gebhart/patrepeval huggingface dataset:
Immunoreceptor tyrosine‐based inhibition motifs: a quest in the past and future (2008)

Since an immunoreceptor tyrosine-based inhibition motif (ITIM) was first identified in the intracytoplasmic domain of Fc gammaRIIB, ITIMs have been found in a large number of inhibitory molecules that were shown to negatively regulate cell activation. Due to their wide tissue distribution and to the variety of their extracellular ligands, ITIM-containing molecules are involved in the control of a large spectrum of biological functions, mostly but not exclusively related to immunity. On the basis of sequence comparison, ITIMs were structurally defined as 6-amino acid sequences containing a tyrosine (Y) with loosely conserved N-terminal (Y-2) and C-terminal (Y+3) residues. Molecular analysis of signaling events demonstrated that when coaggregated with activating receptors, ITIMs are phosphorylated by Src-family tyrosine kinases, which enables them to recruit Src homology 2 domain-containing phosphatases that antagonize activation signals. Because ITIM-dependent negative regulation seems to be a fundamental regulatory mechanism, both in rodents and in humans, and because it can be used either as a target or as a powerful tool in various diseases, we undertook (i) a genome-wide search of potential novel ITIM-containing molecules in humans, mice, frogs, birds, and flies and (ii) a comparative analysis of potential ITIMs in major animal phyla, from mammals to protozoa. We found a surprisingly high number of potential ITIM-containing molecules, having a great diversity of extracellular domains, and being expressed by a variety of immune and non-immune cells. ITIMs could be traced back to the most primitive metazoa. The genes that encode ITIM-containing molecules that belong to the immunoglobulin superfamily or to the C-lectin family seem to derive from a common set of ancestor genes and to have dramatically expanded and diverged in Gnathostomata (from fish to mammals).
Multi-agent Learning for Neural Machine Translation (2019)

Conventional Neural Machine Translation (NMT) models benefit from the training with an additional agent, e.g., dual learning, and bidirectional decoding with one agent decoding from left to right and the other decoding in the opposite direction. In this paper, we extend the training framework to the multi-agent scenario by introducing diverse agents in an interactive updating process. At training time, each agent learns advanced knowledge from others, and they work together to improve translation quality. Experimental results on NIST Chinese-English, IWSLT 2014 German-English, WMT 2014 English-German and large-scale Chinese-English translation tasks indicate that our approach achieves absolute improvements over the strong baseline systems and shows competitive performance on all tasks.
Efficiency and electromechanical resonance in magnetostrictive transducers (1998)

Analysis of the transduction phenomenon of a Tonpilz Terfenol-D magnetostrictive transducer is presented. Transducer efficiency is discussed from electroacoustic and scalar energy perspectives. Equations are presented for identifying the frequency of most efficient transducer operation based on electroacoustic theory [F. V. Hunt, in Electroacoustics: The Analysis of Transduction, and Its Historical Background (Acoustical Society of America, New York, 1982)]. Experimental results are presented that show this analysis to be accurate. However, two nonintuitive results are observed: most efficient transducer operation occurs at a frequency above mechanical resonance; and changes in operating conditions which result in an increase in transducer efficiency cause the frequency of highest efficiency to increase even further above the frequency of mechanical resonance. This motivated a comparison with a scalar energy analysis for development of a better, or at least more intuitive, understanding of the mechanisms which might explain this result. Energy analysis aids in recognizing the distinction between the transducer’s mechanical and electromechanical resonances and that the magnitude of achievable efficiency will be enhanced by separation of electromechanical and mechanical resonances. Coupling the energy and electroacoustic analyses, one arrives at persuasive arguments for explaining the experimental observations regarding magnetostrictive transducer efficiency.
Response to Comment on “Estrogen Receptor Agonist Fate during Wastewater and Biosolids Treatment Processes:  A Mass Balance Analysis” (2003)

