gebhart/patrepeval huggingface dataset:
MDP: A Deinococcus Mn2+-Decapeptide Complex Protects Mice from Ionizing Radiation (2016)

The radioprotective capacity of a rationally-designed Mn2+-decapeptide complex (MDP), based on Mn antioxidants in the bacterium Deinococcus radiodurans, was investigated in a mouse model of radiation injury. MDP was previously reported to be extraordinarily radioprotective of proteins in the setting of vaccine development. The peptide-component (DEHGTAVMLK) of MDP applied here was selected from a group of synthetic peptides screened in vitro for their ability to protect cultured human cells and purified enzymes from extreme damage caused by ionizing radiation (IR). We show that the peptides accumulated in Jurkat T-cells and protected them from 100 Gy. MDP preserved the activity of T4 DNA ligase exposed to 60,000 Gy. In vivo, MDP was nontoxic and protected B6D2F1/J (female) mice from acute radiation syndrome. All irradiated mice treated with MDP survived exposure to 9.5 Gy (LD70/30) in comparison to the untreated mice, which displayed 63% lethality after 30 days. Our results show that MDP provides early protection of white blood cells, and attenuates IR-induced damage to bone marrow and hematopoietic stem cells via G-CSF and GM-CSF modulation. Moreover, MDP mediated the immunomodulation of several cytokine concentrations in serum including G-CSF, GM-CSF, IL-3 and IL-10 during early recovery. Our results present the necessary prelude for future efforts towards clinical application of MDP as a promising IR countermeasure. Further investigation of MDP as a pre-exposure prophylactic and post-exposure therapeutic in radiotherapy and radiation emergencies is warranted.
Linear time and frequency domain turbo equalization (2002)

For coded data transmission over channels introducing inter-symbol interference, one approach for joint equalization and decoding in the receiver is turbo equalization. We rederive existing linear equalization algorithms applicable to turbo equalization for 2/sup m/-ary signal alphabets and compare their computational complexity. Moreover by evaluating the algorithm performance properly, we select for each iteration the most suitable of the two algorithms with lowest computational complexity and achieve at low bit error rates a performance close to that of optimal approaches for equalization, i.e., maximum a-posteriori probability symbol detection.
Human vascular endothelial cells express pattern recognition receptors for fungal glucans which stimulates nuclear factor kappaB activation and interleukin 8 production. Winner of the Best Paper Award from the Gold Medal Forum. (2002)

Fungal cell wall glucans nonspecifically stimulate various aspects of innate immunity via interaction with membrane receptors on macrophages, neutrophils, and natural killer cells. We investigated the binding of water-soluble glucans in primary cultures of normal human coronary or dermal vascular endothelial cells (VECs). Membranes from VECs exhibited saturable binding. Competition studies demonstrated the presence of at least two glucan binding sites on VECs. Glucan phosphate competed for all binding sites with a KD of 3.7 microM for coronary VECs and 11 microM for dermal VECs, respectively. Laminarin, a low molecular weight glucan, competed for 47 to 51 per cent of binding (KD = 2.8-2.9 microM), indicating the presence of at least two binding sites. Glucan (1 microg/mL) stimulated VEC nuclear factor kappaB nuclear binding activity and Interleukin 8 expression--but not that of vascular endothelial growth factor--in a time-dependent manner. This is the first report of pattern recognition receptors for glucan on human VECs. It also provides the first evidence that glucans can directly modulate the functional activity of VECs by stimulating cytokine gene. These results provide new insights into the mechanisms by which the host recognizes and responds to fungal cell wall products and suggests that the response to glucans may not be confined to leukocytes.
Erratum: “Real Time Imaging of Surface Acoustic Waves on Crystals and Microstructures” (2005)

