gebhart/patrepeval huggingface dataset:
Role of the mixed lymphocyte culture (MLC) reaction in marrow donor selection: Matching for transplants from related haploidentical donors (1994)

The utility of the MLC assay as a test of HLA-D region matching and predictor of acute graft-versus-host disease (GvHD) was evaluated in 157 patients receiving marrow grafts from HLA-A, B identical related haploidentical donors. All donors and recipients were tested by HLA-DR serology, by Dw phenotyping with homozygous typing cells (HTC) and by standard MLC. Ninety-nine of the donor-recipient pairs were mismatched for a serologically defined HLA-DR antigen while 109 pairs were mismatched for the HLA-DR region by HTC typing. Donor antirecipient relative responses (RR) in MLC, corresponding to the GvHD vector in marrow transplantation, ranged from -4% to 100%, with a median of 25%. A comparison of reactivity in MLC with presence or absence of matching by Dw phenotyping, however, showed a significant overlap in the distribution of RRs from HLA-Dw matched versus Dw mismatched pairs, suggesting that the MLC was not a reliable predictor of HLA-Dw matching. Using an optimally-defined cutoff of 3% RR, the MLC was correlated with risk of developing clinically significant grades II-IV acute GvHD (p = 0.03) but not with risk of developing severe grades III-IV GvHD (p = 0.18). In contrast, matching by Dw phenotype was a significant predictor of GvHD, with Dw-compatible transplant recipients less likely to develop either grades II-IV (p = 0.004) or III-IV (p = 0.036) GvHD than Dw-incompatible transplant recipients. Overall, these results underscore the difficulty in using the MLC to measure HLA-D region compatibility and predict the risk of severe graft-versus-host disease among patients receiving related haploidentical marrow grafts. HLA-D (HTC) typing results correlate primarily with DRB compatibility, and with the advent of DRB1 allele matching by sequence-specific oligonucleotide probes (SSOP) or by direct sequencing, the precision in donor matching achievable with these methods is far greater than with either HLA-D typing or direct MLC testing.
An Alu‐like RNA promotes cell differentiation and reduces malignancy of human neuroblastoma cells (2010)

Neuroblastoma (NB) is a pediatric cancer characterized by remarkable cell heterogeneity within the tumor nodules. Here, we demonstrate that the synthesis of a pol III-transcribed noncoding (nc) RNA (NDM29) strongly restricts NB development by promoting cell differentiation, a drop of malignancy processes, and a dramatic reduction of the tumor initiating cell (TIC) fraction in the NB cell population. Notably, the overexpression of NDM29 also confers to malignant NB cells an unpredicted susceptibility to the effects of antiblastic drugs used in NB therapy. Altogether, these results suggest the induction of NDM29 expression as possible treatment to increase cancer cells vulnerability to therapeutics and the measure of its synthesis in NB explants as prognostic factor of this cancer type.
Templated Out‐of‐Equilibrium Self‐Assembly of Branched Au Nanoshells (2023)

Out-of-equilibrium self-assembly of metal nanoparticles (NPs) has been devised using different types of strategies and fuels, but achieving finite 3D structures with a controlled morphology through this assembly mode is still rare. Here, a spherical peptide-gold superstructure (PAuSS) is used as a template to control the out-of-equilibrium self-assembly of Au NPs, obtaining a transient 3D-branched Au-nanoshell (BAuNS) stabilized by sodium dodecyl sulphate (SDS). The BAuNS dismantles upon SDS concentration gradient equilibration over time in the sample solution, leading to NPs disassembly and regression to PAuSS. Notably, BAuNS assembly and disassembly promotes temporary interparticle plasmonic coupling, leading to reversible and tunable changes of their plasmonic properties, a highly desirable behavior in the development of optoelectronic nanodevices.
Particle shape as revealed by spectral depolarization (2008)

