gebhart/patrepeval huggingface dataset:
Brorin, a Novel Secreted Bone Morphogenetic Protein Antagonist, Promotes Neurogenesis in Mouse Neural Precursor Cells (2007)

We identified a gene encoding a novel secreted protein in mice and humans and named it Brorin. Mouse Brorin consists of 324 amino acids with a putative secreted signal sequence at its amino terminus and two cysteine-rich domains in its core region. Positions of 10 cysteine residues in the domains of Brorin are similar to those in the cysteine-rich domains of members of the Chordin family. However, the amino acid sequence of Brorin is not significantly similar to that of any other member of the Chordin family, indicating that Brorin is a unique member of the family. Mouse Brorin protein produced in cultured cells was efficiently secreted into the culture medium. The protein inhibited the activity of bone morphogenetic protein 2 (BMP2) and BMP6 in mouse preosteoblastic MC3T3-E1 cells. Mouse Brorin was predominantly expressed in neural tissues in embryos and also predominantly expressed in the adult brain. In the brain, the expression was detected in neurons, but not glial cells. The neural tissue-specific expression profile of Brorin is quite distinct from that of any other member of the Chordin family. Brorin protein promoted neurogenesis, but not astrogenesis, in mouse neural precursor cells. The present findings indicate that Brorin is a novel secreted BMP antagonist that potentially plays roles in neural development and functions.
Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus (2002)

How eukaryotes specify their replication origins is an important unanswered question. Here, we analyze the replicative organization of yeast rDNA, which consists of approximately 150 identical repeats, each containing a potential origin. Using DNA combing and single-molecule imaging, we show that functional rDNA origins are clustered and interspersed with large domains where initiation is silenced. This repression is largely mediated by the Sir2p histone-deacetylase. Increased origin firing in sir2 Delta mutants leads to the accumulation of circular rDNA species, a major determinant of yeast aging. We conclude that rDNA replication is regulated epigenetically and that Sir2p may promote genome stability and longevity by suppressing replication-dependent rDNA recombination.
The human ATP-binding cassette (ABC) transporter superfamily (2001)

The transport of specific molecules across lipid membranes is an essential function of all living organisms and a large number of specific transporters have evolved to carry out this function. The largest transporter gene family is the ATP-binding cassette (ABC) transporter superfamily. These proteins translocate a wide variety of substrates including sugars, amino acids, metal ions, peptides, and proteins, and a large number of hydrophobic compounds and metabolites across extra- and intracellular membranes. ABC genes are essential for many processes in the cell, and mutations in these genes cause or contribute to several human genetic disorders including cystic fibrosis, neurological disease, retinal degeneration, cholesterol and bile transport defects, anemia, and drug response. Characterization of eukaryotic genomes has allowed the complete identification of all the ABC genes in the yeast Saccharomyces cerevisiae, Drosophila, and C. elegans genomes. To date, there are 48 characterized human ABC genes. The genes can be divided into seven distinct subfamilies, based on organization of domains and amino acid homology. Many ABC genes play a role in the maintenance of the lipid bilayer and in the transport of fatty acids and sterols within the body. Here, we review the current knowledge of the human ABC genes, their role in inherited disease, and understanding of the topology of these genes within the membrane.
Pathologic changes in the pericoronal tissues of unerupted third molars. (2001)

Unerupted third molars should be removed before pathologic changes can occur in their pericoronal tissues. This justifies routine removal of unerupted third molars from patients older than 20 years.
A Prospective Study of Benign Breast Disease and the Risk of Breast Cancer (1992)

<h3>Objective.</h3> —To examine the relation between proliferative benign breast disease with and without atypical hyperplasia and the subsequent risk of breast cancer. <h3>Design.</h3> —Case-control study nested within a prospective cohort study. Median follow-up after breast biopsy was 8 years (25th to 75th percentile, 5 to 14 years). <h3>Participants.</h3> —Selected from a prospective cohort of 121 700 US registered nurses followed up from 1976 to 1986. Cases were women with breast cancer who had a prior biopsy for benign breast disease. Controls were randomly selected and matched on year of biopsy and year of birth from among women in the cohort who had a benign breast biopsy but who did not develop breast cancer. Included in the analysis were 121 cases and 488 controls. <h3>Main Outcome Measure.</h3> —Development of breast cancer. <h3>Results.</h3> —Slides from the first benign breast biopsy were reviewed by two breast pathologists blinded to the outcome. The multiply adjusted relative risks (RRs) for breast cancer, relative to women with no proliferative disease, were 1.6 for proliferative disease without atypia (95% confidence interval [Cl], 1.0 to 2.5) and 3.7 for atypical hyperplasia (95% Cl, 2.1 to 6.8). Breast cancer risk was more strongly associated with atypical hyperplasia among premenopausal women (RR = 5.9; 95% Cl, 2.9 to 13.2) than postmenopausal women (RR = 2.3; 95% Cl, 0.9 to 5.9), but the association of breast cancer risk with proliferative disease without atypia did not differ across menopausal status. <h3>Conclusion.</h3> —These results confirm the marked increase in breast cancer risk among women with atypical hyperplasia, particularly in premenopausal women, and suggest that these women should be encouraged to undergo frequent breast cancer screening. (<i>JAMA</i>. 1992;267:941-944)
Molecular cloning and sequence analysis of antigen gene tdpA of Treponema denticola (1991)