The use of acoustic pulses to image materials is well-known in echography or sonar applications. We are extending this field by generating point-excited sound pulses on solid surfaces with ultrashort laser pulses and imaging the resulting surface wave propagation in real time. To see the tiny vibrations of the surface, smaller in amplitude than the dimensions of a single atom, we use another set of laser pulses for scanned probing. The typical surface phonon wavelength is of the order of a few microns, corresponding to frequencies up to 1 GHz. With such a system we can watch coherent acoustic wave packets in two dimensions rippling across crystal surfaces and microscopic landscapes.
myo-Inositol transport by Salmonella enterica serovar Typhimurium (2009)

In Salmonella enterica serovar Typhimurium, the genomic island GEI4417/4436 has recently been identified to be responsible for myo-inositol (MI) utilization. Here, two of the four island-encoded permeases are identified as the MI transporters of this pathogen. In-frame deletion of iolT1 (STM4418) led to a severe growth defect, and deletion of iolT1 (STM4419) to a slight growth defect in the presence of MI. These phenotypes could be complemented by providing the putative transporter genes in trans. Bioluminescence-based reporter assays demonstrated a strong induction of their promoters P(iolT1) and P(iolT2) in the presence of MI but not of glucose. Deletion of iolR, which encodes the negative regulator of most genes involved in MI degradation, resulted in upregulation of P(iolT1) and P(iolT2), indicating that the expression of IolT1 and IolT2 is repressed by IolR. This finding was supported by bandshift assays using purified IolR. Both transporters are located in the membrane when expressed in Escherichia coli. Heterologously expressed IolT1 had its optimal activity at pH 5.5. Together with the strongly reduced MI uptake in the presence of protonophores, this indicates that IolT1 operates as a proton symporter. Using myo-[1,2-[(3)H](N)]inositol, a saturable uptake activity of IolT1 with a K(m) value between 0.49 and 0.79 mM was determined in DH5alpha expressing IolT1, in S. enterica serovar Typhimurium strain 14028, and in mutant 14028 DeltaiolT2. Phylogenetic analysis of IolT1 identified putative MI transporters in Gram-negative bacteria also able to utilize MI.
ISAP – Towards Side-Channel Secure Authenticated Encryption (2017)

Side-channel attacks and in particular differential power analysis (DPA) attacks pose a serious threat to cryptographic implementations. One approach to counteract such attacks are cryptographic schemes based on fresh re-keying. In settings of pre-shared secret keys, such schemes render DPA attacks infeasible by deriving session keys and by ensuring that the attacker cannot collect side-channel leakage on the session key during cryptographic operations with different inputs. While these schemes can be applied to secure standard communication settings, current re-keying approaches are unable to provide protection in settings where the same input needs to be processed multiple times. In this work, we therefore adapt the re-keying approach and present a symmetric authenticated encryption scheme that is secure against DPA attacks and that does not have such a usage restriction. This means that our scheme fully complies with the requirements given in the CAESAR call and hence, can be used like other noncebased authenticated encryption schemes without loss of side-channel protection. Its resistance against side-channel analysis is highly relevant for several applications in practice, like bulk storage settings in general and the protection of FPGA bitfiles and firmware images in particular.
Data from The Prognostic Impact of CD163-Positive Macrophages in Follicular Lymphoma: A Study from the BC Cancer Agency and the Lymphoma Study Association (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; We aimed to assess the prognostic significance of follicular lymphoma–associated macrophages in the era of rituximab treatment and maintenance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We applied immunohistochemistry for CD68 and CD163 to two large tissue microarrays (TMA). The first TMA included samples from 186 patients from the BC Cancer Agency (BCCA) who had been treated with first-line systemic treatment including rituximab, cyclophosphamide, vincristine, and prednisone. The second contained 395 samples from PRIMA trial patients treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone, and randomized to rituximab maintenance or observation. Macrophage infiltration was assessed using Aperio image analysis. Each of the two cohorts was randomly split into training/validation sets.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; An increased CD163-positive pixel count was predictive of adverse outcome in the BCCA dataset [5-year progression-free survival (PFS) 38% vs. 72%, respectively, &lt;i&gt;P&lt;/i&gt; = 0.004 in the training cohort and 5-year PFS 29% vs. 61%, respectively, &lt;i&gt;P&lt;/i&gt; = 0.004 in the validation cohort]. In the PRIMA trial, an increased CD163 pixel count was associated with favorable outcome (5-year PFS 60% vs. 44%, respectively, &lt;i&gt;P&lt;/i&gt; = 0.011 in the training cohort and 5-year PFS 55% vs. 37%, respectively, &lt;i&gt;P&lt;/i&gt; = 0.030 in the validation cohort).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; CD163-positive macrophages predict outcome in follicular lymphoma, but their prognostic impact is highly dependent on treatment received. &lt;i&gt;Clin Cancer Res; 21(15); 3428–35. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Averting the Legacy of Kidney Disease—Focus on Childhood (2016)

