gebhart/patrepeval huggingface dataset:
Insulin-induced remission in new-onset NOD mice is maintained by the PD-1–PD-L1 pathway (2006)

The past decade has seen a significant increase in the number of potentially tolerogenic therapies for treatment of new-onset diabetes. However, most treatments are antigen nonspecific, and the mechanism for the maintenance of long-term tolerance remains unclear. In this study, we developed an antigen-specific therapy, insulin-coupled antigen-presenting cells, to treat diabetes in nonobese diabetic mice after disease onset. Using this approach, we demonstrate disease remission, inhibition of pathogenic T cell proliferation, decreased cytokine production, and induction of anergy. Moreover, we show that robust long-term tolerance depends on the programmed death 1 (PD-1)-programmed death ligand (PD-L)1 pathway, not the distinct cytotoxic T lymphocyte-associated antigen 4 pathway. Anti-PD-1 and anti-PD-L1, but not anti-PD-L2, reversed tolerance weeks after tolerogenic therapy by promoting antigen-specific T cell proliferation and inflammatory cytokine production directly in infiltrated tissues. PD-1-PD-L1 blockade did not limit T regulatory cell activity, suggesting direct effects on pathogenic T cells. Finally, we describe a critical role for PD-1-PD-L1 in another powerful immunotherapy model using anti-CD3, suggesting that PD-1-PD-L1 interactions form part of a common pathway to selectively maintain tolerance within the target tissues.
In silico analysis of complete bacterial genomes: PCR, AFLP–PCR and endonuclease restriction (2004)

This is a new molecular biology resource freely available over the Internet at http://www.in-silico.com
Epidemiology of nosocomial fungal infections (1996)

This paper briefly reviews the current knowledge of the epidemiology and modes of transmission of nosocomial fungal infections and some of the therapeutic options for treating these diseases. In the mid-1980s, many institutions reported that fungi were common pathogens in nosocomial infections. Most, if not all, hospitals care for patients at risk for nosocomial fungal infections. The proportion in all nosocomial infections reportedly caused by Candida spp. increased from 2% in 1980 to 5% in 1986 to 1989. Numerous studies have identified common risk factors for acquiring these infections, most of which are very common among hospitalized patients; some factors act primarily by inducing immunosuppression (e.g., corticosteroids, chemotherapy, malnutrition, malignancy, and neutropenia), while others primarily provide a route of infection (e.g., extensive burns, indwelling catheter), and some act in combination. Non-albicans Candida spp., including fluconazole-resistant C. krusei and Torulopsis (C.) glabrata, have become more common pathogens. Newer molecular typing techniques can assist in the determination of a common source of infection caused by several fungal pathogens. Continued epidemiologic and laboratory research is needed to better characterize these pathogens and allow for improved diagnostic and therapeutic strategies.
Troi 110kv substation and 110 kv branch connection EMP (2005)

This is an environmental assessment for Vietnam's Transmission and Distribution Development Project, in which the Playcu-Phulam transmission line integrates small and medium power generation, such as linking hydropower in the western highlands with the rest of the country. Transmission lines will help create a reliable, economical power supply in the South. Construction activities such as cutting trees, clearing routes, digging foundation holes, transporting material, and tensioning conductors can cause soil erosion. Mitigating options include soil replacing, and tree and grass planting. To offset hunting and poaching, fences will be erected and foresty controllers will increase their supervision and inspections. To prevent fire or explosion caused by hazardous spills, construction crews will be supplied protection equipment. To reduce disease risk in construction camps, medical and hygienic measures for handling water and foodstuffs will be firmly adhered to. During the operational phase, the threat of soil erosion around the towers can be alleviated by building a foundation embankment or contouring on sloping land. Trees posing a safety hazard because they are too close to transmission lines will be cut down periodically. A resettlement action plan recommends solutions for compensation, population relocation, and household restoration.
The Ireland They Dream of: "Eireville, Coolockland" and the Appropriation of Science Fiction and Fantasy Narratives in Short Irish Filmmaking (2003)

