gebhart/patrepeval huggingface dataset:
Dysfunctional Blood and Target Tissue CD4+CD25high Regulatory T Cells in Psoriasis: Mechanism Underlying Unrestrained Pathogenic Effector T Cell Proliferation (2005)

The balance between regulatory and effector functions is important for maintaining efficient immune responses, while avoiding autoimmunity. The inflammatory skin disease psoriasis is sustained by the ongoing activation of pathogenic effector T cells. We found that a CD4(+) T lymphocyte subpopulation in peripheral blood, phenotypically CD25(high), CTLA-4(+), Foxp3(high) (regulatory T (Treg) cells), is deficient in its suppressor activity in psoriasis. This was associated with accelerated proliferation of CD4(+) responder T cells in psoriasis, the majority of which expressed CXCR3. Nevertheless, criss-cross experiments isolated the defect to psoriatic Treg cells. To examine Treg cells in a nonlymphoid tissue of a human T cell-mediated disease, Treg cells were also analyzed and isolated from the site of inflammation, psoriatic lesional skin. At the regulatory vs effector T cells ratios calculated to be present in skin, however, the psoriatic Treg cell population demonstrated decreased suppression of effector T cells. Thus, dysfunctional blood and target tissue CD4(+)CD25(high) Treg cell activity may lead to reduced restraint and consequent hyperproliferation of psoriatic pathogenic T cells in vivo. These findings represent a critical component of human organ-specific autoimmune disease and may have important implications with regard to the possible therapeutic manipulation of Treg cells in vivo.
An Air and Thermally Stable One- Component Catalyst for the Amination of Aryl Chlorides (2003)

[reaction: see text] In this paper we report a new, highly efficient palladacyclic precatalyst that is air, moisture, and thermally stable and obviates the need to employ a glovebox. We have developed a convenient one-component precatalyst for the amination of aryl chlorides that overcomes many of the limitations of those previously described.
Heterodimerization of the transcription factors E2F-1 and DP-1 leads to cooperative trans-activation. (1993)

The E2F transcription factor has been implicated in the regulation of genes whose products are involved in cell proliferation. Two proteins have recently been identified with E2F-like properties. One of these proteins, E2F-1, has been shown to mediate E2F-dependent trans-activation and to bind the hypophosphorylated form of the retinoblastoma protein (pRB). The other protein, murine DP-1, was purified from an E2F DNA-affinity column, and it was subsequently shown to bind the consensus E2F DNA-binding site. To study a possible interaction between E2F-1 and DP-1, we have now isolated a cDNA for the human homolog of DP-1. Human DP-1 and E2F-1 associate both in vivo and in vitro, and this interaction leads to enhanced binding to E2F DNA-binding sites. The association of E2F-1 and DP-1 leads to cooperative activation of an E2F-responsive promoter. Finally, we demonstrate that E2F-1 and DP-1 association is required for stable interaction with pRB in vivo and that trans-activation by E2F-1/DP-1 heterodimers is inhibited by pRB. We suggest that "E2F" is the activity that is formed when an E2F-1-related protein and a DP-1-related protein dimerize.
Llama Antibodies against a Lactococcal Protein Located at the Tip of the Phage Tail Prevent Phage Infection (2005)

Bacteriophage p2 belongs to the most prevalent lactococcal phage group (936) responsible for considerable losses in industrial production of cheese. Immunization of a llama with bacteriophage p2 led to higher titers of neutralizing heavy-chain antibodies (i.e., devoid of light chains) than of the classical type of immunoglobulins. A panel of p2-specific single-domain antibody fragments was obtained using phage display technology, from which a group of potent neutralizing antibodies were identified. The antigen bound by these antibodies was identified as a protein with a molecular mass of 30 kDa, homologous to open reading frame 18 (ORF18) of phage sk1, another 936-like phage for which the complete genomic sequence is available. By the use of immunoelectron microscopy, the protein is located at the tip of the tail of the phage particle. The addition of purified ORF18 protein to a bacterial culture suppressed phage infection. This result and the inhibition of cell lysis by anti-ORF18 protein antibodies support the conclusion that the ORF18 protein plays a crucial role in the interaction of bacteriophage p2 with the surface receptors of Lactococcus lactis.
Functional incorporation of synthetic glycolipids into cells. (1980)

