gebhart/patrepeval huggingface dataset:
Modulating protein function through reversible oxidation: Redox‐mediated processes in plants revealed through proteomics (2012)

It has been clearly demonstrated that plants redox control can be exerted over virtually every cellular metabolic pathway affecting metabolic homeostasis and energy balance. Therefore, a tight link exists between cellular/compartmental steady-state redox level and cellular metabolism. Proteomics offers a powerful new way to characterize the response and regulation of protein oxidation in different cell types and in relation to cellular metabolism. Compelling evidence revealed in proteomics studies suggests the integration of the redox network with other cellular signaling pathways such as Ca(2+) and/or protein phosphorylation, jasmonic, salicylic, abscisic acids, ethylene, and other phytohormones. Here we review progress in using the various proteomics techniques and approaches to answer biological questions arising from redox signaling and from changes in redox status of the cell. The focus is on reversible redox protein modifications and on three main processes, namely oxidative and nitrosative stress, defense against pathogens, cellular redox response and regulation, drawing on examples from plant redox proteomics studies.
Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation (2012)

Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3' untranslated region (UTR) lengths. Different 3'UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3'UTR length, miRNA regulation, and mRNA expression--both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease.
Linet al.Reply: (2007)

A Reply to the Comment by Viktor A. Podolskiy and Evgenii E. Narimanov.Received 8 January 2007DOI:https://doi.org/10.1103/PhysRevLett.98.179402©2007 American Physical Society
Nanoscale ion implantation using focussed highly charged ions (2020)

Abstract We introduce a focussed ion beam (FIB) based ion implanter equipped with an electron beam ion source (EBIS), able to produce highly charged ions. As an example of its utilisation, we demonstrate the direct writing of nitrogen-vacancy centres in diamond using focussed, mask-less irradiation with Ar 8+ ions with sub-micron three dimensional placement accuracy. The ion optical system was optimised and is characterised via secondary electron imaging. The smallest measured foci are below 200 nm, using objective aperture diameters of 5 and 10 µ m, showing that nanoscale ion implantation using an EBIS is feasible.
B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage (2017)

SUMMARY B-1a cells are long-lived, self-renewing innate like B cells that predominantly inhabit the peritoneal and pleural cavities. In contrast to conventional B-2 cells they have a receptor repertoire that is biased towards bacterial and self-antigens, promoting a rapid response to infection and clearing of apoptotic cells. Although B-1a cells are known to primarily originate from fetal tissues the mechanisms by which they arise has been a topic of debate for many years. Here we show that in the fetal liver (FL) versus bone marrow (BM) environment, reduced IL-7R/STAT5 levels promote immunoglobulin kappa ( Igk ) recombination at the early pro-B cell stage. As a result, B cells can directly generate a mature B cell receptor (BCR) and bypass the requirement for a pre-BCR and pairing with surrogate light chain (SLC). This ‘alternate pathway’ of development enables the production of B cells with self reactive, skewed specificity receptors that are peculiar to the B-1a compartment. Together our findings connect seemingly opposing models of B-1a cell development and explain how these cells acquire their unique properties.
Data from The Expression of Adenosine A2B Receptor on Antigen-Presenting Cells Suppresses CD8<sup>+</sup> T-cell Responses and Promotes Tumor Growth (2023)

&lt;div&gt;Abstract&lt;p&gt;Accumulating evidence suggests that inhibiting adenosine-generating ecto-enzymes (CD39 and CD73) and/or adenosine A2A or A2B receptors (R) stimulates antitumor immunity and limits tumor progression. Although activating A2ARs or A2BRs causes similar immunosuppressive and protumoral functions, few studies have investigated the distinct role of A2BR in cancer. Here, we showed that A2BR expression by hematopoietic cells was primarily responsible for promoting tumor growth. Deletion of A2BR profoundly enhanced anticancer T-cell immunity. Although T-cell A2BR plays an insignificant role for A2BR-mediated immunosuppression and tumor promotion, A2BR deficiency in tumor-bearing mice caused increased infiltration of myeloid and CD103&lt;sup&gt;+&lt;/sup&gt; dendritic cells, which was associated with more effective cross-priming of adoptively transferred tumor antigen–specific CD8&lt;sup&gt;+&lt;/sup&gt; T cells. A2BR deletion also intrinsically favored accumulation of myeloid and CD11b&lt;sup&gt;dim&lt;/sup&gt; antigen-presenting cells (APC) in the tumor microenvironment. Both myeloid-specific or CD11c-specific conditional deletion of A2BR delayed primary tumor growth. Myeloid, but not CD11c-specific conditional, depletion delayed lung metastasis. Pharmacologic blockade of A2BR improved the antitumor effect of adoptive T-cell therapy. Overall, these results suggested that A2BR expression on myeloid cells and APCs indirectly suppressed CD8&lt;sup&gt;+&lt;/sup&gt; T-cell responses and promoted metastasis. These data provide a strong rationale to combine A2BR inhibition with T-cell–based immunotherapy for the treatment of tumor growth and metastasis.&lt;/p&gt;&lt;/div&gt;
Physiological, veterinary and clinical effects of hypothalamic releasing hormones (RH), especially LH-RH (1974)

