gebhart/patrepeval huggingface dataset:
Immune responsiveness in mutant mice lacking T-cell receptor alpha beta+ cells. (1995)

Immune responses of mice with T-cell receptor (TCR)gamma delta+ T cells but lacking TCR alpha beta+ cells because of a disruption in the TCR alpha gene, were analysed against alloantigens, soluble protein antigen, killed Mycobacterium tuberculosis and exogenous superantigen. Rejection of skin allografts mismatched for classical major histocompatibility complex (MHC) plus multiple minor H antigens was virtually abrogated but the presence of mismatched Qa-1 non-classical MHC antigens on donor tissue resulted in a significant proportion of TCR alpha-/- mice rejecting such grafts. In view of the proposed role for gamma delta T cells in mycobacterial responses, and particularly against self- or mycobacterial heat-shock protein HSP 65, we examined these responses in TCR alpha-/- mice. Local responses after immunization were low in lymph nodes and no component of these was directed against mycobacterial HSP 65. However, splenic T cells from mutant mice responded strongly to either purified protein derivative (PPD) or M. tuberculosis. Our findings indicate that TCR alpha-/- mice are selectively compromised: while responses to (undefined) mycobacterial antigens were substantial, responses to some other target antigens such as MHC alloantigens and HSP 65, believed to be preferentially recognized by gamma delta receptors, were poor or absent. However, the fact that the mutant mice more readily rejected allografts that are mismatched for the non-classical MHC antigen Qa-1 in addition to classical MHC and minor-H incompatibility, indicates that in some mice the residual immune response, presumed to be by gamma delta cells, is sufficient to cause skin graft rejection and that recognition of non-classical MHC antigens may play an important part in the response.
A “Molecular Eraser” for Dip‐Pen Nanolithography (2007)

The DPN eraser: Dip-pen-nanolithography- (DPN-) generated nanostructures can be repaired using a conductive atomic force microscope (AFM) and an adsorbate-coated AFM tip. This molecule-based erasing technique was used to transform a pattern of MHA in the form of the letters “DRN” into “DPN” (see figure). The technique facilitates removal and subsequent backfilling with a second molecule type. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2007/z600679_s.pdf or from the author. 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.
BioCapacitor: A novel principle for biosensors (2015)

Studies regarding biofuel cells utilizing biocatalysts such as enzymes and microorganisms as electrocatalysts have been vigorously conducted over the last two decades. Because of their environmental safety and sustainability, biofuel cells are expected to be used as clean power generators. Among several principles of biofuel cells, enzyme fuel cells have attracted significant attention for their use as alternative energy sources for future implantable devices, such as implantable insulin pumps and glucose sensors in artificial pancreas and pacemakers. However, the inherent issue of the biofuel cell principle is the low power of a single biofuel cell. The theoretical voltage of biofuel cells is limited by the redox potential of cofactors and/or mediators employed in the anode and cathode, which are inadequate for operating any devices used for biomedical application. These limitations inspired us to develop a novel biodevice based on an enzyme fuel cell that generates sufficient stable power to operate electric devices, designated "BioCapacitor." To increase voltage, the enzyme fuel cell is connected to a charge pump. To obtain a sufficient power and voltage to operate an electric device, a capacitor is used to store the potential generated by the charge pump. Using the combination of a charge pump and capacitor with an enzyme fuel cell, high voltages with sufficient temporary currents to operate an electric device were generated without changing the design and construction of the enzyme fuel cell. In this review, the BioCapacitor principle is described. The three different representative categories of biodevices employing the BioCapacitor principle are introduced. Further, the recent challenges in the developments of self-powered stand-alone biodevices employing enzyme fuel cells combined with charge pumps and capacitors are introduced. Finally, the future prospects of biodevices employing the BioCapacitor principle are addressed.
Upliftment of socio-economical life style of farmers through farmer's data network (2015)

