gebhart/patrepeval huggingface dataset:
Detection of a homozygous four base pair deletion in the protein X gene in a case of pyruvate dehydrogenase complex deficiency (1998)

While the presence of a lipoyl-containing protein (protein X) separate from lipoyl transacetylase in the pyruvate dehydrogenase complex (PDC) has been known for some time, until recently only the cDNA for the yeast enzyme has been cloned. We have cloned, sequenced and characterized the cDNA encoding the human protein X and localized the protein X gene to chromosome 11p13. We also report here a new case of protein X deficiency identified immunologically, with decreased activity of PDC and without mutations in the E1alpha subunit or E1beta subunit. We report that the cDNA and gene of this patient for protein X has a homozygous 4 bp deletion, specifically in the putative mitochondrial targeting signal sequence which results in a premature stop codon. This is the first documented case of a molecular defect in pyruvate dehydrogenase protein X.
Boundary-sampled halfspaces (2021)

We present a novel representation of solid models for shape design. Like Constructive Solid Geometry (CSG), the solid shape is constructed from a set of halfspaces without the need for an explicit boundary structure. Instead of using Boolean expressions as in CSG, the shape is defined by sparsely placed samples on the boundary of each halfspace. This representation, called Boundary-Sampled Halfspaces (BSH), affords greater agility and expressiveness than CSG while simplifying the reverse engineering process. We discuss theoretical properties of the representation and present practical algorithms for boundary extraction and conversion from other representations. Our algorithms are demonstrated on both 2D and 3D examples.
A Smartphone-based Microplate Reader for Point-of-Care ELISA Quantification (2016)

We designed a hand-held and cost-effective smartphone-based microplate reader for quantification of colorimetric ELISA tests. This mobile-device, combined with machine learning, achieved >99% accuracy for the measurement of mumps, measles, and herpes-simplex-virus IgG ELISA tests.
Synthesis of Polynitrocubanes. (1987)

Abstract : The objective of this research is to prepare polynitrocubanes for possible application as either explosives or propellants. During this reporting period, we have explored the synthesis of fluorodinitroethyl and trinitroethyl substituted cubane esters and amines. This work has led to the synthesis of the first cubane with more than two nitro groups. One of the highlights of this research is the synthesis of tetrakis (fluorodinitroethyl)-1,2,4,7-cubanetetracarboxylate, the first cubane explosive that is balanced to carbon monoxide water, nitrogen and hydrogen fluoride. This is an exciting advance because tetrakis (fluorodinitroethyl)-1,2,4,7-cubanetetracarboxylate is quite thermally stable. A second interesting cubane is N-nitro-N'-nitroso-bis(N,N'-fluorodinitroethyl)-1,4-diamino-cubane, a very interesting derivative of diamino-cubane that will be discussed later in this report. Work over the past year has resulted in: Synthesis of several highly nitrated cubanes; Synthesis of other tetrasubstituted energetic cubanes; and Several advances in cubane methodology have been made. To meet the ultimate goal of synthesis of polynitrocubanes, we are proceeding with studies on direct nitration of the cubyl ring system.
Significant influence of the design of the rowing ergometer on elite athlete kinematics (2010)

Rowing injuries and performance have been attributed to the kinematics and kinetics of ergometer rowing. The aim of this study was to investigate these parameters on two commonly used rowing ergometers: one with a fixed-head design and one with a floating-head design. Using electromagnetic motion sensors and load cells, the kinematics and kinetics of ten elite male athletes (mean age, 22.8±3.5 years) rowing on the two different ergometers were assessed. This revealed that the floating-head design produced a greater stroke length ( p&lt;0.05) but higher stroke rate ( p&lt;0.01) for the same rowing intensity. This was combined with significantly different rowing kinematics in which the fixed head had greater anterior pelvic rotation ( p&lt;0.05) and greater femoral flexion ( p&lt;0.05). The implications of these changes with respect to injury require further interpretation through a mathematical model. Since a full analysis comparing rowing kinematics on water with rowing ergometers has not been made here, no conclusions regarding which ergometer simulates rowing on water can be made.
ChemInform Abstract: New Amino Acids for the Topographical Control of Peptide Conformation: Synthesis of All the Isomers of α,β‐Dimethylphenylalanine and α,β‐Dimethyl‐1,2,3,4‐tetrahydroisoquinoline‐3‐ carboxylic Acid of High Optical Purity. (1994)