Synthetic glycolipids containing an alpha-mannoside group linked by a hydrophilic spacer arm to cholesterol were incorporated into bovine erythrocytes by exchange from glycolipid-containing liposomes. When the distance between the sugar and the cholesterol moieties was approximately 26 A, functional incorporation of these glycolipids could be easily detected, as revealed by the concanavalin A-mediated agglutination of these cells. Bovine erythrocytes are not themselves susceptible to concanavalin A-mediated agglutination. The minimal concentration of concanavalin A required for agglutination of modified erythrocytes, containing 9.15 x 10(6) glycolipid molecules per cell, was 4 microgram/ml. Under these conditions, only approximately 4% of the membrane-bound cholesterol had been exchanged for the synthetic glycolipid. The observed aggregation was reversible in the presence of alpha-methyl mannoside and did not occur when beta-galactosyl-containing glycolipids were used in place of their alpha-mannoside isomers. These studies demonstrate a technique of sugar incorporation into cell membranes which should be of great advantage in studies on the roles of cell surface sugars in biological recognition. Furthermore, they demonstrate that the sugars need only be a short distance (26 A) from the membrane in order to functionally bind concanavalin A.
Precision of In-Hospital Triage in Mass-Casualty Incidents after Terror Attacks (2006)

Primary triage, even when carried out by experienced trauma physicians, can be unreliable in a MCI.
Activation-dependent contractility of rat hepatic lipocytes in culture and in vivo. (1993)

Hepatic lipocytes are perisinusoidal cells that have been thought to be analogous to tissue pericytes, a cell type with purported vasoregulatory properties. However, we and others have recently demonstrated that lipocytes acquire markers of smooth muscle cells or myofibroblasts only after liver injury, via a process termed "activation." In this study, we document lipocyte contractility on collagen lattices and examine the importance of activation in this process. In culture, lipocytes became contractile only after spreading and activating, coincident with expression of smooth muscle alpha actin, a marker of activation (1990. Virchows Arch. B Cell Pathol. 59:349). After 5 d in culture, lipocytes induced rapid and sustained contraction of collagen lattices (to 43.7 +/- 2.3% of their original size 24 h after detachment). There was no contraction of lattices containing hepatocytes. Scanning electron microscopy demonstrated intimate associations of lipocyte cell membranes and collagen fibrils. Reduction in cell volume during contraction was also prominent. Lattice contraction by lipocytes was proportional to cell number. Serum was a potent stimulator of lipocyte contraction, as were endothelin types 1, 2, and 3; the effect of serum and endothelin 1 were additive. Neither thrombin, angiotensin-II, serotonin, nor the cytokines PDGF and TGF beta induced contraction. Cytochalasin B treatment resulted in concentration-dependent inhibition of contraction. As a test of the in vivo relevance of the culture findings, lipocytes were isolated from fibrotic animals and examined immediately after adherence. Whereas lipocytes from normal liver were initially compact, smooth muscle alpha actin negative and noncontractile, cells from animals with hepatic injury due to CCl4 displayed an activated appearance, expressed smooth muscle alpha actin, and were contractile immediately after adherence. Additionally, IFN-gamma, an agent which blocks lipocyte activation (1992. Hepatology. 16:776), inhibited lipocyte contraction. The data document that normal (i.e., quiescent) lipocytes are not contractile, but that activation is associated with the development of contractility. These findings suggest that a role for lipocytes in organ contraction or vasoregulation may be confined to injured, not normal liver.
Combining body pose, gaze, and gesture to determine intention to interact in vision-based interfaces (2014)

Vision-based interfaces, such as those made popular by the Microsoft Kinect, suffer from the Midas Touch problem: every user motion can be interpreted as an interaction. In response, we developed an algorithm that combines facial features, body pose and motion to approximate a user's intention to interact with the system. We show how this can be used to determine when to pay attention to a user's actions and when to ignore them. To demonstrate the value of our approach, we present results from a 30-person lab study conducted to compare four engagement algorithms in single and multi-user scenarios. We found that combining intention to interact with a 'raise an open hand in front of you' gesture yielded the best results. The latter approach offers a 12% improvement in accuracy and a 20% reduction in time to engage over a baseline 'wave to engage' gesture currently used on the Xbox 360.
Chemical Structure of Lipid A. The Primary Immunomodulatory Center of Bacterial Lipopolysaccharides. (2002)

