gebhart/patrepeval huggingface dataset:
Ube3a expression is not altered in Mecp2 mutant mice (2006)

Rett syndrome (RTT) is a neurodevelopmental disorder characterized by cognitive regression, loss of purposeful hand movements and speech, stereotypies, ataxia, seizures, mental retardation and acquired microcephaly. Mutations in MECP2, encoding methyl-CpG-binding protein 2, are responsible for approximately 90% of classic RTT cases. RTT displays phenotypic overlap with Angelman syndrome, a disorder caused by loss of expression of the imprinted gene UBE3A. MeCP2 binds to methylated DNA and may alter the expression of imprinted genes, thereby suggesting a mechanistic link between the two disorders. Here, we tested the hypothesis that MeCP2 deficiency affects expression of Ube3a in mouse models of RTT. As Ube3a is only imprinted in brain, we evaluated Ube3a expression in brains of 15 different litters of neonatal or 8-week-old male Mecp2 mutant mice by real-time quantitative RT-PCR and western blot analysis. We found no significant differences between Mecp2(tm1.1Bird/Y) or Mecp2(tm1.1Jae/Y) mutants and their wild-type male siblings that served as negative controls. In positive control mice carrying a maternally inherited Ube3a deletion, Ube3a sense transcript and protein levels were drastically reduced. Our data contrast with two recent reports of substantially decreased Ube3a expression in brain tissues of MeCP2-deficient mice. We, therefore, challenge the conclusion that decreased UBE3A/Ube3a expression contributes to the pathophysiology of RTT.
The Biology of Chromatin Remodeling Complexes (2009)

The packaging of chromosomal DNA by nucleosomes condenses and organizes the genome, but occludes many regulatory DNA elements. However, this constraint also allows nucleosomes and other chromatin components to actively participate in the regulation of transcription, chromosome segregation, DNA replication, and DNA repair. To enable dynamic access to packaged DNA and to tailor nucleosome composition in chromosomal regions, cells have evolved a set of specialized chromatin remodeling complexes (remodelers). Remodelers use the energy of ATP hydrolysis to move, destabilize, eject, or restructure nucleosomes. Here, we address many aspects of remodeler biology: their targeting, mechanism, regulation, shared and unique properties, and specialization for particular biological processes. We also address roles for remodelers in development, cancer, and human syndromes.
De ima(r)ginarios y memorias olvidadas. Reflexiones sobre redes de comunicación e interculturalidad (2005)

The following reflections support some researching criteria around the Political Ecology of
Communications, which null writing degree is located in the mapping of the family genealogy
in the construction of the life projects and in the dwelling and coexisting logics.
We are going to debate some concepts close to intercultural communication (emplacements,
displacements, itineraries, borders) that will allow us to sustain the multidiversity as an
approach of space-temporal articulation of the displaced groups in the new global community.
Thus, we are going the re-locate the value of their personal memoirs in the construction of new
citizenship environments that, acknowledging the technological possibilities, will put them to
serve the intercultural communication, dis-covering the inter-mediation spaces of the family
genealogies: the value of the intersubjectivity in the setting-up of the social subject (gender,
generation, culture and territory), the interdependence in the definition of their vital space and
time (public/private, personal/collective, past/present/future), the intertextuality in the narration
of the life story account (representations of the oral, iconic, kinesic; of the rational/symbolic/
emotive); the interdisciplinarity and interactivity, as opportunities to describe wefts, itineraries
and polyphonic narratives that will give account of our ontological multiculturality.
Ising Machines—Quantum-Inspired Machines for Combinatorial Optimization— (2022)

本稿では，近年国内外で活発に研究開発されているイジングマシンについて述べる．イジングマシンとは，イジング問題と呼ばれる組合せ最適化問題に特化した専用計算機である．世界初の商用量子コンピュータである量子アニーラがイジングマシンの一種であり，それをGoogleとNASAが創設した量子人工知能研究所が購入したことをきっかけに，イジングマシンが注目を集めるようになった．現在では，超伝導や光といった特殊なハードウェアだけでなく，従来の半導体デジタル計算機を利用して実用性を高めたものも多く，ドメイン指向コンピューティングの新たな潮流となっている．後者は主にアルゴリズムに特徴があり，中には量子計算にインスパイアされて発見されたものもある．そもそも量子アニーラに端を発した研究という経緯もあり，メディアはこれらを「疑似量子コンピュータ」と呼ぶことがある．イジングマシンと似たものとして，ホップフィールドニューラルネットワークをご存じの読者は多いだろう．実際，ホップフィールドニューラルネットワークの派生物であるボルツマンマシンなどは，現在のイジングマシンとの関係が深い．そこで，本稿の前半では，特殊ハードウェアから疑似量子コンピュータまで，現在開発中の多種多様なイジングマシンをホップフィールドニューラルネットワークやその派生物との類似に触れながら紹介する．後半は，筆者が提案し，現在も研究開発中である疑似量子コンピュータ，シミュレーテッド分岐マシンについて解説する．
Process Investigations for the Global Studio Project Version 3.0 (2007)