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.
Deformation Microstructure Developed by Nanoindentation of a MAX Phase Ti<sub>2</sub>AlC (2018)

Deformation microstructure that developed during nanoindentation of a MAX phase Ti2AlC was characterized by the scanning probe microscopy and the transmission electron microscopy. To investigate the plastic anisotropy, nanoindentation measurements were made on grains with the normal parallel to ‹3362›, ‹0001›, and ‹1120›. The basal slip, {0001} ‹1120›, was found to be predominant as the deformation mechanism for all the indentation directions. It was also indicated that, upon nanoindentation along ‹0001› and ‹1120›, non-basal slips occurred underneath the indenter. The slip system of the non-basal dislocations was identified to be (1216)[1211] by analyzing the dislocations. Furthermore, fine-scaled kink-bands were found to form underneath the residual impression. The formation of the kink-band was accompanied by delamination, i.e., micro-cracking along the basal plane, suggesting that the delamination plays an important role for kink-band formation in Ti2AlC.
Supplementary Information Figure S5 from Dissecting Therapeutic Resistance to ERK Inhibition (2023)

&lt;p&gt;Analysis of active ERK2 G169D mutant binding to SCH772984&lt;/p&gt;
Table S1 from <i>Ex Vivo</i> Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids (2023)

&lt;p&gt;MC38 MDOTS correlation statistics&lt;/p&gt;
Alternative Chemistries for Free Radical-Initiated Targeting and Immobilization (2023)

Stimuli-responsive biomaterials are an emerging strategy that leverage common pathophysiological triggers to target drug delivery to limit or avoid toxic side effects. Native free radicals, such as reactive oxygen species (ROS), are widely upregulated in many pathological states. We have previously demonstrated that native ROS are capable of crosslinking and immobilizing acrylated polyethylene glycol diacrylate (PEGDA) networks and coupled payloads in tissue mimics, providing evidence for a potential targeting mechanism. To build on these promising results, we evaluated PEG dialkenes and dithiols as alternative polymer chemistries for targeting. The reactivity, toxicity, crosslinking kinetics, and immobilization potential of PEG dialkenes and dithiols were characterized. Both the alkene and thiol chemistries crosslinked in the presence of ROS, generating high molecular weight polymer networks that immobilized fluorescent payloads in tissue mimics. Thiols were especially reactive and even reacted with acrylates in the absence of free radicals, and this motivated us to explore a two-phase targeting approach. Delivering thiolated payloads in a second phase, after the initial polymer net formation, allowed greater control over the payload dosing and timing. Two-phase delivery combined with a library of radical-sensitive chemistries can enhance the versatility and flexibility of this free radical-initiated platform delivery system.
Crystallographic orientation dependence of compositional transition and valence band offset at SiO2/Si interface formed using oxygen radicals (2010)

The chemical and electronic-band structures of SiO2/Si interfaces formed utilizing oxygen radicals were investigated by measuring angle-resolved photoelectron spectra arising from Si 2p and O 1s core levels and a valence band with the same probing depth. We clarified that (1) the SiO2/Si interfaces formed exhibited an almost abrupt compositional transition, (2) the valence band offsets at the Si(111)/Si, Si(110)/Si, and Si(551)/Si interfaces are almost the same and are 0.07 eV smaller than that at the SiO2/Si(100) interface.
Study of Discrepancies Between Recorded and Actual Blood Flow in Hemodialysis Patients (2013)

Adequate blood flow (Qb) is necessary for effective hemodialysis (HD). Aim of the study was to examine relationship between the actually delivered Qb (dQb) and reported Qb (rQb) with dialysis machine. One hundred HD patients with arteriovenous fistula were enrolled. Delivered Qb was measured at the beginning and end of each HD session. dQb/rQb < 1 indicated a discrepancy between actual dQb and rQb reported using a dialysis machine. In addition, dQb/rQb was examined in HD patients using needles of different gauges during treatment. The average levels of dQb/rQb at start and end of HD session were 1.01 ± 0.04 and 0.98 ± 0.05, respectively. In the 16 gauge and 17 gauge needle groups, the percentage of patients with dQb/rQb < 1 increased in accordance with the increase in rQb or as the HD session progressed. In the 15 gauge needle group, the percentage of patients with dQb/rQb < 1 was <50% at any level of rQb. Selection of needle gauge is important factors for determining actual dQb in HD patients.
Aftertreatment System Integration on a Tier 2 Evolution Locomotive: Analysis and Field Test Results (2014)