India is a country dominated by villages. Agriculture is the main occupation in India. Development of any country is dependent on the healthy status of farmers. Farmer is suffering from various problems mainly due to the lack of unity among farmers and no union to support farmers. Technology is not reaching the farmers directly. This paper discusses an innovative solution which proposes the joint effort of Non Government social Organization and Engineers, to help farmers and ease the task of Government and avoid losses occurring due to mismanagement. This idea suggests that, initially a data network has to be created to link each farmer's data of each village to all Talukas, Each Taluk to Districts and to state. This is carried out by software projects using DBMS and VB.Net. Projects are the part of engineering curriculum and societal need based projects help in enhancement of learning. A Non-Government Organization manages to collect the information about each farmer's requirement such as seeds, fertilizers and manures. This information is passed to manufacturers and with the assistance and co-operation of Government and concerned banks, materials will be supplied to NGO who in-turn manages to supply to each village farmers. Similarly, at the harvest time, crop yield estimation of each village is done through the network. This information is provided to large buyers and exporters, through NGO and money transaction is again through NGO to each farmer. It is estimated that by this supply chain management farmer will get his market at his door steps. Precision agriculture information is stored in the database. Farmer can get the timely suggestions and assistance at village level NGO only through the software. Thus we can expect that farmer's life style can be improved by this supply chain management designed through collaborative work of NGO and engineers.
A Readout IC for Capacitive Touch Screen Panels With 33.9 dB Charge-Overflow Reduction Using Amplitude-Modulated Multi-Frequency Excitation (2021)

This article presents a readout integrated circuit (ROIC) for capacitive touch-screen panels (TSPs) employing an amplitude-modulated multiple-frequency excitation (AM-MFE) technique. To prevent charge overflow, which occurs periodically at the beat frequency of the excitation frequencies, the ROIC modulates the amplitude of the excitation voltages at a mixing frequency derived from the excitation frequencies. Thus, the ROIC can sense the charge signal without charge overflow and maximize the signal-to-noise ratio (SNR) by increasing the amplitude of the excitation voltages up to the sensing range of the readout circuit. The proposed ROIC was fabricated in a 0.13- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> standard CMOS process and was measured with a 32-in 104 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\times $ </tex-math></inline-formula> 64 touch-screen panel using 1 and 10 mm metal pillars. It reduces charge overflow up to 33.9 dB compared to operation without AM-MFE. In addition, the ROIC achieves a frame rate of 2.93 kHz, and SNRs of 41.7 and 61.6 dB with 1 and 10 mm metal pillars, respectively.
Properties of Tl2Ba2Ca2Cu3Ox Thin Films with a Critical Temperature of 122 K Prepared by Excimer Laser Ablation (1990)

Superconducting thin films with a single Tl 2 Ba 2 Ca 2 Cu 3 O x (2223) phase were fabricated on MgO(100) substrates using excimer laser ablation and post annealing. The films had a highly c -axis-oriented structure and showed zero resistance at 122 K. Diamagnetism also appeared at 122 K and a 95% transition was achieved at 110 K. The critical current density of the film at 77 K was 1.5×10 5 A/cm 2 at 0 T.
Spatially mapping T cell receptors and transcriptomes (2022)

Abstract T cells mediate antigen-specific immune responses to disease through the specificity and diversity of their T-cell receptors (TCRs). Although determining the spatial distributions of T cell clonotypes in tissues is essential to understanding T cell maturation and behavior, spatial sequencing methods remain unable to profile the TCR repertoire. We have developed Slide-TCR-seq, a 10-μm-resolution method to sequence whole transcriptomes and TCRs within the spatial context of intact tissues. We first confirmed the ability of Slide-TCR-seq to map the characteristic architecture of T cells and their receptors in mouse spleen. In human reactive lymph node and tonsil, we identified spatially distinct TCR repertoires both between germinal center (GC) and non-GC regions as well as between GCs. We then spatially profiled T cell clonotypes and their infiltration in renal cell carcinoma specimens before and following immune checkpoint blockade, which identified uniquely distributed T cell clonotypes and transcriptional states, highlighting the infiltration and expression heterogeneity both between clonotypes and within a T cell clonotype. Our method is anticipated to facilitate dissection of the immune microenvironment, yielding insights into the complex spatial relationships between T cell clonotypes, neighboring cell types, and gene expression that drive T cell development and response to disease. This work was supported in part by the NIH U19AI082630, the Dana-Farber/Harvard Cancer Center Kidney Cancer SPORE (NCI P50CA101942), and the NCI IMAT grant.
Nonclassical CH−π Supramolecular Interactions in Artemisinic Acid Favor a Single Conformation, Yielding High Diastereoselectivity in the Reduction with Diazene (2014)