リポ多糖 (LPS) は、大多数のグラム陰性菌外膜の主要な構成成分であり、昆虫あるいは植物から人間へと進化する多様な真核生物における、先天性 (または自然) 免疫に関係する非常に強い促進物質であることが明らかにされてきた。敗血症ショックといった免疫反応が重篤な病的な形として現れたという所見に基づき、このクラスのバクテリアの表面分子は内毒素と名づけられた。化学 (組成) 分析、質量分析およびNMR解析を用いることで、様々なグラム陰性菌由来のLPSの化学構造が詳細に明らかにされた。細胞外にポリあるいはオリゴ糖鎖領域を持つLPSは、リピドAと呼ばれる特徴的な糖脂質によって菌体の外膜に結合している。リピドA部分はLPSにおける主要な免疫活性中心であることが証明された。メジャータイプのリピドA構造の全体像に関しては、完全あるいは改定された総説が発表されている (1、2)。この総説では、中心構造と生物活性の相関について、哺乳類における食細胞システムの免疫活性化の観点から議論する。一般的な強いアゴニスト的な (高い内毒素的な) タイプのリピドAのグループに加えて、いくつかの天然あるいは合成のリピドAは、特定の哺乳類の食細胞に対する活性化が顕著に低いかまたは全くないことが明らかにされた。後者のよりヘテロなグループのうちのいくつかにはLPS/リピドAの強い免疫促進活性を打ち消すように働くものがある。グラム陰性菌のLPSは3種の要素、リピドAの糖鎖の部分 (リピドA骨格)、先端の極性官能基の数と電荷および結合、そしてリピドA骨格に直接的あるいは間接的に結合している様々なアシル残基の数と位置および化学的な性質、により構造的な多様性が生じる。これら構造の全ての多様性のなかで、アシル化のパターンが、様々な生物システムにおける強いアゴニストあるいはアンタゴニスト的な免疫増強活性に対しては最も重要であることが示されている。
Collaborative storyboarding through democratization of content production (2014)

Pervasive computing allows immediate image and sound capturing, interaction with content, participation in content productions, and thus virtually anyone can become a multimedia content producer on the spot. With our research focus on collaborative content production, we designed a platform called "Poligatari" which aims at bringing professional content producers and amateur filmmakers together.
IL-6 Undergoes Transition fromin vitro Autocrine Growth Factor toin vivo Growth Inhibitor ofB Lymphoma Cells (1997)

IL-6 is a multifunctional cytokine involved in differentiation and proliferation of immune cells. Moreover, it has diverse effects on the proliferation of tumor cells in vivo and in vitro. Although stimulating cell growth of multiple myeloma cells, it inhibits the proliferation of B16 melanoma cells and lung cancer cells. B9.55 cells, B-cell lymphoma, are IL-6-dependent cells, definitely requiring exogenous IL-6 for growth. When the cDNA for IL-6 was transfected into B9.55 cells, they began growing in an autocrine pattern without exogenous IL-6. To investigate the effects of IL-6 on B9.55 lymphoma in vivo, IL-6-transfected B9.55 cells (B9.G7) or neotransfected B9.55 cells (B9.vec) were injected subcutaneously into syngeneic mice. Initially, B9.G7 outgrew B9.vec,but after 3 weeks, B9.G7 grew slower than B9.vec. In addition, 5 μg of recombinant human IL-6 was injected daily into the tumor site. Reduced tumor sizes of IL-6-treated rats, similar to those observed in mice which received B9.G7,indicated that IL-6 itself is the mediator of tumor regression. When B9.G7 cells were injected into the irradiated normal mice, tumor regression was released compared with the untreated normal control, suggesting that radiosensitive host components were involved in the regression of B9.G7 cell growth. However, the tumor regression of B9.G7 cells was not released in SCID mice. Histologically, B9.G7 tumor demonstrated severe necrosis and apoptotic cells with infiltration of host inflammatory cells. Above data indicate that IL-6 functions as an autocrine growth factor for B9.G7 cells in vitro,but behaves as an autocrine inhibiting factor in vivo. These contrasting effects of IL-6 on tumor cells in vitro and in vivo will be facilitative in understanding the interaction of cytokines and host immune systems.
Designed Biosynthesis of 36-Methyl-FK506 by Polyketide Precursor Pathway Engineering (2012)