Ruth Barton, The Ireland They Dream of: "Eireville, Coolockland" and the Appropriation of Science Fiction and Fantasy Narratives in Short Irish Filmmaking, The Canadian Journal of Irish Studies, Vol. 29, No. 2, Irish Cinema / Le cinéma irlandais (Fall, 2003), pp. 41-45
Analyzing a Multilateral-Well Failure in the East Wilmington Field of California (1998)

Summary As the industry pursues optimum cost drilling techniques, more focus is being applied to multilateral (ML) technology. The presently available literature invariably focuses on the cost and efficiency benefits of drilling ML wells. What is missing in the media, however, are the benefits associated with publication of the negative aspects or costly failures of higher-technology, multiple-lateral projects that require a mechanical tieback, cement, or a pressure seal at the junction of the laterals (i.e., Class 3-, 4-, or 5-type wells, respectively). This paper presents a case study of a Class 4 ML well attempted by THUMS Long Beach Co. in the East Wilmington field of California.
Neurofibromatosis Type II of the Head and Neck (1989)

• Neurofibromatosis type II (NF-II) has been traditionally referred to as "acoustic" neurofibromatosis and is not known to be genetically distinct from classic von Recklinghausen's disease (NF-I). Neurofibromatosis type II is due to a lesion on chromosome 22q, while von Recklinghausen's neurofibromatosis is from a defect on chromosome 17. The approximate incidence of NF-II is one in 50000, with bilateral acoustic neuromas occurring in over 90% of those with the abnormal gene. We studied a 17-year-old boy with NF-II who presented with bilateral acoustic neuromas and a concomitant primary nasopharyngeal meningioma. Less than 30 nasopharyngeal meningiomas have been documented, and the presence of both tumor types in the same individual is unique in the literature. (<i>Arch Otolaryngol Head Neck Surg</i>1989;115:380-383)
You're one in a googol: optimizing genes for protein expression (2009)

A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.
Traces of post-transcriptional RNA modifications in deep sequencing data (2011)

Many aspects of the RNA maturation leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. This includes, in particular, genomically non-encoded nucleotides and chemical modifications. The latter leave their signatures in the form of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures focusing on particular types of deviations can help to unravel post-transcriptional modification, maturation and degradation processes. Here, we focus on small RNA sequencing data that is produced in large quantities aimed at the analysis of microRNA expression. Starting from the recovery of many well known modified sites in tRNAs, we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which surprisingly can be found in a diverse collection of transcripts including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.
Mitochondrial permeability transition in CNS trauma: Cause or effect of neuronal cell death? (2004)

Experimental traumatic brain injury (TBI) and spinal cord injury (SCI) result in a rapid and significant necrosis of neuronal tissue at the site of injury. In the ensuing hours and days, secondary injury exacerbates the primary damage, resulting in significant neurologic dysfunction. It is believed that alterations in excitatory amino acids (EAA), increased reactive oxygen species (ROS), and the disruption of Ca(2+) homeostasis are major factors contributing to the ensuing neuropathology. Mitochondria serve as the powerhouse of the cell by maintaining ratios of ATP:ADP that thermodynamically favor the hydrolysis of ATP to ADP + P(i), yet a byproduct of this process is the generation of ROS. Proton-pumping by components of the electron transport system (ETS) generates a membrane potential (DeltaPsi) that can then be used to phosphorylate ADP or sequester Ca(2+) out of the cytosol into the mitochondrial matrix. This allows mitochondria to act as cellular Ca(2+) sinks and to be in phase with changes in cytosolic Ca(2+) levels. Under extreme loads of Ca(2+), however, opening of the mitochondrial permeability transition pore (mPTP) results in the extrusion of mitochondrial Ca(2+) and other high- and low-molecular weight components. This catastrophic event discharges DeltaPsi and uncouples the ETS from ATP production. Cyclosporin A (CsA), a potent immunosuppressive drug, inhibits mitochondrial permeability transition (mPT) by binding to matrix cyclophilin D and blocking its binding to the adenine nucleotide translocator. Peripherally administered CsA attenuates mitochondrial dysfunction and neuronal damage in an experimental rodent model of TBI, in a dose-dependent manner. The underlying mechanism of neuroprotection afforded by CsA is most likely via interaction with the mPTP because the immunosuppressant FK506, which has no effect on the mPT, was not neuroprotective. When CsA was administrated after experimental SCI at the same dosage and regimen used TBI paradigms, however, it had no beneficial neuroprotective effects. This review takes a comprehensive and critical look at the evidence supporting the role for mPT in central nervous system (CNS) trauma and highlights the differential responses of CNS mitochondria to mPT induction and the implications this has for therapeutically targeting the mPT in TBI and SCI.
Remission of transformed myelodysplastic syndrome with fibrosis after danazol therapy (2002)