ADVERTISEMENT RETURN TO ISSUEPREVCorrespondence/Rebut...Correspondence/RebuttalNEXTResponse to Comment on "Estrogen Receptor Agonist Fate during Wastewater and Biosolids Treatment Processes: A Mass Balance Analysis"R. David Holbrook, John T. Novak, Thomas J. Grizzard, and Nancy G. LoveView Author Information Department of Civil and Environmental Engineering Virginia Polytechnic Institute and State University Blacksburg, Virginia 24061-0246Cite this: Environ. Sci. Technol. 2003, 37, 20, 4821–4822Publication Date (Web):September 18, 2003Publication History Published online18 September 2003Published inissue 1 October 2003https://pubs.acs.org/doi/10.1021/es030079ihttps://doi.org/10.1021/es030079iarticle-commentaryACS PublicationsCopyright © 2003 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views249Altmetric-Citations-LEARN 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 PDF (25 KB) Get e-AlertscloseSUBJECTS:Assays,Biotechnology,Extraction,Wastewater,Water treatment Get e-Alerts
Advances in counselling and surveillance of patients at risk for pancreatic cancer: Table 1 (2007)

Even with significant advances in imaging and our understanding of pancreatic cancer genetics, the survival rates for pancreatic cancer remain quite dismal. Although still at an early stage, there are efforts in place to develop surveillance and prevention strategies for people at high risk for pancreatic cancer. This comprehensive review article summarises the predispositions that put people at a high risk of developing pancreatic cancer and the current status in the counselling and surveillance of these people using not only available medical literature, but also incorporating international expert opinion.
Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae (2014)

Lignocellulosic biomass is a sustainable and abundant starting material for biofuel production. However, lignocellulosic hydrolysates contain not only glucose, but also other sugars including xylose which cannot be metabolized by the industrial workhorse Saccharomyces cerevisiae. Hence, engineering of xylose assimilating S. cerevisiae has been much studied, including strain optimization strategies. In this work, we constructed genetically encoded xylose biosensors that can control protein expression upon detection of xylose sugars. These were constructed with the constitutive expression of heterologous XylR repressors, which function as protein sensors, and cloning of synthetic promoters with XylR operator sites. Three XylR variants and the corresponding synthetic promoters were used: XylR from Tetragenococcus halophile, Clostridium difficile, and Lactobacillus pentosus. To optimize the biosensor, two promoters with different strengths were used to express the XylR proteins. The ability of XylR to repress yEGFP expression from the synthetic promoters was demonstrated. Furthermore, xylose sugars added exogenously to the cells were shown to regulate gene expression. We envision that the xylose biosensors can be used as a tool to engineer and optimize yeast that efficiently utilizes xylose as carbon source for growth and biofuel production.
Danazol treatment of myelodysplastic syndromes (2008)

Peripheral cytopenias are common in patients with myelodysplastic syndromes. We previously successfully treated three such patients with improvement of some cytopenias with the impeded androgen danazol. To confirm this finding and elucidate the mechanism of response, we treated an additional 22 patients with myelodysplasia with oral danazol (600-800 mg daily) for 3-12 months. Eleven of 22 evaluable patients taking danazol met our criteria for improvement of peripheral counts, mainly thrombocytopenia. Chromosome analysis, marrow culture studies and serial bone marrow biopsies revealed no alteration of the abnormal clone or normal haematopoiesis in patients on danazol therapy. This suggested that improvement in blood counts was not related to modulation of ineffective haematopoiesis. Investigation of the thrombocytopenia in these patients revealed that most patients presented with markedly elevated platelet associated IgG (PAIgG), elevated plasma platelet-bindable IgG (PBIgG), and an elevated number of monocyte Fc gamma receptors. Treatment with danazol was associated with a decline in monocyte Fc gamma receptor number without significantly altering the elevated PAIgG or PBIgG levels. These results are similar to our observations in patients treated with danazol for chronic idiopathic thrombocytopenia purpura (ITP). Our data suggest that a component of the thrombocytopenia occurring in patients with myelodysplasia may be due to enhanced peripheral blood cell destruction by abnormal macrophages. Danazol may modulate cytopenia by decreasing the number of monocyte Fc gamma receptors. Danazol treatment was associated with minimal toxicity, but clinically meaningful responses were rare.
Increased expression of tenascin in the dermis in scleroderma (1992)