The polyketide synthase (PKS) biosynthetic code has recently expanded to include a newly recognized group of extender unit substrates derived from α,β-unsaturated acyl-CoA molecules that deliver diverse side chain chemistry to polyketide backbones. Herein we report the identification of a three-gene operon responsible for the biosynthesis of the PKS building block isobutyrylmalonyl-CoA associated with the macrolide ansalactam A from the marine bacterium Streptomyces sp. CNH189. Using a synthetic biology approach, we engineered the production of unnatural 36-methyl-FK506 in Streptomyces sp. KCTC 11604BP by incorporating the branched extender unit into FK506 biosynthesis in place of its natural C-21 allyl side chain, which has been shown to be critical for FK506's potent immunosuppressant and neurite outgrowth activities.
Differentially private data release for data mining (2011)

Privacy-preserving data publishing addresses the problem of disclosing sensitive data when mining for useful information. Among the existing privacy models, ∈-differential privacy provides one of the strongest privacy guarantees and has no assumptions about an adversary's background knowledge. Most of the existing solutions that ensure ∈-differential privacy are based on an interactive model, where the data miner is only allowed to pose aggregate queries to the database. In this paper, we propose the first anonymization algorithm for the non-interactive setting based on the generalization technique. The proposed solution first probabilistically generalizes the raw data and then adds noise to guarantee ∈-differential privacy. As a sample application, we show that the anonymized data can be used effectively to build a decision tree induction classifier. Experimental results demonstrate that the proposed non-interactive anonymization algorithm is scalable and performs better than the existing solutions for classification analysis.
The relationship between AIDS and immunologic tolerance. (1992)

A hypothesis is presented in which the immunodeficiency and cell loss leading to acquired immune deficiency syndrome and the clonal deletion associated with immunologic tolerance occur through a common mechanism. In a previous publication we proposed that the interaction of human immunodeficiency virus (HIV) with CD4 delivers activation signals that disrupt immune system regulation. In this article, we compare the biology of HIV infection with recent discoveries concerning the "two-signal" molecular mechanism for thymic selection. We propose that two-signal activation is normally followed by clonal expansion and the programmed death of most or all daughter cells through mechanisms that are proportional to the strength and duration of the activation signals. In the thymus, self-reactive cells are trapped in the continuous presence of both antigen signals (signal 1) and costimulatory signals (signal 2), leading to clonal deletion. In mature lymphocytes, we propose that HIV infection contributes a chronic high-affinity signal 2, which shifts the equilibrium of antigen-activated T-cell populations further toward programmed death. This leads to incremental memory cell deficits and gradual clonal deletion at a rate dependent on the frequency of antigen exposure and the ability of an HIV quasispecies to induce signal 2.
Association Between Pulmonary Fibrosis and Coronary Artery Disease (2004)

These findings support an association between fibrotic lung disorders and CAD. Further research is necessary to confirm this relationship and to explore the pathologic processes underlying, and potentially linking, these 2 conditions.
Synthesis of Macrocyclic Cage Compounds by Diamine−Dihalide One-Step Coupling Reaction (2000)

Macropolycyclic cage compounds were synthesized by a direct reaction between diamines and bis(bromomethyl) compounds. The procedure for constructing the polycyclic cage structure is simple and straightforward. The macropolycyclic compounds obtainable from this cyclization procedure are three-dimensional cage compounds, and any other isomers were not obtained except for two examples. Benzene, pyridine, and aliphatic units could be introduced into the cage structure. The macrocycles that have strong cation affinity were obtained as their potassium complexes.
Efficient Generation of Functional Dopaminergic Neurons from Human Induced Pluripotent Stem Cells Under Defined Conditions (2010)

