gebhart/patrepeval huggingface dataset:
Fragmentation of Singly Protonated Peptides via Interaction with Metastable Rare Gas Atoms (2008)

The effects of metastable energy level and peptide sequence on the fragmentation patterns of singly charged peptide ions dissociated in collisions with metastable rare gas atoms were studied. Fragmentation spectra of singly charged peptide ions were shown to be more structure-informative and very different from those obtained in low-energy collision-induced dissociation. Unusual odd-electron radical a- and x-ions were observed. Several fragment ions corresponding to a side-chain loss were also observed, which allowed differentiation between leucine and isoleucine. The fragmentation mechanism depends on electronic energy transferred during interaction with metastable gas atoms and proceeds either via Penning ionization with formation of radical odd-electron doubly charged molecular cation or via high-energy excitation of internal degrees of freedom of the peptide cation.
A SiGe BiCMOS 16-element phased-array transmitter for 60GHz communications (2010)

The demonstration of multi-Gb/s links in the 60GHz band has created new opportunities for wireless communications [1,2]. Due to the directional nature of millimeter-wave (mm-Wave) propagation, beam steering enables longer-range non-line-of-sight (NLOS) links at these frequencies. A phased-array architecture is attractive for an integrated 60GHz transmitter (Tx) since it can attain both beam steering and higher EIRP through spatial combining. An all-RF 16-element 40-to-45GHz Tx for satellite applications [3], a 6-element 60GHz Tx with IF-path phase-shift [4], and a bi-directional 4-element 60GHz Tx/Rx with RF phase shifters [5] have been recently demonstrated in silicon. This work presents a fully-integrated phased-array Tx which supports multi-Gb/s NLOS IEEE 802.15.3c links. In addition to beamsteering, the IC has the following major features: an on-chip power sensor at each element, 3 temperature sensors, LO leakage and I/Q phase and amplitude adjustment, front-end OP <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</inf> programmability, and an integrated modulator for pi/2-BPSK/MSK signaling (common mode in 802.15.3c). The IC integrates 2240 NPNs, 323,000 FETs and hundreds of transmission lines and is fabricated in the IBM 8HP 0.12µm SiGe BiCMOS process (f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> = 200GHz).
Considerations for further scaling of metal–insulator–metal DRAM capacitors (2012)

Effective electron tunneling mass mtunnel is extracted from trap-assisted leakage in Sr-rich strontium titanate and rutile titanium oxide films in metal–insulator–metal (MIM) capacitors and compared with theoretical values obtained from first principles calculations of the imaginary band structure. Optimum orientations of films and stoichiometry impacting mtunnel are also discussed. Because future vertical DRAM integration schemes also stipulate maximum thickness of the MIM capacitor, mtunnel is shown to be a critical parameter influencing intrinsic leakage and potentially limiting further scaling.
ErbB3-Targeting Oncolytic Adenovirus Causes Potent Tumor Suppression by Induction of Apoptosis in Cancer Cells (2022)

Cancer is a multifactorial and deadly disease. Despite major advancements in cancer therapy in the last two decades, cancer incidence is on the rise and disease prognosis still remains poor. Furthermore, molecular mechanisms of cancer invasiveness, metastasis, and drug resistance remain largely elusive. Targeted cancer therapy involving the silencing of specific cancer-enriched proteins by small interfering RNA (siRNA) offers a powerful tool. However, its application in clinic is limited by the short half-life of siRNA and warrants the development of efficient and stable siRNA delivery systems. Oncolytic adenovirus-mediated therapy offers an attractive alternative to the chemical drugs that often suffer from innate and acquired drug resistance. In continuation to our reports on the development of oncolytic adenovirus-mediated delivery of shRNA, we report here the replication-incompetent (dAd/shErbB3) and replication-competent (oAd/shErbB3) oncolytic adenovirus systems that caused efficient and persistent targeting of ErbB3. We demonstrate that the E1A coded by oAd/shErbB, in contrast to dAd/shErbB, caused downregulation of ErbB2 and ErbB3, yielding stronger downregulation of the ErbB3-oncogenic signaling axis in in vitro models of lung and breast cancer. These results were validated by in vivo antitumor efficacy of dAd/shErbB3 and oAd/shErbB3.
Presence of Oxytocin and Arginine Vasopressin in Human Ovary, Oviduct, and Follicular Fluid* (1984)