The expression of tenascin, a recently discovered extracellular matrix protein, was studied by immunohistochemical techniques in scleroderma skin and compared with its distribution in normal skin. In progressive systemic sclerosis, a marked increase in tenascin content was observed in the superficial reticular dermis. In localized scleroderma, the deposition of tenascin was increased both in the superficial and deep dermis of involved skin, whereas in clinically uninvolved skin the distribution of tenascin was the same as in normal control skin, i.e. the papillary dermis and peri-appendiceal zone. The distribution of tenascin did not strictly parallel that of fibronectin. These findings and the current knowledge of tenascin biology suggest that the overproduction of tenascin in scleroderma dermis could be secondary to stimulation of fibroblasts by immune cell-derived cytokines, or could be due to abnormal fibroblasts, or a subpopulation of fibroblasts, producing high levels of this extracellular matrix protein.
Post Ion-Implant Photoresist Removal via Wet Chemical Cleans Combined with Physical Force Pretreatments (2007)

A combination of wet chemistry and high-velocity solid CO2 aerosol pre-treatment was used to remove ion-implanted resist from patterned Si structures. The top resist surface is modified by heavy ion-implantation forming a crust ~100nm thick. The aerosol treatment, which is aimed at breaking and partially removing the crusted top layer of implanted resist, produces circular openings in this surface, with diameters on the order of tens to hundreds of micrometers. No resist is detected by either optical microscopy or localized SEM inspection, after immersion in hot SPM mixture, on aerosol-pre-treated wafer fragments. In contrast, resist residue is still observed on similarly pre-treated specimens, after immersion in either N-methyl pyrrolidone or Microstrip2001{trade mark, serif}, even under ultrasonic agitation. Overall, the aerosol pre-treatment is a key step in reducing the amount of resist residue, for both aqueous-based and solvent-based wet cleaning. Full-wafer defect-count results, post aerosol treatment, are reported for poly-Si line widths down to 40 nm.
2,4,6-Trichlorophenylhydrazine Schiff Bases as DPPH Radical and Super Oxide Anion Scavengers (2012)

Syntheses of thirty 2,4,6-trichlorophenylhydrazine Schiff bases 1-30 were carried out and evaluated for their in vitro DPPH radical and super oxide anion scavenging activities. Compounds 1-30 have shown a varying degree of DPPH radical scavenging activity and their IC50 values range between 4.05-369.30 µM. The compounds 17, 28, 18, 14, 8, 15, 12, 2, 29, and 7 exhibited IC50 values ranging between 4.05±0.06-24.42±0.86 µM which are superior to standard n-propylgallate (IC50=30.12±0.27 µM). Selected compounds have shown a varying degree of superoxide anion radical scavenger activity and their IC50 values range between 91.23-406.90 µM. The compounds 28, 8, 17, 15, and 14, showed IC50 values between 91.23±1.2-105.31±2.29 µM which are superior to standard n-propylgallate (IC50=106.34±1.6 µM).
Efficient suppression of murine arthritis by combined anticytokine small interfering RNA lipoplexes (2008)

Our results present a novel option for in vivo RNAi-based antiinflammatory immunotherapy. Our findings indicate that intravenous administration of a lipoplex cocktail containing several anticytokine siRNA is a promising novel antiinflammatory therapy for RA, as well as a useful and simple tool for understanding the pathophysiology of RA and for evaluating new therapeutic candidates.
Flexible and Grid-less Wavelength Selective Switch using LCOS Technology (2011)