Remote detection of airborne biological agents is a problem of contemporary interest. At issue is the discrimination of scatter from such harmful species and the scatter from naturally occurring particles such as hydrosols, pollen, and dust. The feature that our detection scheme attempts to exploit is that the species of interest typically have a characteristic size and shape that produce a unique signature in the depolarization of the scattered light. Through the use of <i>T</i>-matrix calculations we demonstrate the effect and show processing algorithms for quantifying and interpreting the measurements. Simulations suggest that it is possible to retrieve an estimate of the aspect ratio from a measurement of the spectral behavior of the linear depolarization in either the forward-scatter or back-scatter regime.
Layered Stereo by Cooperative Grouping with Occlusion. (2020)

Human stereo vision uses occlusions as a prominent cue, sometimes the only cue, to localize object boundaries and recover depth relationships between surfaces adjacent to these boundaries. However, many modern computer vision systems treat occlusions as a secondary cue or ignore them as outliers, leading to imprecise boundaries, especially when matching cues are weak. In this work, we introduce a layered approach to stereo that explicitly incorporates occlusions. Unlike previous layer-based methods, our model is cooperative, involving local computations among units that have overlapping receptive fields at multiple scales, and sparse lateral and vertical connections between the computational units. Focusing on bi-layer scenes, we demonstrate our model's ability to localize boundaries between figure and ground in a wide variety of cases, including images from Middlebury and Falling Things datasets, as well as perceptual stimuli that lack matching cues and have yet to be well explained by previous computational stereo systems. Our model suggests new directions for creating cooperative stereo systems that incorporate occlusion cues in a human-like manner.
Editorial Comment (1985)

Professor and Director George L. Schultz Laboratories for Orthopaedic Research UMDNJ-New Jersey Medical School Newark, New Jersey Professor and Director Section of Orthopaedic Surgery UMDNJ-New Jersey Medical School Newark, New Jersey
Industrial Biotechnology—An Industry at an Inflection Point (2020)

Industrial biotechnology is poised for dramatic growth. A confluence of consumer demand; attractive feedstock quantity, quality, and price; and technical innovation has created a perfect situation for the industry to significantly expand. Since the 2004 Werpy and Peterson paper, “Top Value Added Chemicals from Biomass,” the biobased manufacturing industry and the technologies that make these processes and products possible has evolved significantly. 1 New technology continues to advance, and there is increasing consumer and industry demand for biobased materials. Paired with increasing on-farm efficiency and sustainability considerations, these are all factors that are driving the bioeconomy forward. This paper reviews these factors and illustrates where the technology can head, identifying opportunities for utilizing corn-based sugars as a feedstock for near-term, high-impact products in the biorenewable space. Furthermore, this paper suggests what policies should be considered to move the industry towards the future.
Electrodeposition of Iron from Molten Mixed Chloride/Fluoride Electrolytes (2007)

The electrochemical behaviour of dissolved Fe2O3 and the electrodeposition of iron in molten CaCl2-CaF2 (80-20 mol %) and other mixed chloride/fluoride electrolytes was studied at 827 {degree sign}C and 890 {degree sign}C by cyclic voltammetry, chronoamperometry and galvanostatic electrolysis, and deposits were characterized by XRD and SEM. Pure iron was obtained in these melts at current efficiencies greater than 90 %. High cathodic current densities (~0.5 A cm2) were achieved by using a rotating cathode. The work is related to studies of the possible development of new processes for the production of iron and steel with large reductions of CO2 emissions.
Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold. (1993)

The three-dimensional profile method expresses the three-dimensional structure of a protein as a table, the profile, which represents the local environment of each residue. The score of an amino acid sequence, aligned with the three-dimensional profile, reflects its compatibility with the profiled structure. In the original implementation, each local environment was characterized by its polarity, the area buried of its side chain, and its secondary structure. Here we describe a modified three-dimensional profile algorithm that characterizes the local environment in terms of the statistical preferences of the profiled residue for neighbors of specific residue types, main-chain conformations, or secondary structure. Combined profiles of the original and the three new types were tested on beta/alpha-barrel protein structures. The method identified the following enzymes of unknown three-dimensional structure as probable beta/alpha-barrels, all of which catalyze reactions in the biosynthesis of aromatic amino acids: anthranilate phosphoribosyltransferase (trpD), glutamine amidotransferase (trpG), and phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA).
Development of Viral Vectors for Gene Therapy of β-Chain Hemoglobinopathies: Optimization of a γ-Globin Gene Expression Cassette (1999)