Oxytocin and arginine vasopressin (AVP) immunoreactivity in human ovary, oviduct, and follicular fluid were measured and found to coelute with the authentic peptides using both gel filtration column chromatography and reverse phase thin layer chromatography. In ovarian tissue, mean oxytocin and AVP concentrations were 0.48 and 0.24 ng/mg protein, respectively. These values are approximately 4000-fold higher than peripheral plasma levels. The concentration of oxytocin in the corpus luteum was approximately 6-fold greater (3.12 ng/mg protein) than that in ovarian tissue with no corpus luteum. In contrast, no significant difference in the concentration of AVP was found between corpus luteal and the remaining ovarian tissues. Follicular fluid contained 299 and 131 pg/ml oxytocin and AVP, respectively. These levels were 30-fold greater than the serum level of either peptide, suggesting ovarian synthesis of the neurohypophyseal hormones. In addition, immunoreactive oxytocin and AVP were detected in the oviducts (1.01 and 0.24 ng/mg protein, respectively); however, neither peptide was detectable in myometrial tissue (less than 0.02 ng/mg protein). Our results demonstrate the presence of high concentrations of oxytocin and AVP in human ovarian and oviductal tissues as well as follicular fluid and suggest that neurohypophyseal peptides have a paracrine role in the regulation of ovarian or oviductal functions.
The Specific Acid-Catalyzed and Photochemical Isomerization of a Robust Fulleroid to a Methanofullerene (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Specific Acid-Catalyzed and Photochemical Isomerization of a Robust Fulleroid to a MethanofullereneRosario Gonzalez, Jan C. Hummelen, and Fred WudlCite this: J. Org. Chem. 1995, 60, 8, 2618–2620Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/jo00113a049https://doi.org/10.1021/jo00113a049research-articleACS PublicationsRequest reuse permissionsArticle Views493Altmetric-Citations44LEARN 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
Strong binding of ditrisarubicin B to DNA. (1988)

DNA binding characteristics of ditrisarubicin B were studied by the fluorescence titration technique. Ditrisarubicin B bound to calf thymus DNA with an affinity higher than any we have ever seen among anthracyclines. The apparent association constant (Kapp) of ditrisarubicin B was 2.36 X 10(8) M-1, which is 22.7 times larger than that of doxorubicin. The apparent number of binding sites (napp) of ditrisarubicin B per nucleotide of DNA was 0.164, and this value is identical with that of doxorubicin. Betaclamycin A, which has a trisaccharide chain at C-7 but no carbohydrate at C-10 in the aglycone, interacted with DNA to give a Kapp of 5.92 X 10(6) M-1 and napp of 0.178. These results suggest to us that the high affinity of ditrisarubicin B for DNA is caused by the existence of a glycosidic chain at C-10.
Quantitative and Morphological Studies on Starch of Apple Fruit during Development (1990)

The starch content of apple fruit (Males domestica Borkh `Jonagold ') during development varied depending on the location in the flesh. The most prominent feature was the higher starch content and lower decrease rate in the outer part of the flesh than in the inner and middle part of the flesh. Light microscopy observations coincided well with the analytical data . Examination with a scanning electron microscope showed that starch granules were spherical in shape with a smooth surface and were composed of several fragments . The distribution pattern of the granule size in every part of the flesh did not reveal any significant changes during fruit development. Furthermore, at the late stage of development , the magnitude of the decrease of the mean diameter of starch granules could not account for the decrease of the starch content. These facts indicate that starch degradation of `Jonagold' fruit starts mainly from inside of the granules.
Highly efficient deep‐blue fluorescent dopant for achieving low‐power OLED display satisfying BT.2020 chromaticity (2018)