The increasing spectral efficiency of Optical Transmission systems is constrained by the limitations of wavelength switching and is driving a requirement for significantly more flexible approaches to routing of the optical traffic. We present the intrinsic Grid-free capabilities of LCOS and show how it can be used practically in a flexible Grid architecture to maximize total fiber capacity.
Proton in a Confined Space: Structural Studies of H+⊂Crypt‐111 Iodide and Some Halogen‐Bonded Derivatives (2017)

Abstract Invited for the cover of this issue is the group of Giuseppe Resnati at the Politecnico di Milano. The image depicts proton cryptation by crypt‐111, the smallest cryptand and an effective proton sponge. Read the full text of the article at 10.1002/chem.201701699 .
Predicting the Suction Gas Superheating in Reciprocating Compressors (2014)

A considerable portion of the cooling capacity losses on a household compressor occurs due to heating of the gas entering through the suction tube, which is called as superheating. A better understanding of the flow and heat transfer phenomena involved is crucial to improve compressor efficiency. In this work, it is presented a numerical simulation study using a commercial code to analyze a transient three-dimensional, compressible and non-isothermal flow, which has been used for modeling the problem. The computational domain considered the suction tube, a portion of the compressor cavity and the suction muffler. Prescribed transient mass flow rates obtained by simpler 0D/1D models have been used as boundary conditions while the cavity gas and wall temperatures were prescribed based on experimental methods. The results showed that the mean temperature of the gas entering into the compressor was 40°C, while the mean temperature of the gas leaving the suction muffler was 63°C, presenting 23°C of superheating.
Interferon Signature in the Blood in Inflammatory Common Variable Immune Deficiency (2013)

About half of all subjects with common variable immune deficiency (CVID) are afflicted with inflammatory complications including hematologic autoimmunity, granulomatous infiltrations, interstitial lung disease, lymphoid hyperplasia and/or gastrointestinal inflammatory disease. The pathogenesis of these conditions is poorly understood but singly and in aggregate, these lead to significantly increased (11 fold) morbidity and mortality, not experienced by CVID subjects without these complications. To explore the dysregulated networks in these subjects, we applied whole blood transcriptional profiling to 91 CVID subjects, 47 with inflammatory conditions and 44 without, in comparison to subjects with XLA and healthy controls. As compared to other CVID subjects, males with XLA or healthy controls, the signature of CVID subjects with inflammatory complications was distinguished by a marked up-regulation of IFN responsive genes. Chronic up-regulation of IFN pathways is known to occur in autoimmune disease due to activation of TLRs and other still unclarified cytoplasmic sensors. As subjects with inflammatory complications were also more likely to be lymphopenic, have reduced B cell numbers, and a greater reduction of B, T and plasma cell networks, we suggest that more impaired adaptive immunity in these subjects may lead to chronic activation of innate IFN pathways in response to environmental antigens. The unbiased use of whole blood transcriptome analysis may provides a tool for distinguishing CVID subjects who are at risk for increased morbidity and earlier mortality. As more effective therapeutic options are developed, whole blood transcriptome analyses could also provide an efficient means of monitoring the effects of treatment of the inflammatory phenotype.
Headshape Digitization using an Ultrasound 3D Acquisition System (2004)