Danazol has been used with success in some hematological diseases, but there is no report of this treatment in acute leukemia. We report here a case of remission of myelodysplastic syndrome with myelofibrosis in transformation after danazol therapy in a 72-yr-old man. The role of danazol in remission induction is briefly discussed.
Nitric oxide and nitric oxide‐generating compounds inhibit hepatocyte protein synthesis (1991)

Hepatocytes are stimulated to produce nitric oxide (NO.) from L-arginine in response to conditioned Kupffer cell medium or a combination of cytokines. Associated with the production of NO.in hepatocytes, there is a profound decrease in total protein synthesis ([3H]leucine incorporation). This report demonstrates that authentic NO.and the NO.-generating compound S-nitroso-N-acetylpenicillamine inhibit hepatocyte total protein synthesis in a reversible and concentration-dependent fashion. In parallel with the suppression of hepatocyte total protein synthesis, authentic NO.inhibits the production of two specific hepatocyte proteins, albumin and fibrinogen, without influencing the quantity of albumin mRNA. Although authentic NO.induces a rapid increase in cGMP levels in hepatocytes, the addition of the cGMP analog 8-bromoguanosine 3':5' cyclic monophosphate to unstimulated HC cultures does not reproduce the inhibition of total protein synthesis. These data show that NO.is the hepatocyte L-arginine metabolite that inhibits protein synthesis. Furthermore, these findings indicate that NO.does not inhibit hepatocyte protein synthesis solely through the activation of soluble guanylate cyclase but appears to affect a translational or posttranslational process.
A CRITICAL ANALYSIS OF ON‐CAMPUS INTERVIEWING (1989)

Understanding how to effectively and lawfully gain information from a prospective employee is an important skill for business managers to master. The decision to hire an individual results in long‐term consequences‐turn‐over rates, levels of productivity, training costs, and company image. Because getting the right person in the right job is so important to the success of any business, many managers personally want to interview the potential employee. Yet few can boast of making a perfect hiring decision. In fact, half of all new hires in America stay with a company no more than six months; and each mis‐hire can cost 30 to 50 per cent above annual salary in lost productivity and expense of replacement (Bacas, 1987).
Phase I Clinical Trial of Locoregional Administration of the Oncolytic Adenovirus ONYX-015 in Combination with Mitomycin-C, Doxorubicin, and Cisplatin Chemotherapy in Patients with Advanced Sarcomas (2009)

Despite many advances in cancer therapy, metastatic disease continues to be incurable in the majority of cancer patients. There is an need for more efficient and less toxic treatments in this setting. Oncolytic virotherapy represents a novel promising direction in the treatment of cancer. Based on preclinical and clinical data, combination with standard chemotherapy has the potential to further increase the antitumor activity of oncolytic virotherapy in a synergistic manner. We present the design of a phase I clinical trial combining intratumoral injections of the oncolytic adenovirus ONYX-015 with systemic chemotherapy in patients with advanced sarcomas.
Lock Cohorting (2015)