Progress toward gene therapy of β-chain hemoglobinopathies has been limited in part by poor expression of globin genes in virus vectors. To derive an optimal expression cassette, we systematically analyzed the sequence requirements and relative strengths of theAγ- and β-globin promoters, the activities of various erythroid-specific enhancers, and the importance of flanking and intronic sequences. Expression was analyzed by RNase protection after stable plasmid transfection of the murine erythroleukemia cell line, MEL585. Promoter truncation studies showed that theAγ-globin promoter could be deleted to −159 without affecting expression, while deleting the β-globin promoter to −127 actually increased expression compared with longer fragments. Expression from the optimal β-globin gene promoter was consistently higher than that from the optimal Aγ-globin promoter, regardless of the enhancer used. Enhancers tested included a 2.5-kb composite of the β-globin locus control region (termed a μLCR), a combination of the HS2 and HS3 core elements of the LCR, and the HS-40 core element of the -globin locus. All three enhancers increased expression from the β-globin gene to roughly the same extent, while the HS-40 element was notably less effective with theAγ-globin gene. However, the HS-40 element was able to efficiently enhance expression of a Aγ-globin gene linked to the β-globin promoter. Inclusion of extended 3′ sequences from either the β-globin or the Aγ-globin genes had no significant effect on expression. A 714-bp internal deletion ofAγ-globin intron 2 unexpectedly increased expression more than twofold. With the combination of a −127 β-globin promoter, anAγ-globin gene with the internal deletion of intron 2, and a single copy of the HS-40 enhancer, γ-globin expression averaged 166% of murine -globin mRNA per copy in six pools and 105% in nine clones. When placed in a retrovirus vector, this cassette was also expressed at high levels in MEL585 cells (averaging 75% of murine -globin mRNA per copy) without reducing virus titers. However, recombined provirus or aberrant splicing was observed in 5 of 12 clones, indicating a significant degree of genetic instability. Taken together, these data demonstrate the development of an optimal expression cassette for γ-globin capable of efficient expression in a retrovirus vector and form the basis for further refinement of vectors containing this cassette.
Ultrasonic dyeing of wool fabric with aqueous extract of Ratanjot (Onosma echioides) natural dye (2021)

The purpose of this study is to compare the conventional and ultrasonic dyeing methods in terms of its colour strength and colour fastness properties of wool fabric dyed with Ratanjot root. The results suggested that dyeing of wool fabric with natural dye Ratanjot (Onosma echioides) using ultrasonic waves, significantly improved the dye uptake percentage to 12.31 per cent from conventional heating methods. The fastness grade were found to be higher with ultrasonic than conventional heating. Additionally, the fabric dyed using ultrasonic waves gave a deeper shade and good colour intensity even at lower dyeing time (75min) and temperature (60°C). Therefore, ultrasound wave represents a promising technique for increasing diffusion of dye by the effect of cavitation, as well as for improving the effectiveness of processes when compared to conventional heating
Zu Unrecht vernachlässigt. Zur bleibenden Relevanz des katholischen Eigentumsverständnisses (2015)

Die katholische Traditionsbildung zu Eigentum und Besitz richtet sich an ord- nungspolitischen Vorstellungen aus. Die Nutzung von Eigentum und Besitz wird in einer engen Verbindung und Spannung zu den Rechten der Armen ausgelegt und unter einen legitimatorischen Vorbehalt gestellt. Ein absolu- tes Eigentumsrecht kennt deshalb die Soziallehre der Kirche nicht. Die Ord- nungsvorstellungen der Kirche gerieten durch verschiedene historische Er- eignisse und Bewegungen unter Druck und verloren an Plausibilität. Die päpstlichen Sozialenzykliken ab 1891 lösen sich von einem abstrakten Recht auf Eigentum und vollziehen den Weg hin zu einer Verzahnung die- ses Rechts mit der menschlichen Arbeit und anderen konditionalen Beding- ungen. Die jüngsten Transformationen der kapitalistischen Wirtschaftsweise machen deutlich, dass die Soziallehre der Kirche heute verstärkt eine kri- tische Auseinandersetzung zu Eigentum und Besitz führen müsste. The Catholic tradition of property and ownership is geared to regulatory requirements. The use of property and ownership is interpreted in a narrow connection with the rights of the poor, and in tension to it, and is placed under a reservation of legitimation. An absolute right of ownership is not known by the social doctrine of the Church. The concept of order of the Church got under pressure by the various historical events and movements, and lost its plausibility. The papal social encyclicals since 1891 release from an abstract right of property, and complete the path to a gear tooth with the law of human labor and other conditional terms. The recent transformations of the capitalist economy make clear that the social doctrine of the Church should now increasingly lead to a critical discussion on property and ownership.
Selling privacy at auction (2011)