Localization of neuromagnetic sources requires co-registration in order to map data registered by magnetoencephalography (MEG) onto the corresponding anatomic structure. Co-registration on the other hand often involves head shape digitization, which is usually carried out using a 3D digitization system that has a reference point which is not fixed at the subjects head. Therefore, the major drawback of such systems is that head motion artefacts during the digitization process cannot be compensated. We instead use the Zebris 3D Motion Analyzer for headshape digitization outside the magnetically shielded room providing a much more comfortable measurement, especially for patients. The foremost advantage, however, is that this system makes use of a 3D ultrasound acquisition device providing three or more reference markers that can be fixed on the surface of the subject's head. Using these reference markers we are able to compensate for any head movements during head shape acquisition. Furthermore, we developed a new 3D localization software to control the Zebris system that is now integrated in our MEG measurement environment (4D-Neuroimaging). With our software we automatically can check the quality of the digitization process, and it may also be used to localize attached head location coils or surface electrodes that are used for the MEG acquisition. Our tests show that the headshape digitization system works reliably and provides an acquisition accuracy of about 1mm, while it automatically compensates for any head motion artefacts.
[Receptor occupancy and antipsychotic drug action measured by PET and SPECT]. (2001)

Positron emission tomography (PET) and single photon emission computed tomography (SPECT) studies have demonstrated consistent findings of high dopamine D2 receptor occupancy (> 65-70%) in patients treated with antipsychotic drugs. Further, the risk of extrapyramidal side effects has been shown high in patients with occupancy above 80%. On the basis of these findings, an optimal interval for D2 receptor occupancy between 70% and 80% has been suggested. It has also been shown that several atypical antipsychotics induce marked occupancy of central 5-HT2 and D2 receptors in vivo. However, a low D2 occupancy has been observed in patients with clinical dose of clozapine or quetiapine. The antipsychotic effect of these atypical drugs with a low D2 receptor occupancy has been widely discussed with respect to actions on other receptor systems, limbic selectivity of antipsychotic action and episodic transient occupancy. The recent advances in PET/SPECT and developments of new radioligands have made it possible to evaluate antipsychotic drug actions directly in humans. The empirical data from occupancy measurements will enable us to open future directions of investigation of antipsychotic action and improvement of antipsychotic treatment.
Photonic crystal semiconductor lasers (2005)

Semiconductor lasers based on two-dimensional photonic crystals are described. It is shown that unprecedented type of lasers with perfect single mode over a large area and high output power surface-emission can be realized.
Cervical Flexion and Extension Radiographs in Acutely Injured Patients (1999)

Flexion and extension lateral radiographs of the cervical spine may suggest signs of ligamentous and soft tissue injuries in a potentially unstable spine. However, patients with acute injuries and severe pain and muscle spasms may not be able to move their necks effectively, severely compromising the diagnostic yield of the radiographs. In addition, there are reports of serious neurologic injuries occurring with the use of these radiographs in acutely injured patients. The purpose of this study was to determine the effectiveness and yield of obtaining cervical spine flexion and extension radiographs in the emergency department on acutely injured patients. Review of all patients with cervical flexion and extension radiographs presenting to a Level 1 trauma center was performed. All radiographs were judged based on the adequacy of flexion and extension movement and positive findings indicative of instability by the radiologist in the emergency room. The radiographs of one patient (0.34%) revealed positive findings of instability. Of the 290 flexion and extension radiographs, 97 (33.5%) of them showed such little or inadequate flexion or extension movement that cervical stability could not be assessed. Flexion and extension cervical radiographs should not be obtained routinely in the emergency department because 1/3 of these studies will be inadequate because of pain and muscle spasms experienced by patients. Patients with cervical injuries may not be able to fully flex and extend their necks; this may lead to false reassurance to patients who actually have had an inadequate study to diagnose potential instability.
A Modern Memory Management System for OpenMP (2016)

Modern computers with multi-/many-core processors and accelerators feature a sophisticated and deep memory hierarchy, potentially including distinct main memory, high-bandwidth memory, texture memory and scratchpad memory. The performance characteristics of these memories are varied, and studies have demonstrated the importance of using them effectively.In this paper, we propose an extension of the OpenMP API to address the needs of programmers to efficiently optimize their applications to use new memory technologies in a platform-agnostic and portable fashion. Our proposal separately exposes the characteristics of memory resources (such as kind) and the characteristics of allocations (such as alignment), and is fully compatible with existing OpenMP constructs.