Results of an effort to integrate an aftertreatment system for the simultaneous reduction of NOx and PM emissions on a Tier 2 Evolution Locomotive are presented. The paper provides detail on the solution that was realized to meet packaging constraints and also highlights aftertreatment performance limitations that resulted from these design decisions. Analysis results showing the predicted impact on engine performance are presented and compared to results obtained from field testing of the integrated system.
Antibacterial FANA oligonucleotides as a novel approach for managing the Huanglongbing pathosystem (2021)

Candidatus Liberibacter asiaticus (CLas), a bacterium transmitted by the Asian citrus psyllid, Diaphorina citri, is the causal agent of citrus greening disease, or Huanglongbng (HLB). Currently, vector population suppression with insecticides and tree removal are the most effective strategies for managing the HLB pathosystem. In this study, we assessed the bactericidal capabilities of 2'-deoxy-2'-fluoro-D-arabinonucleic acid antisense oligonucleotides (FANA ASO) both in vitro and in vivo by (1) confirming their capacity to penetrate insect cells, (2) silencing bacterial essential genes, and (3) quantifying reductions in bacterial titer and D. citri transmission. We confirmed that FANA ASO are able to penetrate insect cells without the use of a delivery agent. Expression of an essential gene in the D. citri endosymbiont, Wolbachia (wDi), significantly decreased by 30% following incubation with a wDi-specific FANA ASO. Viability of isolated wDi cells also decreased in response to the FANA ASO treatment. Delivery of a CLas-specific FANA ASO to infected adult D. citri in feeding assays resulted in significant silencing of a CLas essential gene. CLas relative density and transmission were significantly lower among D. citri fed FANA ASO in diet compared to untreated insects. Root infusions of a CLas-specific FANA ASO into infected Citrus trees significantly reduced CLas titer during a 30-day trial. Our results suggest that FANA ASO targeting insect-transmitted plant bacteria or insect endosymbionts may be useful tool for integrated management of agricultural pathogens.
Nondestructive optical methods of food quality evaluation (1984)

Quality control is an important aspect of food production and processing from the point of view of providing foods of acceptable nutritional value, and for providing safety of products. Several characteristics such as size, shape, density, maturity, moisture content, oil content, flavor, firmness, tenderness, color, defects, blemishes, etc., are routinely used in the quality control of agricultural and biological food products. Until recently, most analytical techniques used in quality control required isolation of the food component of interest. The original properties of the product are, therefore, destroyed during sample preparation and analysis. Oftentimes, such analyses are expensive, time consuming, and require sophisticated instrumentation, and hence are not suited for "on-line" quality control of food products. Recent progress in the development of instrumentation utilizing the optical properties of food products has provided several nondestructive techniques for quality evaluation. Most optical methods of nondestructive nature make use of the characteristic absorption spectra of components of interest. Such methods are highly sensitive, rapid, and reproducible, and have been successively used in routine "on-line" quality control of a large number of samples. In this article, theoretical considerations in the development of nondestructive analytical techniques based on the optical properties of several agricultural and biological products are briefly reviewed. A major emphasis is placed on quality control methods that are particularly useful in maturity and/or ripeness evaluation of food products, the detection of external and internal defects, and the subsequent development of automatic sorting machines for on-line measurement of quality.
Presence of SH2 domains of phospholipase C gamma 1 enhances substrate phosphorylation by increasing the affinity toward the epidermal growth factor receptor. (1992)