We isolated and characterized an immunogenic protein of an oral spirochete, Treponema denticola Johnson. A genomic DNA library constructed with bacteriophage lambda EMBL3 as a vector was immunologically screened with a rabbit antiserum against the whole cells. Using Western immunoblot analysis, we found a particular clone encoding an antigen with a molecular weight of 53,000; we designated the antigen as T. denticola protein A (TdpA). Complete sequence determination revealed an open reading frame of 1,419 bp and a signal peptide sequence that was homologous to that of bacterial lipoprotein. Southern hybridization analysis revealed that the tdpA gene is highly conserved in six tested strains of T. denticola species. Furthermore, we found that sera from some periodontitis patients contained antibody against the TdpA protein, although the reactivities of the antibodies varied among individuals.
Activating enhancer-binding protein-2α induces cyclooxygenase-2 expression and promotes nasopharyngeal carcinoma growth (2014)

Activating enhancer-binding protein-2α (AP-2α) regulates the expression of many cancer-related genes. Here, we demonstrated a novel mechanism by which AP-2α up-regulated cyclooxygenase-2 (COX-2) expression to promote the growth of nasopharyngeal carcinomas (NPCs). High expression of AP-2α in NPC cell lines and tumor tissues from NPC patients was detected and significantly correlated with COX-2 expression. Overexpression of AP-2α and COX-2 in tumor tissues was associated with advanced tumor stage, clinical progression, and short survival of patients with NPCs. Knockdown of AP-2α by siRNA markedly inhibited COX-2 expression and PGE2 production in NPC cells. Exogenous expression of AP-2α up-regulated the COX-2 and PGE2. Knockdown of AP-2α also significantly suppressed cell proliferation in NPC cells in vitro and tumor growth in a NPC xenograft mouse model. Moreover, we found that p300 played an important role in the AP-2α/COX-2 pathway. AP-2α could co-localize and interact with p300 in NPC cells. Overexpression of the p300, but not its histone acetyltransferase (HAT) domain deletion mutant, promoted the acetylation of AP-2α and its binding on the COX-2 promoter, thereby up-regulated COX-2 expression. Our results indicate that AP-2α activates COX-2 expression to promote NPC growth and suggest that the AP-2α/COX-2 signaling is a potential therapeutic target for NPC treatment.
Security implications in Kerberos by the introduction of smart cards (2012)

Public key Kerberos (PKINIT) is a standardized authentication and key establishment protocol which is used by the Windows active directory subsystem. In this paper we show that card-based public key Kerberos is flawed. In particular, access to a user's card enables an adversary to impersonate that user even after the adversary's access to the card is revoked. The attack neither exploits physical properties of the card, nor extracts any of its secrets.
Heteroaromatic N-Oxides. X. Synthesis and Reactions of Benzothiazole 3-Oxide (1970)

Benzothiazole 3-oxide (II) was synthesized, starting from its 2-methyl derivative, via the corresponding aldoxime, carbonitrile, imido ester and carboxylic acid. The reaction of the N-oxide II ; deoxygenations, reactions with various nucleophilic agents (tosyl chloride, Ac2O, C6H5MgBr, NaHSO3, NH2NH2·H2O and KCN·BzCl) involving some 1, 3-dipolarophiles (benzyne, C6H5NCO and tetracyanoethylene), and quaternizations were investigated and compared with those of the corresponding imidazole N-oxide.
Antidiabetic agents: a new class of reversible carnitine palmitoyltransferase I inhibitors (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntidiabetic agents: a new class of reversible carnitine palmitoyltransferase I inhibitorsRobert C. Anderson, Michael Balestra, Philip A. Bell, Rhonda O. Deems, William S. Fillers, James E. Foley, James D Fraser, William R. Mann, Markus Rudin, and Edwin B. VillhauerCite this: J. Med. Chem. 1995, 38, 18, 3448–3450Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/jm00018a003https://doi.org/10.1021/jm00018a003research-articleACS PublicationsRequest reuse permissionsArticle Views267Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Design, Synthesis, and Structure−Activity Relationship of 6-Alkynylpyrimidines as Potent Adenosine Kinase Inhibitors (2002)

