinoma cell lines. However, a 24-hour treatment with TZDs (10uM) in serum free medium do not suppress COX-2 expression in both cell lines. Because PPARγ ligands have the capacity to act via PPARγ independent pathways, we determined whether the suppressive effect of both pioglitazone and rosiglitazone are PPARγ dependent. By overexpressing a dominant negative PPARγ via transfection in NSCLC, we found that the suppressive effect of the PPARγ ligands on PGE2 is PPARγ independent. In order to understand the mechanism underlying COX-2 independent suppression of PGE2 by TZDs, we performed experiments to address the downstream events that regulate PGE2. We first assessed the PGE synthase activity, which makes PGE2 from its precursor PGH2. We demonstrated that PGE synthase activity is not altered by either TZD. Next, we examined whether pioglitazone and rosiglitazone can regulate biological inactivation of PGE2. The first step of metabolism of prostaglandins is catalyzed by 15-PGDH enzyme, which produces biologically inactive 15-keto-prostaglandins from active PGE2. Western blot analysis of this enzyme using 15-PGDH antibody reveals that 24-hour treatment of both TZDs (10uM) increase 15-PGDH protein expression in both A427 and A549 cell lines. The enzyme activity was assayed by measuring the transfer of tritium from 15(S)-[15-3H]-PGE2 to glutamate by coupling 15-PGDH with glutamate dehydrogenase. We found that the pioglitazone treatment significantly and rosiglitazone treatment moderately increase the 15-PGDH activity in NSCLC. Because both pioglitazone and rosiglitazone fail to inhibit COX-2 while inhibiting PGE2 production, they bypass the potential overproduction of pulmonary leukotrienes, some of which may be inducers of tumor progression. This new understanding will allow the foundation for the future development of drugs that may directly inhibit PGE2 levels in NSCLC. (Supported by the UCLA Lung Cancer SPORE-P50CA90388)
A DDA Octree Traversal Algorithm for Ray Tracing (1991)

A spatial traversal algorithm for ray tracing that combines the memory efficiency of an octree and the traversal speed of a uniform voxel space is described. A new octree representation is proposed and an implementation of the algorithm based on that representation is presented. Performance of the implementation and other spatial structure traversal algorithms are examined.
A Meta-Analysis of Transcutaneous Electrical Nerve Stimulation for Chronic Low Back Pain. (2016)

Treatment of chronic low back pain with TENS demonstrated significant pain reduction. The application of TENS may lead to less pain medication usage and should be incorporated into the treatment armamentarium for chronic low back pain.
IC‐P‐017: AMYLOID PET IS MORE THAN JUST POSITIVE OR NEGATIVE: AMYLOID LEVEL IMPACTS RISK OF CLINICAL PROGRESSION IN NORMAL INDIVIDUALS (2019)

Ab-amyloid (Ab) PET positivity is an important predictor of clinical progression. However, the level of Ab deposition likely provides additional prognostic information over a binary report. We aimed to determine the effect of Abburden on the progression risk to MCI or dementia in cognitively normal (CN) individuals and its longitudinal association with change in cognition. We included 447 CN (age 72±6 years) from the AIBL study with ≥3 years follow-up. Abburden was expressed in Centiloids (CL) and divided into five categories: <15 CL negative, 15–25 CL uncertain, 26–50 CL moderate, 51–100 CL high, >100 CL very high. Cox proportional hazards analysis and linear mixed effect models were used to assess risk of clinical progression to MCI or dementia and to examine association between Ab burden and change in cognition. At baseline, 64% individuals were negative, 9% uncertain, 9% moderate, 14% high and 3% very high for Abburden. Forty-six individuals progressed to MCI or dementia during follow-up (mean±SD 71±27 months). An Ab burden greater than 50 CL significantly increased the risk of progression (Table 1) and was also associated with the greatest decline in AIBL PACC (Figure 1, PreAD Cognitive Composite) score during follow-up (negative 0.010 SD/yr, p=0.84; uncertain 0.073, p=0.65; moderate −0.237, p=0.10; high −0.449, p<0.001; very high −1.654, p<0.001).
The Effect of Coal Drying on the Behaviour of Alkali and Alkaline Earth Metallic Species during Victorian Brown Coal Combustion (2010)

The purpose of this work was to determine whether coal pre-drying will affect the behaviour of alkali and alkaline earth metallic (AAEM) species during combustion. A drop tube furnace was used to generate chars and ashes from both wet and dry coal. Raw coal, char and ash were then analysed for the presence of AAEM species (i.e. Na, Mg, Ca, K) using x-ray fluorescence (XRF), x-ray diffraction (XRD) and scanning electron microscopy with energy dispersive spectroscopy (SEM/EDX). Experimental results were complemented with FACTSage, an equilibrium modelling package. The pyrolysis rate was found to be the same for both dry and wet coal. The major AAEM species present in the coal sample investigated were found to be Mg and Na. Na was found to volatilise significantly, while Mg was not. The major components of the ash produced were MgO, NaCl and, at lower furnace temperatures, Na2SO4. The char contained organically-bound Cl and Na, as well as MgO and NaCl, and small amounts of S, Ca, Al and Si. There were no discernible differences between the composition of chars and ashes formed from the combustion of dry and wet coal. Any differences are likely to be caused by the fact that the furnace temperature will be increased if pre-dried coal is used as a feed stock. The use of pre-dried coal in an industrial boiler could increase slag formation, but studies at higher furnace temperatures would be required to confirm this.
Plasma-Enhanced Chemical Vapor Deposition of n-Heptane and Methyl Methacrylate for Potential Cell Alignment Applications (2012)