src homology region 2 and 3 (SH2 and SH3) domains are conserved noncatalytic regions originally described in cytoplasmic tyrosine kinases and subsequently identified in phospholipase C gamma 1 (PLC gamma 1), GTPase-activating protein of ras, and other signaling proteins. Although numerous studies indicate that SH2 domains promote protein-protein interactions by specific binding to tyrosine phosphorylated proteins, the function of SH3 domains is not known. The SH2 domain of PLC gamma 1 binds to certain tyrosine-phosphorylated growth factor receptors, and following phosphorylation on Tyr783 the enzymatic activity of PLC gamma 1 is enhanced, leading to phosphatidylinositol hydrolysis. To determine the functional role of the SH2 domain(s) on substrate phosphorylation in quantitative terms, we have expressed in Escherichia coli PLC gamma 1 constructs encoding the region containing Tyr783 and Tyr771, their two flanking SH2 domains and the SH3 domain, and five different deletion mutants of this region. These six proteins were purified and subjected to quantitative phosphorylation by the epidermal growth factor receptor (EGFR). Analysis of the kinetics of substrate phosphorylation revealed similar Vmax for the phosphorylation of the various mutant proteins. However, the affinity was enhanced for substrates containing SH2 domains: from S0.5 (average apparent Km) of 110 microM to S0.5 of 20 microM with the addition of a single SH2 domain and S0.5 of 3-4 microM for mutants containing two SH2 domains. The presence of the SH3 domain did not influence the apparent Km of substrate phosphorylation. These results demonstrate that the presence of the SH2 domain in PLC gamma 1 lowers the apparent Km (increases the affinity) of substrate phosphorylation by the EGFR, thereby facilitating PLC gamma 1 phosphorylation and activation.
Aberration-correction results from a segmented microelectromechanical deformable mirror and a refractive lenslet array (1998)

Quadratic aberration is successfully corrected with a segmented microelectromechanical deformable mirror in conjunction with a refractive lenslet array. Use of the lenslet array greatly improves the effective fill factor of the correcting element. Experimental results show correction approaching the diffraction limit for an extreme spherical aberration.
Differential down-modulation of HLA class I and II molecule expression on human tumor cell lines upon in vivo transfer (2011)

Previous evidence from our laboratory showed that Epstein-Barr virus-immortalized lymphoblastoid B cells undergo a prominent down-modulation of HLA-II molecule expression when injected intraperitoneally in SCID mice, while HLA-I remains almost unaffected. Since this phenomenon can alter the experimental outcome of therapeutic protocols of adoptive cell therapy, we decided to evaluate the behavior of MHC antigens in a panel of cell lines belonging to the B- and T-cell lineages, as well as in epithelial tumor cell lines. Cells were administered in mice either intraperitoneally or subcutaneously and recovered 4 days later for HLA molecule expression analysis. Collected data showed a highly heterogeneous in vivo behavior of the various cell lines, which could alternatively down-modulate, completely abrogate or maintain unchanged the expression of either MHC-I or MHC-II molecules. Moreover, the site of injection impacted differentially on these aspects. Although such phenomena still lack a comprehensive clarification, epigenetic mechanisms are likely to be involved as epigenetic drugs could partially counteract MHC down-modulation in vivo. Nonetheless, it has to be pointed out that careful attention must be paid to the assessment of therapeutic efficacy of translational protocols of adoptive immunotherapy, as modulation of MHC molecules on human target cells when transferred in a mouse environment could readily interfere with the desired and expected therapeutic effects.
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions (2016)

Massively parallel reporter assays (MPRAs) enable nucleotide-resolution dissection of transcriptional regulatory regions, such as enhancers, but only few regions at a time. Here we present a combined experimental and computational approach, Systematic high-resolution activation and repression profiling with reporter tiling using MPRA (Sharpr-MPRA), that allows high-resolution analysis of thousands of regions simultaneously. Sharpr-MPRA combines dense tiling of overlapping MPRA constructs with a probabilistic graphical model to recognize functional regulatory nucleotides, and to distinguish activating and repressive nucleotides, using their inferred contribution to reporter gene expression. We used Sharpr-MPRA to test 4.6 million nucleotides spanning 15,000 putative regulatory regions tiled at 5-nucleotide resolution in two human cell types. Our results recovered known cell-type-specific regulatory motifs and evolutionarily conserved nucleotides, and distinguished known activating and repressive motifs. Our results also showed that endogenous chromatin state and DNA accessibility are both predictive of regulatory function in reporter assays, identified retroviral elements with activating roles, and uncovered 'attenuator' motifs with repressive roles in active chromatin.
Microtron-based Intense Neutron Source (2016)