Adenosine (ADO) is an extracellular signaling molecule within the central and peripheral nervous system. Its concentration is increased at sites of tissue injury and inflammation. One of the mechanisms by which antinociceptive and antiinflammatory effects of ADO can be enhanced consists of inhibition of adenosine kinase (AK), the primary metabolic enzyme for ADO. Novel nonnucleoside AK inhibitors based on 4-amino-6-alkynylpyrimidines were prepared, and the importance of the length of the linker at the 5-position for high affinity AK inhibition was demonstrated. Compounds with 2- and 3-atom linkers were the most potent AK inhibitors. Optimization of their physicochemical properties led to 31a and 37a that effectively reduced pain and inflammation in animal models.
DLD pillar shape design for efficient separation of spherical and non-spherical bioparticles (2014)

Particle sorting methods in microfluidic platforms are gaining momentum for various biomedical applications. Bioparticles are found in different shapes and sizes. However, conventional separation techniques are mainly designed for separation of spherical particles. Thus, there is a need to develop new methods for effective separation of spherical and non-spherical bioparticles for various applications. Deterministic lateral displacement (DLD) microfluidic methods have become popular for high separation resolution, simplicity, and predictability. However, shape sorting in the DLD separation methods is not well researched. Recently, we explored this area and found that pillar shapes in DLD significantly affect bioparticle separation. In this work, we designed a group of different pillar shapes with protrusions and groove structures with the hypothesis that pillar protrusions will induce particle rotation while pillar grooves will confine the particle rotational movement in a directed path for effective separation in a DLD pillar array. Using combinations of protrusions and grooves, 3-dimensional spherical particles, 2-dimensional planar disc-shaped red blood cells and 1-dimensional rod-shaped bacteria were separated and two interesting phenomena were observed. Firstly, the arrangement of pillar protrusions and grooves induces inertial movements, enhancing the separation of spherical particles. Secondly, non-spherical particles experience dominant rotational movements due to the protrusions and grooves which help in changing their orientations. This gives an opportunity to perform efficient separation based on the desired orientation (the longest dimension of the particles) by restricting or containing their movement within a specific DLD path.
A new simulation method and its application to knowledge-based systems for railway scheduling (2002)

A simulation method is proposed to emulate human experts' simulating processes of train movements on a computer. Computer simulation is one of the possible tools applicable for design, planning, scheduling, and control of rail and transit systems. Although conventional simulation has been successfully applied to systems design and facility planning, scheduling, and online rescheduling still depend heavily on flexible simulation and the intelligent decision-making abilities of experts. The simulation method consists of three major components: partial simulation, basic command, and strategic knowledge. Since the method can be integrated with the intelligent scheduling abilities of experts, two knowledge-based systems are developed using it: DIAPLAN and ESTRAC-III. Through the experience of applying both systems to large and complicated rail and transit systems operated in the real world, it was confirmed that the method can successfully emulate experts' simulating processes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Native fluorescence detection of nucleic acids and DNA restriction fragments in capillary electrophoresis (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNative fluorescence detection of nucleic acids and DNA restriction fragments in capillary electrophoresisRobert E. Milofsky and Edward S. YeungCite this: Anal. Chem. 1993, 65, 2, 153–157Publication Date (Print):January 15, 1993Publication History Published online1 May 2002Published inissue 15 January 1993https://doi.org/10.1021/ac00050a011RIGHTS & PERMISSIONSArticle Views205Altmetric-Citations53LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (663 KB) Get e-Alerts Get e-Alerts
Making the most out of spectral redundancy in GSM: cheap CCI suppression (2001)

FRESH (frequency-shift) filtering prior to Viterbi demodulation in GSM basestations and/or handsets can theoretically completely suppress 1 cochannel interferer with one antenna, 3 interferers with a diversity antenna pair, and 2M-1 interferers with M antennas. It also can partially suppress larger numbers of interfering signals. Network-level simulations reported in this paper clearly demonstrate that FRESH filtering prior to demodulation in GSM basestations and/or handsets provides a cost-effective means of substantially improving system performance regardless of the antenna subsystem used. In all cases considered, single antenna, pair of diversity antennas, fully adaptive array of four antennas per 120 /spl deg/ sector, and switched-beam array of four 30 /spl deg/ antennas per 120 /spl deg/ sector, FRESH filtering substantially reduces BER and FER (thereby improving quality) and/or reduces required SNR (thereby increasing range) and/or enables reduced frequency reuse factor (thereby increasing capacity).
Development platform for self-organizing wireless sensor networks (1999)

