gebhart/patrepeval huggingface dataset:
Response to “Interaction between HIV gp41 fusion peptide and T cell receptor: putting the puzzle pieces back together” (2007)

In his letter, Dr. Alexander Sigalov suggests an alternative interpretation to our results mapping the domain of FP1–32 that mediates the interaction with the TCR to the FP5–13 region (1). He suggests that, in addition to FP5–13, the C-terminus domain of FP1–32 contains a region capable of inserting itself into the membrane and interacting with the CD3 subunits of the TCR, thereby impairing TCR function. We consider this alternative explanation unlikely for several reasons. First, we have synthesized and investigated FP17–32 and found it inactive in all assays (unpublished data). Second, a mutant FP1–32 termed V2E shows a diminished ability to interfere with the activation of T cells both in vivo and in vitro (2), despite the fact that the mutation in V2E is located in the N-terminus and not in the C-terminus of FP1–32. Thus, if any inhibitory activity resides on the C-terminus of FP1–32, it must be secondary to the activity of the N-terminus. Thirdly, the current working model describing the mechanism of action of FP1–32 during membrane fusion in HIV infection suggests that FP1–16 inserts into the target T-cell membrane, while the FP17–32 region does not insert, but remains positioned parallel to the cell membrane (ref 1, Fig. 1) (3, 4). This positioning of the different domains of FP1–32 does not allow the FP17–32 region to insert into the membrane and interact with the CD3 subunits of the TCR complex as suggested by Sigalov. The alternative interpretation suggested by Sigalov is based on the different potency manifested by FP1–32, FP1–16 and FP5–13 in Figs. 1 and 7 of our manuscript (1). However, a careful comparison of Figs. 1 and 7 reveals that FP1–32 and FP5–13 have similar inhibitory efficiencies; moreover FP1–32 and FP1–16 (Fig. 2) have similar activities in vivo. Thus, we attribute the differences in the efficiency of FP1–16 and FP1–32 not as an indicator of the existence of another independent inhibitory region, but as the result of the different solubility and state of aggregation of the different peptides; this effect seems to be more important for in vitro assays (Fig. 1), but less important for in vivo assays (Fig. 2). Indeed, FP1–32 is known to form oligomers (2, 4); this multi-merization is facilitated by the C-terminus increasing fusogenic activity of FP1–32 (3, 4). Whether multimer-ization plays a role in the immunomodulatory activities of FP and its peptides is still unknown. Nevertheless, we believe that the above-mentioned data rule out the alternative interpretation put forward by Sigalov, that the C terminus region of FP1–32 plays a significant role in its immunomodulatory activity.
(Keynote) History and Future Directions in SiGe HBT BiCMOS Technology and Its Applications (2012)

The development of SiGe BiCMOS has mirrored silicon semiconductor development as the technology transitioned from Ge transistors, to silicon transistors, to ion-implanted base, to polysilicon emitter transistors, and finally to SiGe HBTs and SiGe BiCMOS. While the physics of the graded base SiGe HBT transistor was established early on in 1954 by Herb Kroemer it was not until the 1980s that SiGe HBTs were first realized. At the core of the SiGe Heterojunction Bipolar transistor development is the SiGe Epitaxy. In fact the SiGe HBT drove the development of the SiGe:B S/D processes now used for stressors in advanced CMOS since it was the first commercial technology with SiGe layers. SiGe HBT BiCMOS continues to find large volume production opportunities in applications that require mostly RF/Analog and less digital content (Big-A/little-D). Scaling has driven the speed performance ( f MAX ) towards terahertz levels to open up yet more applications. Many challenges still exist in the technology.
Supplementary Tables 1-6 from Basal Subtype and MAPK/ERK Kinase (MEK)-Phosphoinositide 3-Kinase Feedback Signaling Determine Susceptibility of Breast Cancer Cells to MEK Inhibition (2023)

Supplementary Tables 1-6 from Basal Subtype and MAPK/ERK Kinase (MEK)-Phosphoinositide 3-Kinase Feedback Signaling Determine Susceptibility of Breast Cancer Cells to MEK Inhibition
The All Diode Pumped, Yb3+ Based, 10 J, 10 Hz, Sub-picosecond CPA Laser of the Petawatt-Field-Synthesizer (2021)