In this paper we present an overview of current plans for the global studio project version 3.0. version 3.0 applies a new experimental process with a higher degree of collaboration and that relies less on the central team, as compared to the extended workbench model. We expect that the use of an architecture for component integration and the identification of domain experts for each component will significantly reduce the amount of upfront architecture and requirements work usually required from the central team in the extended workbench model.
Toxicological consultation data management system based on experience of Pomeranian Center of Toxicology (2015)

Information about Poison Control Center consultations access should be better spread among medical service providers. The extent of poison information collected by Polish Poison Control Centers should be limited and unified. This should contribute to the increased percentage of properly documented consultations. Additional duties stemming from the need of digital archiving of consults provided, require the involvement of additional staff, leading to the increased operation costs incurred by Poison Control Centers.
Ethical considerations of using a single minor donor for three bone marrow harvests for three HLA‐matched siblings with primary immunodeficiency (2019)

Allogeneic hematopoietic stem cell transplantation is curative for primary immunodeficiencies. Bone marrow from an unaffected human leukocyte antigen (HLA)-identical sibling donor is the ideal graft source. For minor donors, meaningful consent or assent may not be feasible, and permission from parents or legal guardians is considered acceptable. Adverse events, albeit extremely small, can be associated with bone marrow harvest in pediatric donors. Donor safety concerns potentially increase with multiple bone marrow harvests. Very little is known about multiple bone marrow harvests from pediatric donors. We describe the ethical considerations and clinical decision-making in an unusual clinical situation where three patients with the same primary immunodeficiency were HLA identical to one another and their younger sibling, who underwent bone marrow harvests three times between 1.3 and 4 years of age, resulting in successful transplantation for all three patients. We hope that this experience will provide guidance to providers and families in a similar situation.
A Brief Introduction to Time-to-Digital and Digital-to-Time Converters (2010)

This paper presents a short review of time-to-digital and digital-to-time converters (TDCs and DTCs, respectively) adopting a time-mode signal-processing perspective. The primary definitions, operating principles, and basic building blocks are presented. The discussion applies to most, if not all, DTCs and TDCs. A series of voltage-controlled delay units are used as the primary building block of these converter circuits. When configured in a servo-loop manner, a very short time resolution is achievable with excellent manufacturing robustness. Such designs can be synthesized in field-programmable gate arrays (FPGAs) or constructed in custom silicon. TDCs and DTCs are not new, as they have extensively been used for making very accurate and repeatable time measurements in both the physics-related and semiconductor industry. Today, TDCs and DTCs are finding new applications in phase-locked loops and frequency synthesizers.
A simple distributed PRMA for MANETs (2002)

With the rapid development of Global Positioning System (GPS) technology and its applications, synchronization between terminals in mobile ad hoc environments becomes feasible at a low cost. Thus, slotted-channel-based medium access control (MAC) schemes like time division multiple access (TDMA) also become interesting for mobile ad hoc networks (MANETs). In this paper, we extend the classical centralized and slotted packet reservation multiple access (PRMA) scheme to a simple distributed PRMA (D-PRMA) as a MAC scheme for MANETs, with emphasis on voice application support. The major efforts of D-PRMA include 1) a simple slot reservation mechanism for voice traffic at the level of "talkspurt" without relying on any central entity and 2) a simple solution for the hidden and exposed terminal problems uniquely present in wireless ad hoc environments. The performance of D-PRMA has been investigated by analysis and computer simulations in comparison with IEEE 802.11. The results show that D-PRMA is much more suitable than IEEE 802.11 for voice application.
Chemicals and Fuels from Bio‐Based Building Blocks (2016)