Abstract In this work, novel blue‐fluorescent dopants with a heteroaromatic ring skeleton instead of the conventional pyrene skeleton were investigated. Bottom‐emission organic light‐emitting diodes (OLEDs) fabricated using the novel blue‐fluorescent dopants in light‐emitting layers achieved better deep‐blue chromaticity than OLEDs based on a conventional pyrene‐based dopant, while maintaining both high external quantum efficiency (EQE) and comparable reliability. The attainment of deep‐blue chromaticity without losing high EQE was ascribed to the improvement of the efficiency of energy transfer from the host to the dopant. Furthermore, it was estimated that using this novel dopant in a top‐emission OLED panel that satisfies BT.2020 chromaticity enables the power consumption of the whole panel to be 24% lower than that of the panel with a conventional dopant.
Sequential sequencing by synthesis and the next-generation sequencing revolution (2023)

The impact of next-generation sequencing (NGS) cannot be overestimated. The technology has transformed the field of life science, contributing to a dramatic expansion in our understanding of human health and disease and our understanding of biology and ecology. The vast majority of the major NGS systems today are based on the concept of 'sequencing by synthesis' (SBS) with sequential detection of nucleotide incorporation using an engineered DNA polymerase. Based on this strategy, various alternative platforms have been developed, including the use of either native nucleotides or reversible terminators and different strategies for the attachment of DNA to a solid support. In this review, some of the key concepts leading to this remarkable development are discussed.
Delayed opportunistic infections in hematopoietic stem cell transplantation patients: a surmountable challenge (2012)

Changes in the transplantation procedure and the implementation of effective supportive care strategies have decreased the incidence of infectious complications early after conditioning therapy for allogeneic hematopoietic stem cell transplantation (HCT) and have extended the duration of risks later. Therefore, the types of infections that cause significant morbidity and the timing of risks have changed. These late infections are caused by all types of organisms, bacterial, viral, and fungal, but risks are predictable and surmountable with the use of tailored prevention strategies. Specifically, recent studies document prolonged risks for bacterial infections in the setting of GVHD, especially those caused by encapsulated organisms and those secondary to impaired Ab responses. Both prophylaxis and vaccination strategies can be used as a means to prevent infections, which typically manifest in the respiratory tract. Multiple viruses cause infection later after HCT, including several herpesviruses (eg, CMV and varicella zoster virus) and other respiratory viruses such as influenza and adenovirus. These infections can cause severe disease with diagnostic challenges, but prevention strategies using enhanced monitoring and/or prophylaxis may be effective. Finally, fungi also cause disease late after HCT, especially filamentous fungi (eg, Aspergillus species and Mucormycoses) and Pneumocystis jiroveci; prophylactic strategies may be used successfully to prevent invasive infection. Late infections and methods to prevent them are reviewed herein.
CD38: A target in relapsed/refractory acute lymphoblastic leukemia—Limitations in treatment and diagnostics (2022)

Daratumumab, an anti-CD38 antibody, is used experimentally in the treatment of relapsed acute lymphoblastic leukemia (ALL). We treated five patients suffering from relapsed ALL with daratumumab. Four patients had T ALL, three of whom achieved complete remission (CR) after treatment and underwent stem cell transplant (SCT). Two of them had a second relapse and died 6 and 8 months after SCT, respectively. One transplanted T ALL patient remained in CR2 15 months after relapse. In the remaining T-ALL patient, the disease progressed under daratumumab treatment, and the patient died early after the first relapse. The B-cell precursor ALL patient with a second CD19-negative relapse, whose disease turned out to be resistant to the combination of daratumumab with chemotherapy, later achieved CR3 with inotuzumab ozogamicin, underwent SCT and remained in CR3. Leukemia burden should be monitored after daratumumab, and care should be taken not to misclassify leukemic cells with false negativity of surface CD38; using an antibody reacting with nondaratumumab epitopes is advantageous.
Learning Language and Multimodal Privacy-Preserving Markers of Mood from Mobile Data (2021)

Paul Pu Liang, Terrance Liu, Anna Cai, Michal Muszynski, Ryo Ishii, Nick Allen, Randy Auerbach, David Brent, Ruslan Salakhutdinov, Louis-Philippe Morency. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.
Regulation of CCN2/Connective tissue growth factor expression in the nucleus pulposus of the intervertebral disc: Role of Smad and activator protein 1 signaling (2010)