We present the laboratory performance and key technologies of the all diode pumped, Yb 3+ based, 10 J, 10 Hz, sub-picosecond CPA laser chain that was developed to pump the picosecond OPCPA stages of the Petawatt-Field-Synthesizer.
(2×2) reconstructions of the {111} polar surfaces of GaAs (1986)

Ab initio total-energy calculations were used to examine (2\ifmmode\times\else\texttimes\fi{}2) reconstruction models for the (111) and (1\ifmmode\bar\else\textasciimacron\fi{}1\ifmmode\bar\else\textasciimacron\fi{}1\ifmmode\bar\else\textasciimacron\fi{}) surfaces of GaAs. For the (111) surface the lowest-energy Ga-vacancy geometry is determined; several mechanisms for Ga-vacancy formation are examined and other reconstructions are discussed. For the (1\ifmmode\bar\else\textasciimacron\fi{}1\ifmmode\bar\else\textasciimacron\fi{}1\ifmmode\bar\else\textasciimacron\fi{}) surface it is shown that the As-vacancy model is unlikely and other geometries are considered.
Decoding the Morphological Diversity in Two Dimensional Crystalline Porous Polymers by Core Planarity Modulation (2016)

Two new chemically stable triazine- and phenyl-core-based crystalline porous polymers (CPPs) have been synthesized using a single-step template-free solvothermal route. Unique morphological diversities were observed for these CPPs [2,3-DhaTta (ribbon) and 2,3-DhaTab (hollow sphere)] by simply altering the linker planarity. A detailed time-dependent study established a significant correlation between the molecular level structures of building blocks with the morphology of CPPs. Moreover, a DFT study was done for calculating the interlayer stacking energy, which revealed that the extent of stacking efficiency is responsible for governing the morphological diversity in these CPPs.
ChemInform Abstract: A Simple Method for the Assignment of the Relative Stereochemistry of 2‐Substituted Clavams. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Analysis of T cell lines from rejecting renal allografts. (1993)

Acute rejection after renal allotransplantation is characterized by the presence of a mononuclear cell infiltrate in the interstitium with involvement of tubuli. In a previous study on renal histology we showed that tubular damage by graft infiltrating cells (GIC) is a sign of clinically significant rejection. We cultured proximal tubular epithelial cells (PTEC) and T cells bearing the interleukin 2 (IL-2) receptor from biopsies after transplantation. In vitro outgrowth of T cells from the biopsy was significantly (P = 0.0014) related to histological signs of graft rejection. Of the T cell lines generated from 25 biopsies, only five lines showed no or low cytotoxicity against donor PTEC. Three cell lines were cytotoxic towards donor PTEC, but not against PHA stimulated donor splenocytes, suggesting tissue specificity of GIC. Treatment of PTEC with interferon (IFN) gamma for 72 hours to upregulate MHC class I and to induce MHC class II expression did not necessarily result in an increased susceptibility to lysis. However, three PTEC lines displayed an increment of susceptibility to lysis after IFN gamma treatment. Analysis of one T cell line from the same graft revealed a high percentage of CD4 positive cells, compatible with a class II restricted cytotoxicity. This was confirmed by blocking experiments using anti-CD4, anti-CD8, anti-class I, and anti-class II antibodies. Blocking experiments were done with 12 of these 25 lines. Anti-CD3 and anti-CD18 antibodies inhibited cytotoxicity in every case, showing that cytotoxicity was T cell mediated.(ABSTRACT TRUNCATED AT 250 WORDS)
Cyclo[8]isoindoles: Ring‐Expanded and Annelated Porphyrinoids (2011)

Cyclo[8]isoindol, das über eine sattelförmige Struktur verfügt (siehe Bild, 2), wurde durch oxidative Kupplung von Bicyclo[2.2.2]octadien(BCOD)-kondensierten 2,2′-Bipyrrolen und anschließende Retro-Diels-Alder-Reaktion eines BCOD-kondensierten Cyclo[8]pyrrols (1) synthetisiert. Schlüsseltrends bei den optischen Spektren ringanellierter Cyclo[8]pyrrole werden anhand von magnetischen Circulardichroismus-Spektren und theoretischen Rechnungen beschrieben.
Extracellular Vesicles from High-Grade Glioma Exchange Diverse Pro-oncogenic Signals That Maintain Intratumoral Heterogeneity (2016)