We initiate the study of markets for private data, through the lens of differential privacy. Although the purchase and sale of private data has already begun on a large scale, a theory of privacy as a commodity is missing. In this paper, we propose to build such a theory. Specifically, we consider a setting in which a data analyst wishes to buy information from a population from which he can estimate some statistic. The analyst wishes to obtain an accurate estimate cheaply, while the owners of the private data experience some cost for their loss of privacy, and must be compensated for this loss. Agents are selfish, and wish to maximize their profit, so our goal is to design truthful mechanisms. Our main result is that such problems can naturally be viewed and optimally solved as variants of multi-unit procurement auctions. Based on this result, we derive auctions which are optimal up to small constant factors for two natural settings: When the data analyst has a fixed accuracy goal, we show that an application of the classic Vickrey auction achieves the analyst's accuracy goal while minimizing his total payment. When the data analyst has a fixed budget, we give a mechanism which maximizes the accuracy of the resulting estimate while guaranteeing that the resulting sum payments do not exceed the analyst's budget.
A STUDY OF ORAL ATROPINE IN HEALTHY ADULT SUBJECTS (1974)

SUMMARY The effect of administering atropine by intramuscular and oral routes was compared by measuring the depression of salivation in nine healthy adult subjects. The ratio of oral to intramuscular dose for the same peak effect was found to be 1.86 (SD 0.50, SE 0.16).
Modification of the pH Profile and Tetrabenazine Sensitivity of Rat VMAT1 by Replacement of Aspartate 404 with Glutamate (1996)

Vesicular monoamine transporters (VMAT) catalyze transport of serotonin, dopamine, epinephrine, and norepinephrine into subcellular storage organelles in a variety of cells. Accumulation of the neurotransmitter depends on the proton electrochemical gradient (Delta micro H+) across the organelle membrane and involves VMAT-mediated exchange of two lumenal protons with one cytoplasmic amine. Mutagenic analysis of the role of two conserved Asp residues located in transmembrane segments X and XI of rat VMAT type I reveals an important role of these two residues in catalysis. Replacement of Asp 431 with either Glu or Ser inhibits VMAT-mediated [3H]serotonin transport. The mutated proteins are unimpaired in ligand recognition as measured with the high affinity ligand [3H]reserpine or coupling to the proton electrochemical gradient as judged by its ability to accelerate [3H]reserpine binding. Therefore, the Asp residue is needed as such in this position and even a conservative replacement with Glu generates a protein that can catalyze only partial reactions but cannot complete the transport cycle. Replacement of Asp 404 with either Ser or Cys inhibits all VMAT-mediated reactions measured. However, replacement with Glu generated a protein that catalyzed [3H]serotonin transport with modified properties. Whereas the mutated protein binds [3H]reserpine to normal levels and the pH optimum of this reaction is only slightly affected, the optimum pH for transport activity shifted to the acid side and became very sharp; in addition the sensitivity to the inhibitor tetrabenazine increased significantly in this mutated protein. The results point to the need of a carboxyl moiety in position 404. A slight change in its relative location or in the environment around it has a significant effect on the pK of group(s) involved in steps after ligand recognition and coupling to the first H+.
A 3-D single-electron-memory cell structure with 2F/sup 2/ per bit (1997)