The high diastereoselectivity of the hydrogenation of artemisinate by diazene to form dihydroartemisinate (diastereoselective ratio, dr, 97:3) necessary for efficient production of artemisin has been rationalized by state-of-the-art DFT calculations and identification of the noncovalent interactions by coupled ELF/NCI analysis. Remarkably, a single conformer of artemisinate is responsible for the high diastereoselectivity of the reaction. NMR studies confirm the preference for a single conformation that is found to be identical to that predicted by the calculations. The calculations and ELF/NCI analyses show that the hydrogenation of the exocyclic activated C═C double bond has a low energy barrier and that the lowest transition state and the preferred conformation of free artemisinate develop the same network of weak noncovalent interactions between the electron donor groups (oxygen and exocyclic C═C double bond) and CH bonds of the cis-decalene group of the artemisinate, which rationalize the high diastereoselectivity unusual for a strongly exothermic reaction.
Cutinase from Fusarium solani pisi Hydrolyzing Triglyceride Analogs. Effect of Acyl Chain Length and Position in the Substrate Molecule on Activity and Enantioselectivity (1995)

Triglyceride analogues were synthesized in which one of the primary acyl ester functions has been replaced by an alkyl group and the secondary acyl ester bond has been replaced by an acyl amino bond. The chain length at either position was varied, and both (R)- and (S)-enantiomers of each compound were synthesized. These pseudo triglycerides contain only one hydrolyzable ester bond, and they are ideally suited to studying the influence of the chain length at the 1-, 2-, and 3-position on lipase activity and on stereopreference. These substrates were used to characterize cutinase from Fusarium solani pisi. Our results show that the activity of cutinase is very sensitive to the length and distribution of the acyl chains and that the highest activities are found when the chains at positions 1 and 3 contain three or four carbon atoms. The enzyme preferentially hydrolyzes the (R)-enantiomers, but this preference is strongly dependent on the acyl chain length distribution, with (R) over (S) activity ratios varying from about 30 to 1. This enantioselectivity was found in three different assay systems: a mixed micellar, a reverse micellar, and a monolayer study. Our data suggest that at least two alkyl chains of the pseudo triglycerides must be fixed during hydrolysis. Therefore, these substrates were used to characterize mutants of cutinase with mutations in putative lipid binding domains. Two mutants (A85F and A85W) have increased activities. The results obtained with these mutants suggest an interaction of the acyl chain of the scissile ester bond with a surface loop, comprising residues 80-90, in the enzyme-substrate complex.
Structure, Dynamics, and Antimicrobial and Immune Modulatory Activities of Human LL-23 and Its Single-Residue Variants Mutated on the Basis of Homologous Primate Cathelicidins (2011)