A lack of experimental models of tumor heterogeneity limits our knowledge of the complex subpopulation dynamics within the tumor ecosystem. In high-grade gliomas (HGG), distinct hierarchical cell populations arise from different glioma stem-like cell (GSC) subpopulations. Extracellular vesicles (EV) shed by cells may serve as conduits of genetic and signaling communications; however, little is known about how HGG heterogeneity may impact EV content and activity. In this study, we performed a proteomic analysis of EVs isolated from patient-derived GSC of either proneural or mesenchymal subtypes. EV signatures were heterogeneous, but reflected the molecular make-up of the GSC and consistently clustered into the two subtypes. EV-borne protein cargos transferred between proneural and mesenchymal GSC increased protumorigenic behaviors in vitro and in vivo Clinically, analyses of HGG patient data from the The Cancer Genome Atlas database revealed that proneural tumors with mesenchymal EV signatures or mesenchymal tumors with proneural EV signatures were both associated with worse outcomes, suggesting influences by the proportion of tumor cells of varying subtypes in tumors. Collectively, our findings illuminate the heterogeneity among tumor EVs and the complexity of HGG heterogeneity, which these EVs help to maintain. Cancer Res; 76(10); 2876-81. ©2016 AACR.
How to build a WebFountain: An architecture for very large-scale text analytics (2004)

WebFountain is a platform for very large-scale text analytics applications. The platform allows uniform access to a wide variety of sources, scalable system-managed deployment of a variety of document-level “augmenters” and corpus-level “miners,” and finally creation of an extensible set of hosted Web services containing information that drives end-user applications. Analytical components can be authored remotely by partners using a collection of Web service APIs (application programming interfaces). The system is operational and supports live customers. This paper surveys the high-level decisions made in creating such a system.
The Complete Automation of Cell Culture: Improvements for High-Throughput and High-Content Screening (2011)

Genomic approaches provide enormous amounts of raw data with regard to genetic variation, the diversity of RNA species, and protein complement. High-throughput (HT) and high-content (HC) cellular screens are ideally suited to contextualize the information gathered from other "omic" approaches into networks and can be used for the identification of therapeutic targets. Current methods used for HT-HC screens are laborious, time-consuming, and prone to human error. The authors thus developed an automated high-throughput system with an integrated fluorescent imager for HC screens called the AI.CELLHOST. The implementation of user-defined culturing and assay plate setup parameters allows parallel operation of multiple screens in diverse mammalian cell types. The authors demonstrate that such a system is able to successfully maintain different cell lines in culture for extended periods of time as well as significantly increasing throughput, accuracy, and reproducibility of HT and HC screens.
Voiding defects in acute radiation cystitis driven by urothelial barrier defect through loss of E-cadherin, ZO-1 and Uroplakin III (2021)

Long term-side effects from cancer therapies are a growing health care concern as life expectancy among cancer survivors increases. Damage to the bladder is common in patients treated with radiation therapy for pelvic cancers and can result in radiation (hemorrhagic) cystitis (RC). The disease progression of RC consists of an acute and chronic phase, separated by a symptom-free period. Gaining insight in tissue changes associated with these phases is necessary to develop appropriate interventions. Using a mouse preclinical model, we have previously shown that fibrosis and vascular damage are the predominant pathological features of chronic RC. The goal of this study was to determine the pathological changes during acute RC. We identified that radiation treatment results in a temporary increase in micturition frequency and decrease in void volume 4-8 weeks after irradiation. Histologically, the micturition defect is associated with thinning of the urothelium, loss of urothelial cell-cell adhesion and tight junction proteins and decrease in uroplakin III expression. By 12 weeks, the urothelium had regenerated and micturition patterns were similar to littermate controls. No inflammation or fibrosis were detected in bladder tissues after irradiation. We conclude that functional bladder defects during acute RC are driven primarily by a urothelial defect.
Psychophysical Exams as Early Indicators of Diabetic Retinopathy (2010)