Summary form only given. A 3-dimensional (3-D) single-electron memory cell, which achieves an area of 2F/sup 2/ per bit (where F is the feature size of the fabricated structures), is proposed. In the proposed vertically united cell (VUC), two cells are stacked vertically which only adds a few steps to the whole fabrication process. The results obtained demonstrate that the single-electron memory has a cost advantage over conventional memories in terms of giga-scale memories. Moreover, with the aim of producing single-electron memory LSI, MOS devices are fabricated on the same wafer as the VUCs, and this set-up shows successful operation.
The Modified Surface Killing Assay Distinguishes between Protective and Nonprotective Antibodies to PspA (2019)

Pneumococcal surface protein A (PspA) elicits antibody protective against lethal challenge by <i>Streptococcus pneumoniae</i> and is a candidate noncapsular antigen for inclusion in vaccines. Evaluation of immunity to PspA in human trials would be greatly facilitated by an <i>in vitro</i> functional assay able to distinguish protective from nonprotective antibodies to PspA. Mouse monoclonal antibodies (MAbs) to PspA can mediate killing by human granulocytes in the modified surface killing assay (MSKA). To determine if the MSKA can distinguish between protective and nonprotective MAbs, we examined seven MAbs to PspA. All bound recombinant PspA, as detected by enzyme-linked immunosorbent assay and Western blotting; four gave strong passive protection against fatal challenge, two were nonprotective, and the seventh one only delayed death. The four that were able to provide strong passive protection were also most able to enhance killing in the MSKA, the two that were not protective in mice were not effective in the MSKA, and the MAb that was only weakly protective in mice was weakly effective in the MSKA (<i>P < </i>0.001). One of the four most protective MAbs tested reacted to the proline-rich domain of PspA. Two of the other most protective MAbs and the weakly protective MAb reacted with a fragment from PspA's α-helical domain (αHD), containing amino acids (aa) 148 to 247 from the N terminus of PspA. The fourth highly protective MAb recognized none of the overlapping 81- or 100-aa fragments of PspA. The two nonprotective MAbs recognized a more N-terminal αHD fragment (aa 48 to 147).<b>IMPORTANCE</b> The most important finding of this study is that the MSKA can be used as an <i>in vitro</i> functional assay. Such an assay will be critical for the development of PspA-containing vaccines. The other important findings relate to the locations and nature of the protection-eliciting epitopes of PspA. There are limited prior data on the locations of protection-eliciting PspA epitopes, but those data along with the data presented here make it clear that there is not a single epitope or domain of PspA that can elicit protective antibody and there exists at least one region of the αHD which seldom elicits protective antibody. Moreover, these data, in concert with prior data, strongly make the case that protective epitopes in the αHD are highly conformational (≥100-amino-acid fragments of the αHD are required), whereas at least some protection-eliciting epitopes in the proline-rich domain are encoded by ≤15-amino-acid sequences.
Regulation of Ribulose-1,5-Bisphosphate Carboxylase Activity in Response to Changing Partial Pressure of O2 and Light in Phaseolus vulgaris (1986)

The regulation of ribulose-1,5-bisphosphate (RuBP) carboxylase (rubisco) activity in Phaseolus vulgaris was studied under moderate CO(2) and high light, conditions in which photosynthesis in C(3) plants can be insensitive to changes in O(2) partial pressure. Steady state RuBP concentrations were higher, the calculated rate of RuBP use was lower and the activation state of rubisco was lower in low O(2) relative to values observed in normal O(2). It is suggested that the reduced activity of rubisco observed here is related to feedback effects which occur when the rate of net CO(2) assimilation approaches the maximum capacity for starch and sucrose synthesis (triose phosphate utilization). The activation state of rubisco was independent of O(2) partial pressure when light or CO(2) was limiting for photosynthesis. Reduced activity of rubisco was also observed at limiting light. However, in this species light dependent changes in the concentration of an inhibitor of rubisco controlled the apparent V(max) of rubisco in low light while changes in the CO(2)-Mg(2+) dependent activation of rubisco controlled the apparent V(max) in high light.