An up-to-date and two volume overview of recent developments in the field of chemocatalytic processes for the transformation of renewable material into essential chemicals and fuels. Experts from both academia and industry discuss catalytic processes currently under development as well as those already in commercial use for the production of bio-fuels and bio-based commodity chemicals. As such, they cover drop-in commodity chemicals and fuels, as well as bio-based monomers and polymers, such as acrylic acid, glycols, polyesters and polyolefins. In addition, they also describe reactions applied to waste and biomass valorization and integrated biorefining strategies. With its comprehensive coverage of the topic, this is an indispensable reference for chemists working in the field of catalysis, industrial chemistry, sustainable chemistry, and polymer synthesis.
Vav1 Sustains the In Vitro Differentiation of Normal and Tumor Precursors to Insulin Producing Cells Induced by all-Trans Retinoic Acid (ATRA) (2020)

All-trans retinoic acid (ATRA) promotes the development and the function of insulin producing cells and induces partial differentiation of pancreatic tumor cells. A number of evidences clearly indicate that the ATRA mediated signaling may have a substantial role in therapeutic approaches based on restoration of functional β-cells. Among the proteins up-regulated by ATRA, Vav1 is involved in maturation and function of haematopoietic cells and is essential for retinoids induced differentiation of tumor promyelocytes. The presence of Vav1 in solid tissues, including pancreas, is considered ectopic and no role in the differentiation of human epithelial cells has so far been described. We demonstrated here that Vav1 sustains the maturation to β-cells of the normal precursors human Biliary Tree Stem/progenitor Cells (hBTSCs) induced by a differentiation medium containing ATRA and that, in the mature normal pancreas, insulin-producing cells express variable levels of Vav1. Using pancreatic ductal adenocarcinoma (PDAC)-derived cells, we also revealed that the ATRA induced up-modulation of Vav1 is essential for the retinoid-induced trans-differentiation of neoplastic cells into insulin producing cells. The results of this study identify Vav1 as crucial molecule in ATRA induced maturation of insulin producing cells and suggest this protein as a marker for new strategies ended to restore functional β-cells. Graphical abstract.
Estrogen and Tamoxifen Modulate Cerebrovascular Tone in Ovariectomized Female Rats (2004)

Postmenopausal estrogen deficiency increases the incidence of cerebrovascular disease. However, hormone replacement therapy is associated with an increased cardiovascular risk. Tamoxifen is a selective estrogen receptor modulator with estrogenic effects on cardiovascular risk factors, but its long-term impacts on cerebral vasculature are unknown. We hypothesized that chronic 17beta-estradiol or tamoxifen treatment exerted similar effects in reducing cerebrovascular tension in ovariectomized rats. We therefore determine whether (1) chronic 17beta-estradiol treatment could influence vasomotor activities, (2) chronic tamoxifen therapy could exert an estrogen-like or estrogen-antagonistic effect, and (3) acute exposure to estrogen could mimic the effect of 17beta-estradiol. Isometric tension was measured in cerebral arteries from female rat groups: control, ovariectomy, ovariectomy plus 17beta-estradiol treatment, ovariectomy plus tamoxifen treatment, and ovariectomized rats treated with tamoxifen and 17beta-estradiol. Ovariectomy enhanced cerebrovascular contractions to endothelin-1 or CaCl2, but not to U46619 or phenylephrine. 17beta-Estradiol therapy reversed these effects. Chronic tamoxifen treatment exerted estrogen-like actions by reversing ovariectomy-induced enhancement of vessel tone without antagonizing the effect of chronic 17beta-estradiol treatment. Ovariectomy enhanced the relaxing potency of nicardipine, and 17beta-estradiol treatment prevented this effect. Acute exposure to 10(-9) mol/L 17beta-estradiol or 10(-8) mol/L tamoxifen did not modulate contractions in rings from nonoperated female rats. In conclusion, ovariectomy differentially enhances agonist-induced cerebrovascular tone, an effect that was reversed by estrogen therapy. Tamoxifen does not act as an estrogen antagonist; instead, it functions as an estrogen agonist during estrogen deficiency. Thus, tamoxifen may confer beneficial effects similar to estrogen in cerebrovascular vessels.
Input Distribution Optimization in OFDM Dual-Function Radar-Communication Systems (2023)