Retinopathy is a serious and common complication of diabetes that represents the leading cause of blindness, among people of working age, in developed countries. It is estimated that the number of people with diabetic retinopathy (DR) will increase from 126.6 million in 2011 to 191 million by 2030. The visual function that seems to be affected first in the course of DR is probably the contrast sensitivity; in addition, being mainly a macular function, the perception of colour is also compromised. Moreover, the duration of the disease, the levels of glycated haemoglobin (HbA<sub>1c</sub>) and the presence of cystoid macular oedema are strongly associated with the impairment of fixation stability in patients with diabetes with clinically significant macular oedema, suggesting the possible diagnostic role of microperimetry. The test of contrast sensitivity and the microperimetry and the chromatic sensitivity tests have proved to be useful, safe, reproducible and inexpensive tools to diagnose the disease early.
Enabling agents to work together (1994)

article Free Access Share on Enabling agents to work together Authors: R. V. Guha Microelectronics and Computer Technology Corp., Austin, TX Microelectronics and Computer Technology Corp., Austin, TXView Profile , Douglas B. Lenat Microelectronics and Computer Technology Corp., Austin, TX Microelectronics and Computer Technology Corp., Austin, TXView Profile Authors Info & Claims Communications of the ACMVolume 37Issue 7July 1994 pp 126–142https://doi.org/10.1145/176789.176804Online:01 July 1994Publication History 97citation767DownloadsMetricsTotal Citations97Total Downloads767Last 12 Months9Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Evaluation of Effect of Mechanical Stress on Stacking Fault Expansion in 4H-SiC P-i-N Diode (2019)

Single Shockley stacking faults (SSFs) expand from basal plane dislocations (BPDs) under forward current operation of 4H-SiC bipolar devices, giving rise to a reliability deterioration mode called “bipolar degradation”. Several groups have proposed models for the expansion of SSFs, in which the SSFs expand when electron-hole pair recombination takes place at BPDs. Maeda proposed a formulation of SSF expansion that includes stacking fault energy. However, the mechanisms by which mechanical stress affects the expansion of SSFs are unclear. In this paper, we evaluated the “expansion threshold current” of bar-shaped SSFs in a mechanical stress field using a p-i-n diode fabricated on 4H-SiC. To confirm the effect of mechanical stress on the threshold current for bar-shaped SSF expansion, a SiC-p-i-n diode was evaluated by the four-point bending method. Experimental results show that the threshold current of SSFs decreases or increases by more than 100 A/cm 2 depending on the direction of the applied stress of SSFs. This result indicates that mechanical stress is an important factor for SiC bipolar device design.
Search for new phenomena in three- or four-lepton events in $pp$ collisions at $\sqrt s$ =13 TeV with the ATLAS detector (2021)

A search with minimal model dependence for physics beyond the Standard Model in events featuring three or four charged leptons (3ℓ and 4ℓ, ℓ=e,μ) is presented. The analysis aims to be sensitive to a wide range of potential new-physics theories simultaneously. This analysis uses data from pp collisions delivered by the Large Hadron Collider at a centre-of-mass energy of s=13 TeV and recorded with the ATLAS detector, corresponding to the full Run 2 dataset of 139 fb−1. The 3ℓ and 4ℓ phase space is divided into 22 event categories according to the number of leptons in the event, the missing transverse momentum, the invariant mass of the leptons, and the presence of leptons originating from a Z-boson candidate. These event categories are analysed independently for the presence of deviations from the Standard Model. No statistically significant deviations from the Standard Model predictions are observed. Upper limits for all signal regions are reported in terms of the visible cross-section.
Magnetic Extraction, Detection, and Isotope Analysis of Metal Ions Using Surface Modified Microspheres for Lab-on-a-Chip Applications (2010)

Abstract Liquid–liquid extraction and ion-exchange chromatography are efficient methods for sequestration of metal ions, but these methods are poorly suitable for microfluidic miniaturization. Here we examine several methods for rapid extraction, fluorometric detection, and the subsequent isotope analysis of lanthanide ions sequestered on surface modified magnetic microspheres as a versatile platform for chemical manipulation. The assays involve immobilization of a mixed-ligand complex of luminescent lanthanide ions at the surface of polystyrene microspheres. Using the ion-exchange properties of these microspheres, this scheme can be extended to the detection of nonluminescent ions. Keywords: magnetic separationsion-exchange chromatographymicrofluidicsfluorometryisotope analysisantenna effect ACKNOWLEDGMENTS IAS and MDK thank P. Rickert and C. J. Mertz for their assistance and M. Jensen, R. Chiarizia, M. L. Dietz, L. Soderholm, and F. Stevens for many useful discussions. KR thanks S. P. Meserole, J. E. Reich, and A. Allen for their assistance. Work at Argonne was performed under the auspices of the Office of Science, Division of Chemical Science, US-DOE under contract No. DE-AC-02-06CH11357 and DTRA DOD contract 08-43151. Notes a For a 2.5 wt% stock aqueous solution. b Median diameter. c Surface area per MM. d Surface density of groups. e Total number of groups per MM. a The standard assay for 1.5 × 10−8 M (23 ppb) Eu3+ and 1.5 mM TTA in 600 µL of 5 × 10−5 HNO3 with 0.12 wt% of the modified MMs. b n = 6.
TGF‐beta signalling in the adult neurogenic niche promotes stem cell quiescence as well as generation of new neurons (2014)