Multicore machines are quickly shifting to NUMA and CC-NUMA architectures, making scalable NUMA-aware locking algorithms, ones that take into account the machine's nonuniform memory and caching hierarchy, ever more important. This article presents lock cohorting , a general new technique for designing NUMA-aware locks that is as simple as it is powerful. Lock cohorting allows one to transform any spin-lock algorithm, with minimal nonintrusive changes,into a scalable NUMA-aware spin-lock. Our new cohorting technique allows us to easily create NUMA-aware versions of the TATAS-Backoff, CLH, MCS, and ticket locks, to name a few. Moreover, it allows us to derive a CLH-based cohort abortable lock, the first NUMA-aware queue lock to support abortability. We empirically compared the performance of cohort locks with prior NUMA-aware and classic NUMA-oblivious locks on a synthetic micro-benchmark, a real world key-value store application memcached, as well as the libc memory allocator. Our results demonstrate that cohort locks perform as well or better than known locks when the load is low and significantly out-perform them as the load increases.
Neointimal Smooth Muscle Cells Display a Proinflammatory Phenotype Resulting in Increased Leukocyte Recruitment Mediated by P-Selectin and Chemokines (2004)

Leukocyte recruitment is crucial for the response to vascular injury in spontaneous and accelerated atherosclerosis. Whereas the mechanisms of leukocyte adhesion to endothelium or matrix-bound platelets have been characterized, less is known about the proadhesive role of smooth muscle cells (SMCs) exposed after endothelial denudation. In laminar flow assays, neointimal rat SMCs (niSMCs) supported a 2.5-fold higher arrest of monocytes and "memory" T lymphocytes than medial SMCs, which was dependent on both P-selectin and VLA-4, as demonstrated by blocking antibodies. The increase in monocyte arrest on niSMCs was triggered by the CXC chemokine GRO-alpha and fractalkine, whereas "memory" T cell arrest was mediated by stromal cell-derived factor (SDF)-1alpha. This functional phenotype was paralleled by a constitutively increased mRNA and surface expression of P-selectin and of relevant chemokines in niSMCs, as assessed by real-time PCR and flow cytometry. The increased expression of P-selectin in niSMCs versus medial SMCs was associated with enhanced NF-kappaB activity, as revealed by immunofluorescence staining for nuclear p65 in vitro. Inhibition of NF-kappaB by adenoviral IkappaBalpha in niSMCs resulted in a marked reduction of increased leukocyte arrest in flow. Furthermore, P-selectin expression by niSMCs in vivo was confirmed in a hypercholesterolemic mouse model of vascular injury by double immunofluorescence and by RT-PCR after laser microdissection. In conclusion, we have identified a NF-kappaB-mediated proinflammatory phenotype of niSMCs that is characterized by increased P-selectin and chemokine expression and thereby effectively supports leukocyte recruitment.
Oncology Micro-Cap Stocks: Caveat Emptor! (2011)

JNCI Vol. 103, Issue 20 | October 19, 2011 Trading based on material nonpublic information is a criminal violation of the Federal Securities Exchange Act of 1934 and is punishable by a maximum sentence of 20 years and a fine of $5 million. Thus, the suggestion by Rothenstein et al. (1) in this issue of the Journal that insider trading is the cause of observed differences in company stock prices before and after public announcements related to oncology drugs is of grave concern. Specifically, Rothenstein et al. (1) analyzed the stock prices in the 120 days leading up to public announcements regarding phase III trials, and they appear to reject the null hypothesis that the outcome of the trial is unrelated to the stock price behavior before the announcement. Indeed, companies that reported a positive trial demonstrated better price performance (an increase of approximately 14%) during that period compared with companies Oncology Micro-Cap Stocks: Caveat Emptor!
Hydroxyethylamine analogs of the p17/p24 substrate cleavage site are tight-binding inhibitors of HIV protease (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroxyethylamine analogs of the p17/p24 substrate cleavage site are tight-binding inhibitors of HIV proteaseDaniel H. Rich, Jeremy Green, Mihaly V. Toth, Garland R. Marshall, and Stephen B. H. KentCite this: J. Med. Chem. 1990, 33, 5, 1285–1288Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/jm00167a003https://doi.org/10.1021/jm00167a003research-articleACS PublicationsRequest reuse permissionsArticle Views420Altmetric-Citations119LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Bactericidal Action of Bicarbonate Ion on Selected Periodontal Pathogenic Microorganisms (1984)