Distributed microsensor networks, built from collections of nodes each having the ability to sensor their environment, process the raw sensor data in cooperation with other neighboring nodes into information and then communicate that information to end users. These systems are designed to be self-organizing in the sense of establishing and maintaining their own network without the need for specialistic operators. In most envisioned applications, wireless communications are the most practical means of interconnection, eliminating the internode cabling. Long periods of autonomous operations in remote environments will need battery or other renewable energy sources. In order to prolong battery life, all node hardware and software functions need to be designed to consume minimal power. In general, a node will expend energy on local processing of sensor data to produce compressed information in order to reduce communications. These network systems are intended to support large numbers of such nodes to cover large geographic areas.
Analysis of the Linux random number generator (2006)

Linux is the most popular open source project. The Linux random number generator is part of the kernel of all Linux distributions and is based on generating randomness from entropy of operating system events. The output of this generator is used for almost every security protocol, including TLS/SSL key generation, choosing TCP sequence numbers, and file system and email encryption. Although the generator is part of an open source project, its source code (about 2500 lines of code) is poorly documented, and patched with hundreds of code patches. We used dynamic and static reverse engineering to learn the operation of this generator. This paper presents a description of the underlying algorithms and exposes several security vulnerabilities. In particular, we show an attack on the forward security of the generator which enables an adversary who exposes the state of the generator to compute previous states and outputs. In addition we present a few cryptographic flaws in the design of the generator, as well as measurements of the actual entropy collected by it, and a critical analysis of the use of the generator in Linux distributions on diskless devices.
Role of IL-4 and IFN-gamma in Schistosoma mansoni egg-induced hypersensitivity granuloma formation. Orchestration, relative contribution, and relationship to macrophage function (1992)

A well defined model of T cell-mediated hypersensitivity-type granulomatous inflammation induced by Schistosoma mansoni eggs was used to assess the role of IL-4 and IFN-gamma in granuloma development. Synchronized pulmonary granulomas were induced and isolated from S. mansoni-infected mice during vigorous (8 wk) and modulated (20 wk) stages of the disease. The sequential production of IL-4 and IFN was determined and related to temporal changes in granuloma macrophage production of IL-1, TNF, and superoxide anion (O2-). During the vigorous stage, IL-4 was produced on days 1 and 2 of granuloma formation, whereas IFN was released in greatest amounts on days 4 to 8. The peak of IL-4 occurred in a window between the peak of IL-1 (1 day) and maximal TNF production (8 to 16 days). Maximal O2- release tended to parallel IFN production. During the modulated stage when the inflammatory response is attenuated, IL-4 production was dramatically reduced as were levels of IL-1 and TNF, but IFN production persisted and maximum O2(-)-producing capacity was only delayed in onset. mAb specific for IL-4 and IFN were used to examine the effect of in vivo depletion of these cytokines on granuloma development. Administration of a single 1.0-mg dose of anti-IL-4 antibodies to mice with synchronously developing granulomas dramatically reduced granuloma size (40 to 50% suppression of area) during an 8-day study period, whereas antibodies to IFN had no effect on size. However, the latter treatment reduced giant cell formation. Our results indicate that granuloma development involves an orchestrated production of cytokines possibly resulting from sequential participation of different Th cell populations. Moreover, IL-4 is a pivotal cytokine in anamnestic cellular recruitment and subject to endogenous regulation.
The Influence of Poly(3-hexylthiophene) Regioregularity on Fullerene-Composite Solar Cell Performance (2008)

A comparison of three samples of poly(3-hexylthiophene) having regioregularities of 86, 90, and 96% is used to elucidate the effect of regioregularity on polymer-fullerene-composite solar cell performance. It is observed that polymer samples with lower regioregularity are capable of generating fullerene composites that exhibit superior thermal stability. The enhanced thermal stability of the composites is attributed to a lower driving force for polymer crystallization in the less regioregular polymer samples, which is supported with two-dimensional grazing incidence X-ray scattering and differential scanning calorimetry measurements. Furthermore, it is demonstrated that all three polymer samples are capable of generating solar cells with equivalent peak efficiencies of approximately 4% in blends with [6,6]-phenyl-C61-butyric acid methyl ester. While it may be non-intuitive that polymers with lower regioregularity can exhibit higher efficiencies, it is observed that the charge-carrier mobility of the three polymers is on the same order of magnitude (10(-4) cm2 V(-1) s(-1)) when measured from the space-charge-limited current, suggesting that highly regioregular and crystalline polythiophenes are not required in order to effectively transport charges in polymer solar cells. Overall, these results suggest a design principle for semicrystalline conjugated polymers in fullerene-composite solar cells in which crystallization-driven phase separation can be dramatically suppressed via the introduction of a controlled amount of disorder into the polymer backbone.