Orthogonal frequency division multiplexing (OFDM) has been widely adopted in dual-function radar-communication (DFRC) systems, where radar and communications are performed simultaneously with a common signal. However, with random communication symbols (CS) in DFRC, the transmit signal has a random ambiguity function that affects the radar's range-velocity estimation performance, whose influence is remained uncovered. Hence, this paper focuses on minimizing the outlier probability (OP) -- the probability of incorrectly estimating a target's range-velocity bin -- in OFDM DFRC w.r.t the CS probability distribution (i.e., the \emph{input distribution}). Conditioned on the CSs, the OP only depends on the CS magnitudes. Hence, we consider the following two schemes for the above optimization: CSs with (1) constant magnitude (phase shift keying input), and (2) random magnitude (Gaussian input). For (1), the problem reduces to the familiar power allocation design across OFDM's subcarriers and symbols, with uniform power allocation across subcarriers and a \emph{windowed} power allocation across symbols being near-optimal. For (2), the mean and variance of the Gaussian distribution at each subcarrier is optimized, with an additional communication constraint to avoid the zero-variance solution where no CSs are carried. We observe that subcarriers with strong communication channels feature strong variance (i.e., favour communications) while the others are characterized by a strong mean (favouring radar). However, the overall power allocation (i.e., the sum of mean and variance) across the OFDM subcarriers and symbols is similar to (1). Simulations show that CSs with random magnitudes degrade the sensing performance, but can be compensated significantly with the proposed input distribution optimization.
The Evolution of Peace Operations from the Nineteenth Century (1999)

(1999). The Evolution of Peace Operations from the Nineteenth Century. Small Wars & Insurgencies: Vol. 10, Peace Operations Between War and Peace, pp. 4-20.
Aerocyanidin, a new antibiotic produced by Chromobacterium violaceum. (1988)

Aerocyanidin, a new antibiotic containing an isonitrile group, has been isolated from fermentations of Chromobacterium violaceum ATCC 53434. Structure 1 was assigned on the basis of spectroscopic characterization of the antibiotic and of a degradation product that results from treatment with base. The antibiotic is primarily active against Gram-positive bacteria.
Non-coding sequence variation reveals fragility within interleukin 2 feedback circuitry and shapes autoimmune disease risk (2023)

Genetic variants associated with human autoimmune diseases commonly map to non-coding control regions, particularly enhancers that function selectively in immune cells and fine-tune gene expression within a relatively narrow range of values. How such modest, cell-type-selective changes can meaningfully shape organismal disease risk remains unclear. To explore this issue, we experimentally manipulated species-conserved enhancers within the disease-associated <i>IL2RA</i> locus and studied accompanying changes in the progression of autoimmunity. Perturbing distinct enhancers with restricted activity in conventional T cells (Tconvs) or regulatory T cells (Tregs)-two functionally antagonistic T cell subsets-caused only modest, cell-type-selective decreases in <i>IL2ra</i> expression parameters. However, these same perturbations had striking and opposing effects <i>in vivo</i> , completely preventing or severely accelerating disease in a murine model of type 1 diabetes. Quantitative tissue imaging and computational modelling revealed that each enhancer manipulation impinged on distinct IL-2-dependent feedback circuits. These imbalances altered the intracellular signaling and intercellular communication dynamics of activated Tregs and Tconvs, producing opposing spatial domains that amplified or constrained ongoing autoimmune responses. These findings demonstrate how subtle changes in gene regulation stemming from non-coding variation can propagate across biological scales due to non-linearities in intra- and intercellular feedback circuitry, dramatically shaping disease risk at the organismal level.
Peripheral blood lymphocytes genetically modified to express the self/tumor antigen MAGE-A3 induce antitumor immune responses in cancer patients (2008)

Dendritic cell (DC) targeting in vivo has recently been shown to confer strong and protective cytotoxic T lymphocyte (CTL)-based immunity in tumor murine models. Our group has recently demonstrated in preclinical models that the infusion of genetically modified lymphocytes (GMLs) expressing the self/tumor antigen TRP-2 is able to elicit functional TRP-2-specific effectors with antitumor activity by targeting DCs in vivo. Here we have analyzed vaccine- and tumor-specific immune responses of 10 melanoma patients treated with autologous GMLs expressing the cancer germline gene MAGE-A3. Three of 10 patients treated with MAGE-A3-GML showed an increase of circulating anti-MAGE-A3 T cells, and developed skin delayed-type hypersensitivity to MAGE-A3. Interestingly, in 2 of these patients, with progressive and measurable tumors at study entry, anti-MAGE-A3 T cells were detected not only in the blood but also within tumors resected after vaccination. These results demonstrate that the infusion of MAGE-A3-GML elicits antitumor T cells, which are capable of trafficking to inflamed tissues and of infiltrating tumors. Clinical studies on a larger group of patients are needed to evaluate the clinical efficacy of such a strategy.
Positional changes of the frontoparietal ossification centers in perinatal craniosynostotic rabbits. (1999)