LL-23 is a natural peptide corresponding to the 23 N-terminal amino acid residues of human host defense cathelicidin LL-37. LL-23 demonstrated, compared to LL-37, a conserved ability to induce the chemokine MCP-1 in human peripheral blood mononuclear cells, a lack of ability to suppress induction of the pro-inflammatory cytokine TNF-α in response to bacterial lipopolysaccharides (LPS), and reduced antimicrobial activity. Heteronuclear multidimensional nuclear magnetic resonance (NMR) characterization of LL-23 revealed similar secondary structures and backbone dynamics in three membrane-mimetic micelles: SDS, dodecylphosphocholine (DPC), and dioctanoylphosphatidylglycerol. The NMR structure of LL-23 determined in perdeuterated DPC contained a unique serine that segregated the hydrophobic surface of the amphipathic helix into two domains. To improve our understanding, Ser9 of LL-23was changed to either Ala or Val on the basis of homologous primate cathelicidins. These changes made the hydrophobic surface of LL-23 continuous and enhanced antibacterial activity. While identical helical structures did not explain the altered activities, a reduced rate of hydrogen-deuterium exchange from LL-23 to LL-23A9 to LL-23V9 suggested a deeper penetration of LL-23V9 into the interior of the micelles, which correlated with enhanced activities. Moreover, these LL-23 variants had discrete immunomodulatory activities. Both restored the TNF-α dampening activity to the level of LL-37. Furthermore, LL-23A9, like LL-23, maintained superior protective MCP-1 production, while LL-23V9 was strongly immunosuppressive, preventing baseline MCP-1 induction and substantially reducing LPS-stimulated MCP-1 production. Thus, these LL-23 variants, designed on the basis of a structural hot spot, are promising immune modulators that are easier to synthesize and less toxic to mammalian cells than the parent peptide LL-37.
Involvement of Catecholamines and Glucocorticoids in Ethanol‐Induced Suppression of Splenic Natural Killer Cell Activity in a Mouse Model for Binge Drinking (1997)

Ethanol (EtOH) suppresses splenic natural killer (NK) cell activity in a mouse binge drinking model. Direct effects of EtOH and its metabolites are not the major cause of this suppression. Also, catecholamines do not completely explain this suppression. This implicates the involvement of other neuroendocrine mediators in this suppression. Previous studies in this laboratory have shown that RU 486 at a dosage of 100 mg/kg did not affect EtOH-induced suppression of NK cell activity. However, in the present study, RU 486 at a dosage of 200 mg/kg partially blocked the suppression of NK cell activity induced by EtOH. Moreover, corticosterone at levels expected in the free (unbound) form in EtOH-treated mice decreased NK cell activity in vitro. Nadolol in combination with RU 486 blocked the suppression of NK cell activity in EtOH-treated mice. Although there were reasons to suspect that EtOH-induced changes in the levels of growth hormone or prolactin might also contribute to the suppression of NK cell activity; evidence obtained herein did not indicate such involvement. Thus, glucocorticoids and catecholamines seem to be involved in EtOH-induced suppression of NK cell activity. Together, with the direct effects of EtOH, these neuroendocrine mediators seem to be sufficient to explain all of the suppression of NK cell activity caused by EtOH.
Complement Factor H Variant Y402H is Not a Risk Factor for Preeclampsia in the Finnish Population (2008)

Neither the Y402H variant, nor mutations in the short consensus repeat domain 20 of the gene is associated with preeclampsia. For examination of possible links to other polymorphisms or detection of small genotypic effects, studies in larger sample sets are warranted.
Reconstruction error in transform/subband coding (2002)

We use the linear gain-plus-additive noise model for the class of PDF-optimized scalar quantizers to develop a frequency domain analysis of transform/subband coding systems. We derive a novel and explicit expression for the PSD of the reconstruction error, and show that this PSD has signal, alias and noise components. We employ this expression to compare different block transforms and subband filters with the rate-distortion optimal source coder, for a 1-D Gauss-Markov source. This paper quantifies, via the 'out-of-band' noise energy in the reconstruction error, the performance gap between DCT-based coders and coders that use subband/wavelet filters.
Ten-year all-cause death after percutaneous or surgical revascularization for men and women with multivessel or left main coronary artery disease: insights from the SYNTAX extended survival study (2020)