Abstract
Observation of the Coexistence of Sodium and Calcium Ions in a DNA G-Quadruplex Ion Channel (2007)

The crystal structure of a DNA quadruplex, d(TGGGGT), crystallized in the presence of calcium and sodium ions, shows the presence of both ions in the central channel of the structure. This was verified by anomalous dispersion maps, which unequivocally showed the presence of calcium ions.
Deadbeat Flux Vector Control for Dynamic Six-Step Operation of Synchronous Machines (2019)

This paper proposes a deadbeat flux vector regulator to control flux along a hexagonal flux trajectory for six-step operation. Since the stator flux is directly controlled at every sampling instant, fast and smooth flux and torque generation is achieved both in steady state and transient operations. A key feature of this control technique is that deviations from the ideal six-step flux trajectory can be detected and corrected at every sample instant resulting in a very fast transient response and good disturbance rejection properties while maintaining six-step operation. Furthermore, this approach allows transitioning in and out of six-step within a few sampling periods. By using flux as the primary control variable, the control law is simple to implement and only relies on a few parameters. Moreover, this paper analyzes discrete time control limitations and stator resistance sensitivity and proposes techniques to mitigate these limitations. The paper presents simulation-based and experimental evaluation of the control approach and compares it to conventional six-step voltage angle torque control.
Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function (2019)

Abstract Adney et al. describe the complete and comprehensive codon substitution mutagenesis of human retrotransposon LINE-1 using a synthetic DNA approach. This experiment is the first of its kind for any transposon... Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a “copy-and-paste” mechanism. ORF1p is an RNA-binding protein, and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication, and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p; only 16% of trialanine mutants retained near-wild-type (WT) activity. All ORF1p mutants formed near-WT levels of mRNA transcripts and 75% formed near-WT levels of protein. Two ORF1p mutants presented a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins, and target DNA throughout the L1 life cycle.
<title>Gram-Gabor approach to optimal image representation</title> (1990)

The Gram determinant technique is applied to signal representation by non-orthogonal bases. A special case of image representation in biological and machine vision using Gabor elementary functions (GEFs) is considered. It is shown that, in general, the Gram determinant is a better approach to computation of the expansion coefficients than the one using bi-orthonormal auxiliary functions. An optimal representation by finite sets of coefficients is attained without a significant computational effort and the resultant reconstruction error converges monotonically with the addition of basis’ components to the reconstruction set. The Gram approach appears to be in a better accord with biological findings, regarding information processing along the visual pathway, compared to the conventional bi-orthogonal scheme.
Catalytic Paper Spray Ionization Mass Spectrometry with Metal Nanotubes and the Detection of 2,4,6-Trinitrotoluene (2017)

Materials are making inroads into mass spectrometry, and an example is the use of advanced materials for enhanced ionization by transformation of a less-ionizable molecule to an easily ionizable one. Here we show the use of Pt nanoparticle-decorated nanotubes as highly active catalysts for the reduction of 2,4,6-trinitrotoluene to 2,4,6-triaminotoluene and subsequent easy detection of the product by in situ ambient ionization mass spectrometry.
Processor Allocation in an N-Cube Multiprocessor Using Gray Codes (1987)