Members of the transforming growth factor (TGF)-β family govern a wide range of mechanisms in brain development and in the adult, in particular neuronal/glial differentiation and survival, but also cell cycle regulation and neural stem cell maintenance. This clearly created some discrepancies in the field with some studies favouring neuronal differentiation/survival of progenitors and others favouring cell cycle exit and neural stem cell quiescence/maintenance. Here, we provide a unifying hypothesis claiming that through its regulation of neural progenitor cell (NPC) proliferation, TGF-β signalling might be responsible for (i) maintaining stem cells in a quiescent stage, and (ii) promoting survival of newly generated neurons and their functional differentiation. Therefore, we performed a detailed histological analysis of TGF-β1 signalling in the hippocampal neural stem cell niche of a transgenic mouse that was previously generated to express TGF-β1 under a tetracycline regulatable Ca-Calmodulin kinase promoter. We also analysed NPC proliferation, quiescence, neuronal survival and differentiation in relation to elevated levels of TGF-β1 in vitro and in vivo conditions. Finally, we performed a gene expression profiling to identify the targets of TGF-β1 signalling in adult NPCs. The results demonstrate that TGF-β1 promotes stem cell quiescence on one side, but also neuronal survival on the other side. Thus, considering the elevated levels of TGF-β1 in ageing and neurodegenerative diseases, TGF-β1 signalling presents a molecular target for future interventions in such conditions.
Serine Octamer Reactions: Indicators of Prebiotic Relevance (2003)

Ursprung der Homochiralität? Serin geht enantioselektive Reaktionen ein, die bedeutsam für den Ursprung von homochiralem Leben sein könnten. Chiralitätsaustausch zwischen Serin, Glyceraldehyd und Glucose führt bevorzugt zu denjenigen Enantiomeren (L-Serin, D-Zucker), die heute auch in lebenden Organismen gefunden werden (siehe Bild).
Multiple presynaptic metabotropic glutamate receptors modulate excitatory and inhibitory synaptic transmission in hippocampal area CA1 (1995)

The metabotropic glutamate receptors (mGluRs) have many important roles in regulation of neuronal excitability and synaptic transmission. In hippocampal area CA1, activation of mGluRs can reduce both excitatory and inhibitory synaptic transmission. The conventional view is that the presynaptic effects are mediated by L-2-amino-4-phosphonobutyric acid (L-AP4)-sensitive, or group III mGluRs (mGluR4, mGluR6, mGluR7, mGluR8). However, some studies suggest that other mGluR subtypes may also be involved in regulation of excitatory and inhibitory synaptic transmission in area CA1. We have found that two pharmacologically distinct presynaptic receptors are involved in the depression of excitatory transmission at the Schaffer collateral--CA1 synapse. Consistent with previous studies, one receptor subtype is an L-AP4- sensitive receptor that is pharmacologically similar to mGluR4 or mGluR7. However, we have found that a second mGluR subtype, which is pharmacologically similar to mGluR1 and mGluR5 (group I mGluRs), can also reduce excitatory synaptic transmission in area CA1. Analysis of effects of agonists of these two receptors on miniature EPSCs and paired-pulse facilitation suggest that both receptors are localized presynaptically. It is also shown that the mGluR that reduces transmission at inhibitory synapses in area CA1 is presynaptically localized, is insensitive to L-AP4, and is sensitive to agonists selective for mGluR1 and mGluR5.
The Advantages of Interrupted Sutures and a Therapeutic Lens in Keratoplasty (1981)

SUMMARY Forty-one consecutive keratoplasties were performed using interrupted sutures with exposed knots in combination with therapeutic lenses applied at the time of surgery. We found that this technique offers the advantages of interrupted sutures and provides maximum comfort. The therapeutic lens prevents problems with faulty re-epithelialization, discourages vascularization, and allows easy and selective suture removal. Early final visual rehabilitation was possible because all sutures were safely removed by 15 weeks.