An L-Band 7.7-9.8 MeV CW relatively inexpensive microtron with a warm accelerating cavity for multi-purpose applications in nuclear medicine and radiation industry is proposed. The microtron with a photo-neutron converter is intended to serve as an intense source of photo-neutrons with yield up to 4·10¹² n/s for nuclear medicine or/and producing of short lived isotopes, as a source of gamma-radiation with dose rates up to 130 kR/min·m with a heavy bremsstrahlung target, and as a source of the electron beam with total energy of 9.8 MeV at the average current up to 4.4 mA for various radiation treatments.
Screening of Algae for Purifying Aquaculture Wastewater (2010)

Algal takes very important role in purifying aquaculture wastewater. The study aimed at screening the fittest algal according to comparison of removal rate of inorganic nitrogen and dissolved phosphorus in simulated aquaculture wastewater, with the test algae including Chlorella Pyrenoidosa, Scenedesmus Obliquus, Selenastrum Reinsch and Anabaena Spiroides. It was found that all of four algae can remove inorganic nitrogen and dissolved phosphorus effectively with the optimum removal rate as 51.9% , 60.9% , 43.3% , 30.2% as well as 22.7% 76.1% , 54.6% and 49.5% respectively. Four algae showed special removal function for different shapes of nitrogen, and nitrate could be removed easily by Scenedesmus Obliquus with the highest removal rate of 64.8%, ammonia-N was easily removed by Selenastrum Reinsch with the highest removal efficiency up to 15.4% while nitrite was removed effectively by Anabaena Spiroides with the highest removal rate as 98.3% . The combination of different algae for aquaculture wastewater treatment is prospective.
The complex tides of the Torres Straits (2012)

In 2008 a pioneering bathymetric LIDAR survey of the Torres Straits was undertaken. Due to the ever finer spatial details in the data and complex tidal regime, extensive water level data was collected at 19 stations to allow the reduction of the LiDAR survey data. A model with the ability to provide the water level at any location and instance in time was developed to replace the traditional tidal correction method of discrete tide zoning. This paper presents the results of this data collection program and describes techniques that were used to analyze and predict water levels in the region, which are some of the most complex ever monitored.
Studies on the α‐Methylglucoside Permease of Escherichia coli (1970)

The sequential events which occur in the membrane of Escherichia coli and lead to the antecedent appearance of α‐methylglucoside 6‐phosphate when cells are exposed to extracellular α‐methylglucoside have been analyzed. It has been shown that phosphorylation is the rate limiting step in α‐methylglucoside phosphate synthesis in vivo . However, phosphorylation of α‐methylglucoside was not found to be the only step occurring in the thickness of membrane. It was shown that a step of transport was necessarily taking place before phosphorylation. In the absence of phosphorylation (due to genetic inactivation of any part of the enzymatic complex devoted to phosphorylation, or to chemical inactivation of one among its components), this step was expressed as a facilitated diffusion of unaltered α‐methylglucoside. The demonstration of this facilitated passage rests on the following evidence: equalization of α‐methylglucoside concentrations in intracellular and extracellular compartments faster than when due to free passive diffusion alone; requirement of the interaction of α‐methylglucoside with a stereospecific site, distinct from E II , with a K m of 20 μM; finally, existence of counterflows suggesting that the passage was ensured by a mobile carrier, mediating both influx and efflux of α‐methylglucoside. This step of stransport was shown to be required in intact cells for a normal efficiency of phosphorylation in vivo . However it was not expressed in vivo as a facilitated diffusion but very likely as a facilitated access to the site of phosphorylation of E II . From these findings, and from an analysis of various mutants, it was concluded that a concerted change of conformation occurs when E II was phosphorylating, which renders the step of transport unlimiting. Some consequences of the dissociation of the α‐methylglucoside phosphate synthesis into two sequential steps are discussed. Mainly this model provides a simple explanation for the polarity exhibited by E II , the absence of phosphorylation of intracellular α‐methylglucoside and its continuous exchange.