TGFbeta, through Smad3 and AP-1, serves as a positive regulator of CTGF expression in the nucleus pulposus. We propose that CTGF is a part of the limited reparative response of the degenerated disc.
Magnetic nanotube composite membranes (2023)

The invention provides a membrane comprising tubes extending through a polymer, wherein substantially all of the tubes are parallel with each other. Also provided is a method for producing a membrane, the method comprising: placing tubes on a substrate, subjecting the tubes to a magnetic field for a time and at a magnetic field strength to cause the tubes to align parallel with each other while simultaneously causing depending ends of the tubes to embed within the substrate; applying polymer to the tubes and substrate in an amount to affix the tubes relative to each other and relative to the substrate, and applying an etchant that cleaves a specific type of the bonds within the polymer to unblock the upstream ends of the nanotubes.
Quantum reference frames and deformed symmetries (2008)

In the context of constrained quantum mechanics, reference systems are used to construct relational observables that are invariant under the action of the symmetry group. Upon measurement of a relational observable, the reference system undergoes an unavoidable measurement ``back-action'' that modifies its properties. In a quantum-gravitational setting, it has been argued that such a back-action may produce effects that are described at an effective level as a form of deformed (or doubly) special relativity. We examine this possibility using a simple constrained system that has been extensively studied in the context of quantum information. While our conclusions support the idea of a symmetry deformation, they also reveal a host of other effects that may be relevant to the context of quantum gravity, and could potentially conceal the symmetry deformation.
Mechanism of dynamic nuclear polarization in high magnetic fields (2001)

Solid-state NMR signal enhancements of about two orders of magnitude (100–400) have been observed in dynamic nuclear polarization (DNP) experiments performed at high magnetic field (5 T) and low temperature (10 K) using the nitroxide radical 4-amino TEMPO as the source of electron polarization. Since the breadth of the 4-amino TEMPO EPR spectrum is large compared to the nuclear Larmor frequency, it has been assumed that thermal mixing (TM) is the dominate mechanism by which polarization is transferred from electron to nuclear spins. However, theoretical explanations of TM generally assume a homogeneously broadened EPR line and, since the 4-amino TEMPO line at 5 T is inhomogeneously broadened, they do not explain the observed DNP enhancements. Accordingly, we have developed a treatment of DNP that explicitly uses electron–electron cross-relaxation to mediate electron–nuclear polarization transfer. The process proceeds via spin flip–flops between pairs of electronic spin packets whose Zeeman temperatures differ from one another. To confirm the essential features of the model we have studied the field dependence of electron–electron double resonance (ELDOR) data and DNP enhancement data. Both are well simulated using a simple model of electron cross-relaxation in the inhomogeneously broadened 4-amino TEMPO EPR line.
Intraneuronal Aβ immunoreactivity is not a predictor of brain amyloidosis-β or neurofibrillary degeneration (2007)

Amyloid beta (Abeta) immunoreactivity in neurons was examined in brains of 32 control subjects, 31 people with Down syndrome, and 36 patients with sporadic Alzheimer's disease to determine if intraneuronal Abeta immunoreactivity is an early manifestation of Alzheimer-type pathology leading to fibrillar plaque formation and/or neurofibrillary degeneration. The appearance of Abeta immunoreactivity in neurons in infants and stable neuron-type specific Abeta immunoreactivity in a majority of brain structures during late childhood, adulthood, and normal aging does not support this hypothesis. The absence or detection of only traces of reaction with antibodies against 4-13 aa and 8-17 aa of Abeta in neurons indicated that intraneuronal Abeta was mainly a product of alpha- and gamma-secretases (Abeta(17-40/42)). The presence of N-terminally truncated Abeta(17-40) and Abeta(17-42) in the control brains was confirmed by Western blotting and the identity of Abeta(17-40) was confirmed by mass spectrometry. The prevalence of products of alpha- and gamma -secretases in neurons and beta- and gamma-secretases in plaques argues against major contribution of Abeta-immunopositive material detected in neuronal soma to amyloid deposit in plaques. The strongest intraneuronal Abeta(17-42) immunoreactivity was observed in structures with low susceptibility to fibrillar Abeta deposition, neurofibrillary degeneration, and neuronal loss compared to areas more vulnerable to Alzheimer-type pathology. These observations indicate that the intraneuronal Abeta immunoreactivity detected in this study is not a predictor of brain amyloidosis or neurofibrillary degeneration. The constant level of Abeta immunoreactivity in structures free from neuronal pathology during essentially the entire life span suggests that intraneuronal amino-terminally truncated Abeta represents a product of normal neuronal metabolism.
Detecting acute distress and risk of future psychological morbidity in critically ill patients: validation of the intensive care psychological assessment tool (2014)