Abstract Background In patients with complex coronary artery disease (CAD), women favored coronary artery bypass grafting surgery (CABG) compared to percutaneous coronary intervention (PCI) at 5 years in the SYNTAX trial, whereas mortality rates after PCI and CABG were not different in men. On the other hand, poor outcomes of women undergoing PCI were not observed in the PRECOMBAT and BEST trials. The long-term optimal revascularization strategy according to gender has not been fully evaluated. Purpose In the SYNTAX Extended Survival (SYNTAXES) study, no significant difference existed in all-cause death between PCI and CABG at 10 years. This study aimed to assess treatment effect of PCI and CABG for 10-year all-cause death according to gender. Methods The SYNTAXES study evaluated vital status up to 10 years in 1,800 patients with de novo three-vessel disease (3VD) and/or left main coronary artery disease (LMCAD) randomized to treatment with CABG or PCI in the SYNTAX trial, and the pre-specified primary endpoint was all-cause death at 10 years. In this prespecified analysis, all-cause death at 10 years according to gender in patients undergoing PCI or CABG was evaluated. Results Of 1800 patients, 402 (22.3%) were women and 1398 (77.7%) were men. In women, the rate of mortality was significantly higher in the PCI arm at 5 years than in the CABG arm (19.3% vs. 10.3%; Log-rank p=0.010, Figure A), but the rates of mortality were not different at 10 years between the PCI and CABG arms (33.0% vs. 32.5%; Log-rank p=0.600, Figure A). In men, the mortality rate tended to be higher in the PCI arm at 10 years than in the CABG arm (27.0% vs. 22.5%; Log-rank p=0.082, Figure B), although the mortality rates were not different at 5 years between the PCI and CABG arms (12.4% vs. 12.3%; Log-rank p=0.957, Figure B). Conclusion The efficacy of CABG observed at 5 years disappeared at 10 years in women, whereas the efficacy of CABG became apparent after 5 years in men. Figure 1 Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): Erasmus University Medical Centre, Rotterdam, Netherlands, reference: MEC-2016-716
A general approach to solving problems on graphs by collective automata (2017)

We propose a general method to solve graph problems by a set of automata (computational agents) located in vertices of undirected ordered connected rooted graph and communicating by passing messages along graph edges. The automata are semi-robots, i.e., their internal memory size is sufficient to store values depending on the number of vertices and edges of the graph (n and m, correspondingly) but is too small to store the complete graph description. Section 2 presents classification of graph-based distributed computational models depending on internal memory size of vertex automaton, vertex automaton operation time, and edge capacity (the number of messages that are passing along an edge simultaneously). We choose for further use the model of maximum parallelism, having zero automaton operation time and unbounded edge capacity. It allows to obtain lower complexity bounds on distributed graph problems. Section 3 describes algorithm complexity assessment rules. Section 4 presents basic message processing procedures and message classification according to paths passed by them and methods of message processing by vertex automaton. We propose to construct algorithms solving graph problems on the base of the procedures considered, and present some examples in further sections. Sections 5-9 describe distributed algorithms for spanning tree construction, for task termination detection (based on detection of absence of messages used by the task), for shortest paths tree construction, for graph vertices enumeration, for collecting graph structure information in the root automaton memory (if it is unbounded). The algorithms proposed has linear time complexity in n and m, and use linear in n and m number of messages. Section 10 considers construction of maximum weight path in a weighted graph, which is the NP problem. We propose the algorithm that for the sake of using unbounded number of messages can solve this problem in linear time in n and m. The conclusion summarizes the paper and draws directions of further research: constructing algorithms for other graph problems and generalization of the approach to directed, non-deterministic and dynamic graphs.
Automated identification of multiple micro-organisms from resequencing DNA microarrays (2006)

There is an increasing recognition that detailed nucleic acid sequence information will be useful and even required in the diagnosis, treatment and surveillance of many significant pathogens. Because generating detailed information about pathogens leads to significantly larger amounts of data, it is necessary to develop automated analysis methods to reduce analysis time and to standardize identification criteria. This is especially important for multiple pathogen assays designed to reduce assay time and costs. In this paper, we present a successful algorithm for detecting pathogens and reporting the maximum level of detail possible using multi-pathogen resequencing microarrays. The algorithm filters the sequence of base calls from the microarray and finds entries in genetic databases that most closely match. Taxonomic databases are then used to relate these entries to each other so that the microorganism can be identified. Although developed using a resequencing microarray, the approach is applicable to any assay method that produces base call sequence information. The success and continued development of this approach means that a non-expert can now perform unassisted analysis of the results obtained from partial sequence data.