The processor allocation problem in an n-dimensional hypercube (or an n-cube) multiprocessor is similar to the conventional memory allocation problem. The main objective in both problems is to maximize the utilization of available resources as well as minimize the inherent system fragmentation. A processor allocation strategy using the buddy system, called the buddy strategy, is discussed first and then a new allocation strategy using a Gray code (GC), called the GC strategy, is proposed. When processor relinquishment is not considered (i.e., static allocation), both of these strategies are proved to be optimal in the sense that each incoming request sequence is always assigned to a minimal subcube. It is also shown that the GC strategy outperforms the buddy strategy in detecting the availability of subcubes. Our results are extended further to implement an allocation strategy using more than one GC and derive the relationship between the GC's used and the corresponding ability of detecting the availability of various subcubes. The minimal number of GC's required for complete subcube recognition in a Q <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</inf> is proved to be less than or equal to C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[n/2]</inf> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> . Several processor allocation strategies in a Q <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</inf> are implemented on the NCUBE/six multiprocessor at the University of Michigan, and their performance is experimentally measured.
Enabling Innovation Below the Communication API (2009)

Innovation in the network is notoriously difficult due to the need to support legacy applications. We argue that this difficulty stems from the API used to access the network. The ubiquitous Sockets API lets applications choose from a number of communication mechanisms, but binds them tightly to their chosen mechanism (e.g. specifying a destination using IPv4). Applications must therefore be modified in order to benefit from new network technologies. To address this problem, we propose a new communication API called NetAPI that lets applications specify their communication intents without binding to particular network mechanisms, enabling evolution below the API. We have built a NetAPI prototype for the iPhone, and use it to show that we can add disconnection tolerance, content shaping and power saving policies under NetAPI without application modifications.
The GS Protein-coupled A2a Adenosine Receptor Controls T Cell Help in the Germinal Center (2017)

T follicular helper (T<sub>FH</sub>) cells have been shown to be critically required for the germinal center (GC) reaction where B cells undergo class switch recombination and clonal selection to generate high affinity neutralizing antibodies. However, detailed knowledge of the physiological cues within the GC microenvironment that regulate T cell help is limited. The cAMP-elevating, G<sub>s</sub> protein-coupled A2a adenosine receptor (A2aR) is an evolutionarily conserved receptor that limits and redirects cellular immunity. However, the role of A2aR in humoral immunity and B cell differentiation is unknown. We hypothesized that the hypoxic microenvironment within the GC facilitates an extracellular adenosine-rich milieu, which serves to limit T<sub>FH</sub> frequency and function, and also promotes immunosuppressive T follicular regulatory cells (T<sub>FR</sub>). In support of this hypothesis, we found that following immunization, mice lacking A2aR (A2aRKO) exhibited a significant expansion of T follicular cells, as well as increases in T<sub>FH</sub> to T<sub>FR</sub> ratio, GC T cell frequency, GC B cell frequency, and class switching of GC B cells to IgG1. Transfer of CD4 T cells from A2aRKO or wild type donors into T cell-deficient hosts revealed that these increases were largely T cell-intrinsic. Finally, injection of A2aR agonist, CGS21680, following immunization suppressed T follicular differentiation, GC B cell frequency, and class switching of GC B cells to IgG1. Taken together, these observations point to a previously unappreciated role of G<sub>S</sub> protein-coupled A2aR in regulating humoral immunity, which may be pharmacologically targeted during vaccination or pathological states in which GC-derived autoantibodies contribute to the pathology.
Reusable Cryptographic Fuzzy Extractors. (2004)

We show that a number of recent definitions and constructions of fuzzy extractors are not adequate for multiple uses of the same fuzzy secret--a major shortcoming in the case of biometric applications. We propose two particularly stringent security models that specifically address the case of fuzzy secret reuse, respectively from an outsider and an insider perspective, in what we call a chosen perturbation attack. We characterize the conditions that fuzzy extractors need to satisfy to be secure, and present generic constructions from ordinary building blocks. As an illustration, we demonstrate how to use a biometric secret in a remote error tolerant authentication protocol that does not require any storage on the client&amp;apos;s side.
Effect of Cholecalciferol Supplementation on Inflammation and Cellular Alloimmunity in Hemodialysis Patients: Data from a Randomized Controlled Pilot Trial (2014)

Clinicaltrials.gov NCT01175798.
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (2007)