The IPAT was found to have good reliability and validity. Sensitivity and specificity analysis suggest the IPAT could provide a way of allowing staff to assess psychological distress among critical care patients after further replication and validation. Further work is also needed to determine its utility in predicting future psychological morbidity.
Nef protein of human immunodeficiency virus type 1 binds its own myristoylated N-terminus (2007)

HIV-1 Nef is a small protein (approx. 25 kDa) that is posttranslationally modified by myristoylation. To explain its complex activities, a 'Nef-cycle' is discussed, which postulates different molecular conformations of Nef. Using recombinant full-length non-myristoylated Nef and synthetic peptides, we demonstrate by fluorescence titration experiments that a peptide representing the myristoylated N-terminus of Nef is specifically bound by Nef. A non-myristoylated N-terminal fragment of Nef or a myristoylated control peptide does not bind to Nef. These results are the first direct experimental evidence of the existence of a myristate-binding pocket in Nef, a prerequisite of the postulated 'closed' Nef conformation.
CD45 modulates T cell receptor/CD3‐induced activation of human thymocytes via regulation of tyrosine phosphorylation (1992)

Stimulation of thymocytes or mature T cells via the T cell receptor (TcR)/CD3 complex activates a cascade of processes inducing cells to enter the cell cycle. A key step is the activation of phosphatidylinositol-specific phospholipase C (PI-PLC) within seconds following TcR/CD3 stimulation, an event which is strongly enhanced by co-ligation of the CD4 (or CD8) accessory molecule with TcR/CD3. In contrast, co-ligation of CD45 inhibits the same TcR/CD3 responses. The machinery which couples the TcR/CD3 complex, CD4, and CD45 to PI-PLC appears to involve regulation of tyrosine phosphorylation, as the TcR/CD3 and CD4 receptors are associated with the tyrosine kinases p59fyn and p56lck, respectively, and CD45 has intrinsic tyrosine phosphatase activity. Here, we have examined the ability of CD45 to regulate signal transduction via TcR/CD3 in human thymocytes. Co-cross-linking CD45 to the TcR/CD3 complex strongly suppressed the tyrosine phosphorylation of several intracellular substrates normally seen following TcR/CD3 stimulation. This effect of CD45 was associated with inhibition of a rise in intracellular calcium following TcR/CD3 ligation. Since TcR/CD3 stimulation of mature T cells induces tyrosine phosphorylation of PLC gamma 1, we investigated this phenomenon in thymocytes, and asked whether ligation of CD45 might regulate this process. By immunoprecipitation we found that TcR/CD3 stimulation induced tyrosine phosphorylation of PLC gamma 1, an effect which was enhanced by co-cross-linking CD4 to TcR/CD3. In contrast, co-ligation of CD45 strongly blocked PLC gamma 1 phosphorylation induced by either stimulus. Consistent with previous findings in mature T cells, CD45 cross-linking was able to partially inhibit TcR/CD3-induced thymocyte proliferation when interleukin 2 was used as a second signal, but almost completely (80%-90%) blocked proliferation when anti-CD28 mAb was used as the second signal, suggesting that CD45 cross-linking may be able to block interleukin 2 production via the CD28 pathway. These effects of CD45 on TcR/CD3 signaling and proliferation in thymocytes point towards a potential role for this pathway in thymic selection.