Organisms representative of soil, skin and fecal flora and of supragingival and subgingival flora were tested for inhibition of growth and killing by various salts (NaHCO3, NaCl, MgSO4). The antimicrobial activities of KHCO3, NaF, sodium lauryl sulfate (SLS) and chloramine T were also compared with that of NaHCO3, and the rate at which NaHCO3 exerts its bactericidal effect was studied. Suspected periodontal pathogens were more susceptible to salts than were control non-oral bacteria. Supragingival plaque organisms showed intermediate susceptibility. Periodontal pathogens were more susceptible to NaHCO3 than to NaCl; NaHCO3 and KHCO3 showed similar activity against all strains tested. Accordingly, the antibacterial activity of NaHCO3 is not simply an osmotic effect and is due to the bicarbonate ion. NaF, SLS and chloramine T had greater antimicrobial activity than NaHCO3. Supragingival bacteria required at least 6-hour exposure to 1.0 M NaHCO3 to produce 99% lethality (decrease colony-forming units by 2 log10), whereas selected periodontal pathogens were killed more rapidly (30-120 minutes). The higher the concentration of bicarbonate, the faster the lethality. Morphologic examination by transmission electron microscopy of organisms exposed to bactericidal salt concentrations revealed marked fibrillar condensations within the cytoplasm and shrinkage of the cytoplasm from the outer membrane. For NaHCO3 to be clinically effective, a high concentration must be introduced into the periodontal pocket and maintained there long enough to kill periodontal pathogens. Furthermore, NaHCO3 must be reapplied often enough to prevent recolonization by these pathogens. An advantage of NaHCO3 over NaF, SLS and other antimicrobial agents is its safety, availability and low cost.
我们到了没——“交叉路口”的女性主义叙事学的未来 (2010)

我们现在已经抵达女性主义叙事学的转折点,在这里,女性主义可以再一次为叙事研究孕育新方法,同时叙事研究对拓展女性主义思想也更显重要。＂交叉路口＂的女性主义可以与跨越时空的叙事模式互为映照,从而创造出一种叙事学。它既是历史的和跨文化的,也是形式和理论的,因此使我们得以将（叙事的）形式读成（性别化的）内容。＂影子情节＂（negative plotting）这个概念有助于我们通过叙事的一个重要侧面来梳理不同文化或不同时期的作者和读者的（性别化）策略。然而,改变女性主义叙事学需要不同领域的国际团体合作与参与方能成功。
E1a-dependent expression of adenovirus genes in OTF963 embryonal carcinoma cells: role of E1a-induced differentiation. (1990)

Some undifferentiated F9 embryonal carcinoma cells allow adenovirus genes to be expressed independently of the E1a oncogene normally required for their activation; this has been attributed to a cellular equivalent of E1a in F9 cells. However, transcription of all early genes was low in undifferentiated OTF963 embryonic carcinoma cells during the first 48 hr after infection with adenovirus type 5 (Ad5). Transcription then increased to about the level seen 16 hr after infection of cells induced to differentiate by retinoic acid (RA) (referred to as RA-dF9 cells), but this increase did not occur in cells infected by the E1a deletion mutant dl312. Addition of E1a in trans, or of RA, had no immediate effect on viral transcription in OTF963 cells, but viral transcription increased about 48 hr after these additions. Ad5 induced transcription of several differentiation-specific genes in OTF963 cells with about the same kinetics as their induction by RA. These genes were superinduced in RA-dF9 cells by cAMP or infection by adenovirus. We suggest the small amount of E1a produced early in infection of OTF963 cells activates cellular genes, some of which are differentiation specific and required for efficient transcription of viral genes, so that E1a both induces and is induced by differentiation. The simple hypothesis of a cellular equivalent to E1a does not adequately explain the complex interactions between viral and cellular genes in OTF963 embryonic carcinoma cells.