A number of computational methods have been proposed for identifying transcription factor binding sites from a set of unaligned sequences that are thought to share the motif in question. We here introduce an algorithm, called cosmo, that allows this search to be supervised by specifying a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may be formulated, for example, on the basis of prior knowledge about the structure of the transcription factor in question. The algorithm is based on the same two-component multinomial mixture model used by MEME, with stronger reliance, however, on the likelihood principle instead of more ad-hoc criteria like the E-value. The intensity parameter in the ZOOPS and TCM models, for instance, is estimated based on a profile-likelihood approach, and the width of the unknown motif is selected based on BIC. These changes allow cosmo to outperform MEME even in the absence of any constraints, as evidenced by 2- to 3-fold greater sensitivity in some simulation studies. Additional improvements in performance can be achieved by selecting the model type (OOPS, ZOOPS, or TCM) data-adaptively or by supplying correctly specified constraints, especially if the motif appears only as a weak signal in the data. The algorithm can data-adaptively choose between working in a given constrained model or in the completely unconstrained model, guarding against the risk of supplying mis-specified constraints. Simulation studies suggest that this approach can offer 3 to 3.5 times greater sensitivity than MEME. The algorithm has been implemented in the form of a stand-alone C program as well as a web application that can be accessed at http://cosmoweb.berkeley.edu. An R package is available through Bioconductor (http://bioconductor.org).
WLC29-4: Two-phase Collision Avoidance to Improve Scalability in Wireless LANs (2006)

IEEE 802.11 DCF exhibits poor scalability due to the large contention overhead. Therefore, the more the number of stations, the less the aggregate throughput. We propose a two-phase collision avoidance scheme to reduce the collision probability and to enhance the throughput performance. In our proposed scheme, contention among stations is resolved in two phases: SuperSlots and SubSlots. Also, our truncated backoff mechanism increases the throughput by reducing the idle time slots. We analyze the performance of our proposed scheme based on the previous analysis of 802.11 DCF. Both the analysis and simulation results exhibit that our proposed scheme achieves higher throughput than the current IEEE 802.11 backoff mechanism, and this differential increases with the number of stations in the network.
Au Bump Interconnection in 20 µm Pitch on 3D Chip Stacking Technology (2003)

The three-dimensional (3D) chip stacking LSI technology under development in Association of Super-Advanced Electronic Technologies (ASET) is a new packaging technology for realizing high-density and high-speed transmission, and superfine flip-chip bonding technologies utilizing 20-µm-pitch micro bumps on Cu through hole electrodes are substantial technologies. There are two key technical issues involved in realizing the 3D chip stacking LSI. One is the provision of the sufficient interconnections, which have low resistivity and which are absolutely connected. Another is the reduction of the thermal stress of the micro bumps by providing encapsulated resin between devices. Regarding the metallurgically stable and low electrical resistance interconnections, electroplated Au bump bonding in 20-µm-pitch by thermo compression bonding process was evaluated on the chip-on-chip(COC) structure. First, the softening of the Au bump by annealing was confirmed, and was expected to decrease the bonding stress of the under bump structure. Second, the lower limit bonding conditions were confirmed to be a bonding force of 24.5 N at 350°C, and the electrical resistance was confirmed to be stable at about 0.55 Ω. The mechanism of Au–Au thermo compression bonding with the solid phase diffusion across the boundary was confirmed. Finally, the life of the 20-µm-pitch interconnection with the underfillresin containing the hyperfine filler particles under temperature cycling tests (TCT) was more than 1000 cycles, which is an acceptable level for a semiconductor package. This research will enable the realization of 3D chip stacking LSI in the near future which features scalability and high performance. The subjects are the verification of the appropriate bump dimensions in order to further improve the reliability and the realization of the interconnection reliability on 3D chip stacking LSI.
Instant-Messagers Really Are About Six Degrees from Kevin Bacon; Big Microsoft Study Supports Small World Theory (2016)

Turns out, it is a small world. The “small world theory,” embodied in the old saw that there are just “six degrees of separation” between any two strangers on Earth, has been largely corroborated by a massive study of electronic communication.
Relapsed Multiple Myeloma Presenting as Intracranial Plasmacytoma and Malignant Pericardial Effusion following Recent Allogeneic Stem Cell Transplantation (2017)

Although rare, both central nervous system and pericardial involvement of myeloma have been well described in the literature. Their simultaneous occurrence in relapsed disease, however, has not been previously reported. This case describes a 54-year-old female who was treated for high-risk multiple myeloma with multiregimen chemotherapy and allogeneic hematopoietic stem cell transplantation. Four months after transplant, she was found to have relapsed disease manifesting as an extraosseous, intracranial plasmacytoma and simultaneous malignant pericardial effusion. Her disease characteristics, treatment course, radiologic and pathologic findings are described in detail, and we review the previous literature to determine the various aspects of her disease that may have contributed to her aggressive clinical course.