It has been suggested that craniosynostosis is caused by abnormally located ossification centers (i.e., bony tubers) in the developing skull prior to suture formation [Mathijssen et al., 1996, 1997]. The present study was designed to test this hypothesis in a rabbit model of human familial, nonsyndromic coronal suture (CS) synostosis. Calvariae were taken from 99 New Zealand White rabbit perinates (55 normal controls, 15 with delayed-onset CS synostosis, and 29 with bilateral or unilateral CS synostosis), ranging in age from 23 to 34 days postconception (synostosis occurs at approximately 23 days in this model). Frontoparietal, interfrontal, and interparietal ossification center distances were obtained using a Wild microscope with camera lucida attachment and a 2-D computer digitization technique. Linear regression analysis was used to compare age-related changes in the perinatal ossification centers among groups. Results revealed that frontoparietal ossification center regression line slopes had similar start points (24-day intercepts) with significantly (P < 0.05) diverging slopes over time. Normal and delayed-onset ossification center distance increased more rapidly than in synostosed perinates. No significant (P > 0.05) differences were noted in regression line slopes among groups for interparietal or interfrontal ossification center distances. Results demonstrated that, in synostosed perinates, frontoparietal ossification center location was similar to normals around the time of synostosis and became displaced later. These findings suggest that ossification center (i.e., bony tuber) displacement seen in infants with craniosynostosis is probably a secondary and compensatory, postsynostotic change and not a primary causal factor of synostosis in this rabbit model.
Homotopy reconstruction for compressive sensing based cooperative transmissions in cognitive radio network (2015)

Compressive sensing (CS) based cooperative transmissions is investigated in cognitive radio networks (CRN). Energy efficiency based optimal relay selection is implemented to determine the measurement numbers in CS. Homotopy reconstruction method that solves a bound constrained quadratic programming (BCQP) problem is studied for signal sparse reconstruction at secondary user destination (SUD) in CRN. Based on the determined measurement numbers, binary phase shift keying (BPSK) modulation signal is sparsely sampled by analog-to-information converters (AICs) equipped at the selected secondary user relays (SURs). The corresponding measurement matrix is constructed in CS-based cooperative transmissions. Homotopy reconstruction method is implemented to obtain dynamic update of the solution for BCQP problem. The updating critical value of homotopy parameter and the updating solution of the reconstructed signals' autocorrelation vector can be both achieved via iteration. Simulation results are presented to validate the effectiveness of the proposed approach. It is shown that, homotopy method recovers original signal approximately in low signal-to-noise ratio (SNR) region. Compared with orthogonal matching pursuit (OMP) reconstruction approach, it provides a balanced solution considering normalized mean square error (NMSE) performance versus computational complexity. Moreover, spectrum sensing overhead plays significant role in CS based cooperative transmissions.
Avid binding by B cells to the Plasmodium circumsporozoite protein repeat suppresses responses to protective subdominant epitopes (2021)

Antibodies targeting the NANP/NVDP repeat domain of the Plasmodium falciparum circumsporozoite protein (CSP<sub>Repeat</sub>) can protect against malaria. However, it has also been suggested that the CSP<sub>Repeat</sub> is a decoy that prevents the immune system from mounting responses against other domains of CSP. Here, we show that, following parasite immunization, B cell responses to the CSP<sub>Repeat</sub> are immunodominant over responses to other CSP domains despite the presence of similar numbers of naive B cells able to bind these regions. We find that this immunodominance is driven by avid binding of the CSP<sub>Repeat</sub> to cognate B cells that are able to expand at the expense of B cells with other specificities. We further show that mice immunized with repeat-truncated CSP molecules develop responses to subdominant epitopes and are protected against malaria. These data demonstrate that the CSP<sub>Repeat</sub> functions as a decoy, but truncated CSP molecules may be an approach for malaria vaccination.