Human induced pluripotent stem cells (iPSCs) reprogrammed from somatic cells represent a promising unlimited cell source for generating patient-specific cells for biomedical research and personalized medicine. As a first step, critical to clinical applications, we attempted to develop defined culture conditions to expand and differentiate human iPSCs into functional progeny such as dopaminergic neurons for treating or modeling Parkinson's disease (PD). We used a completely defined (xeno-free) system that we previously developed for efficient generation of authentic dopaminergic neurons from human embryonic stem cells (hESCs), and applied it to iPSCs. First, we adapted two human iPSC lines derived from different somatic cell types for the defined expansion medium and showed that the iPSCs grew similarly as hESCs in the same medium regarding pluripotency and genomic stability. Second, by using these two independent adapted iPSC lines, we showed that the process of differentiation into committed neural stem cells (NSCs) and subsequently into dopaminergic neurons was also similar to hESCs. Importantly, iPSC-derived dopaminergic neurons were functional as they survived and improved behavioral deficits in 6-hydroxydopamine-leasioned rats after transplantation. In addition, iPSC-derived NSCs and neurons could be efficiently transduced by a baculoviral vector delivering episomal DNA for future gene function study and disease modeling using iPSCs. We also performed genome-wide microarray comparisons between iPSCs and hESCs, and we derived NSC and dopaminergic neurons. Our data revealed overall similarity and visible differences at a molecular level. Efficient generation of functional dopaminergic neurons under defined conditions will facilitate research and applications using PD patient-specific iPSCs.
High Efficiency Counter Mode Security Architecture via Prediction and Precomputation (2005)

Encrypting data in unprotected memory has gained much interest lately for digital rights protection and security reasons. Counter Mode is a well-known encryption scheme. It is a symmetric-key encryption scheme based on any block cipher, e.g. AES. The schemeýs encryption algorithm uses a block cipher, a secret key and a counter (or a sequence number) to generate an encryption pad which is XORed with the data stored in memory. Like other memory encryption schemes, this method suffers from the inherent latency of decrypting encrypted data when loading them into the on-chip cache. One solution that parallelizes data fetching and encryption pad generation requires the sequence numbers of evicted cache lines to be cached on-chip. On-chip sequence number caching can be successful in reducing the latency at the cost of a large area overhead. In this paper, we present a novel technique to hide the latency overhead of decrypting counter mode encrypted memory by predicting the sequence number and pre-computing the encryption pad that we call one-time-pad or OTP. In contrast to the prior techniques of sequence number caching, our mechanism solves the latency issue by using idle decryption engine cycles to speculatively predict and pre-compute OTPs before the corresponding sequence number is loaded. This technique incurs very little area overhead. In addition, a novel adaptive OTP prediction technique is also presented to further improve our regular OTP prediction and precomputation mechanism. This adaptive scheme is not only able to predict encryption pads associated with static and infrequently updated cache lines but also those frequently updated ones as well. Experimental results using SPEC2000 benchmark show an 82% prediction rate. Moreover, we also explore several optimization techniques for improving the prediction accuracy. Two specific techniques, Two-level prediction and Context-based prediction are presented and evaluated. For the two-level prediction, the prediction rate was improved from 82% to 96%. With the context-based prediction, the prediction rate approaches 99%. Context-based OTP prediction outperforms a very large 512KB sequence number cache for many memory-bound SPEC programs. IPC results show an overall 15% to 40% performance improvement using our prediction and precomputation, and another 7% improvement when context-based prediction techniques is used.
Representation of affinity in the case of co‐operativity in protein‐ligand binding (1994)

We have already proposed a "Global Association Function" to represent the global affinity of proteins to a drug; it was first applied in the case of independent binding sites. In this paper, we show that this same function can also be used to assess interactions between sites by varying the number of interacting sites and their co-operativity level. The resulting curves in two application cases are given together with the corresponding Scatchard plot: i) in a system with one single class of identical and interacting sites, ii) in a system with two classes of sites in which either primary or secondary are interacting; unexpectedly, in this latter case we also observed that sometimes positive co-operativity occasionally resulted in a concave-up Scatchard plot which is unusually admitted. In addition, as described in one example, our function is assumption free; this might be an advantage over usual methods, such as discrete parameter methods, because they require additional and empirical hypotheses on their related binding model.