Plasma-enhanced chemical vapor deposited polymers (plasma polymers) are promising candidates for biomaterials applications. In the present study, plasma deposition as a fast and easily scalable method was adapted to deposit coatings from n-heptane and methyl methacrylate monomers onto glass substrates. Linear patterns with line and groove widths between 1.25 and 160 μm were introduced by degrative UV-lithography for cell alignment. Differential interference contrast optical microscopy, profilometry and atomic force microscopy revealed that the patterned surfaces had a smooth, homogeneous appearance and a pattern height of 8 and 45 nm for plasma deposited n-heptane and methyl methacrylate, respectively. UV-lithography increased the oxygen content on the surface drastically as shown by X-ray photoelectron spectroscopy. After immersion in simulated body fluid for 21 days, the pattern was still intact, and the ester groups were also maintained for the most part as shown by infrared spectroscopy. To test the coatings' potential applicability for biomaterial surfaces in a preliminary experiment, we cultured murine preosteoblastic MC3T3-E1 cells on these coatings. Light and electron microscopically, a normal spindle-shaped and aligned cell morphology was observed. At the mRNA level, cells showed no signs of diminished proliferation or elevated expression of apoptosis markers. In conclusion, plasma-enhanced chemical vapor deposited polymers can be patterned with a fast and feasible method and might be suitable materials to guide cell alignment.
A Secreted Aminopeptidase of Pseudomonas aeruginosa (2001)

Using leucine-p-nitroanilide (Leu-pNA) as a substrate, we demonstrated aminopeptidase activity in the culture filtrates of several Pseudomonas aeruginosa strains. The aminopeptidase was partially purified by DEAE-cellulose chromatography and found to be heat stable. The apparent molecular mass of the enzyme was approximately 56 kDa; hence, it was designated AP(56). Heating (70 degrees C) of the partially purified aminopeptidase preparations led to the conversion of AP(56) to a approximately 28-kDa protein (AP(28)) that retained enzyme activity, a reaction that depended on elastase (LasB). The pH optimum for Leu-pNA hydrolysis by AP(28) was 8.5. This activity was inhibited by Zn chelators but not by inhibitors of serine- or thiol-proteases, suggesting that AP(28) is a Zn-dependent enzyme. Of several amino acid p-nitroanilide derivatives examined, Leu-pNA was the preferred substrate. The sequences of the first 20 residues of AP(56) and AP(28) were determined. A search of the P. aeruginosa genomic data base revealed a perfect match of these sequences with positions 39-58 and 273-291, respectively, in a 536-amino acid residue open reading frame predicted to encode an aminopeptidase. A search for sequence similarities with other proteins revealed 52% identity with Streptomyces griseus aminopeptidase, approximately 35% identity with Saccharomyces cerevisiae aminopeptidase Y and a hypothetical aminopeptidase from Bacillus subtilis, and 29-32% with Aeromonas caviae, Vibrio proteolyticus, and Vibrio cholerae aminopeptidases. The residues potentially involved in zinc coordination were conserved in all these proteins. Thus, P. aeruginosa aminopeptidase may belong to the same family (M28) of metalloproteases.
Nowe techniki przetwarzania i interpretacji danych sejsmicznych w zastosowaniu do określenia szcze- gółowej budowy złoża ropy Radoszyn (2001)

Artykul dokumentuje wyniki bardzo szczegolowych studiow i analiz materialow sejsmicznych i wybranych profilowan geofizycznych w otworach, ukierunkowanych na wyjaśnienie architektury facjalnej zloza ropy naftowej Radoszyn, a wiec w pewnym sensie na udokumentowanie przydatności metody sejsmicznej do rozwiązywania bardzo szczegolowych problemow geologicznych. Pozytywne wyniki badan przypisac nalezy przede wszystkim poszerzonemu specjalistycznemu przetwarzaniu sekcji sejsmicznych, a szczegolnie transformacji fazowej i standaryzacji widma czestotliwości oraz interaktywnie prowadzonemu modelowaniu sejsmicznemu, wspomagającemu optymalizacje modelu geometryczno-predkościowego.

THE NEW TECHNOLOGY IN PROCESSING AND INTERPRETATION OF SEISMIC DATA APPLIED TO THE DESCRIPTION OF THE RADOSZYN OIL FIELD (WESTERN POLAND)

Summary 
This paper presents the results of very detailed studies and analyses of seismic data and selected borehole loggings. The principal purpose of these studies was to explain the facies distribution pattern of the Radoszyn oil field. In some measure, they were to confirm the usefulness of seismic methods for solving detailed geological problems. The positive results of these studies should be attributed primarily to the broadened specialist processing of seismic sections, especially to the phasic transformation and frequency spectrum standardization, as well as the interactive seismic modeling aiding the geometrical-velocity model optimization