World Kidney Day 2016 focuses on kidney disease in childhood and the antecedents of adult kidney disease that can begin in earliest childhood. Chronic kidney disease (CKD) in childhood differs from that in adults, as the largest diagnostic group among children includes congenital anomalies and inherited disorders, with glomerulopathies and kidney disease in the setting of diabetes being relatively uncommon. In addition, many children with acute kidney injury will ultimately develop sequelae that may lead to hypertension and CKD in later childhood or in adult life. Children born early or who are small-for date newborns have relatively increased risk for the development of CKD later in life. Persons with a high-risk birth and early childhood history should be watched closely in order to help detect early signs of kidney disease in time to provide effective prevention or treatment. Successful therapy is feasible for advanced CKD in childhood; there is evidence that children fare better than adults if they receive kidney replacement therapy, including dialysis and transplantation, while only a minority of children may require this ultimate intervention. Since there are disparities in access to care, effort is needed so that those children with kidney disease, wherever they live, may be treated effectively, irrespective of their geographic or economic circumstances. Our hope is that World Kidney Day will inform the general public, policy makers and caregivers about the needs and possibilities surrounding kidney disease in childhood. “For in every adult there dwells the child that was, and in every child there lies the adult that will be.”—John Connolly, The Book of Lost Things.
Compartmentalization of the protein repair machinery in photosynthetic membranes (2014)

A crucial component of protein homeostasis in cells is the repair of damaged proteins. The repair of oxygen-evolving photosystem II (PS II) supercomplexes in plant chloroplasts is a prime example of a very efficient repair process that evolved in response to the high vulnerability of PS II to photooxidative damage, exacerbated by high-light (HL) stress. Significant progress in recent years has unraveled individual components and steps that constitute the PS II repair machinery, which is embedded in the thylakoid membrane system inside chloroplasts. However, an open question is how a certain order of these repair steps is established and how unwanted back-reactions that jeopardize the repair efficiency are avoided. Here, we report that spatial separation of key enzymes involved in PS II repair is realized by subcompartmentalization of the thylakoid membrane, accomplished by the formation of stacked grana membranes. The spatial segregation of kinases, phosphatases, proteases, and ribosomes ensures a certain order of events with minimal mutual interference. The margins of the grana turn out to be the site of protein degradation, well separated from active PS II in grana core and de novo protein synthesis in unstacked stroma lamellae. Furthermore, HL induces a partial conversion of stacked grana core to grana margin, which leads to a controlled access of proteases to PS II. Our study suggests that the origin of grana in evolution ensures high repair efficiency, which is essential for PS II homeostasis.
Engineering Human Peripheral Blood Stem Cell Grafts that Are Depleted of Naïve T Cells and Retain Functional Pathogen-Specific Memory T Cells (2014)

Graft-versus-host disease (GVHD) is a frequent major complication of allogeneic hematopoietic cell transplantation (HCT). Approaches that selectively deplete T cells that cause GVHD from allogeneic stem cell grafts and preserve T cells specific for pathogens may improve HCT outcomes. It has been hypothesized that the majority of T cells that can cause GVHD reside within the naïve T cell (TN) subset, and previous studies performed in mouse models and with human cells in vitro support this hypothesis. As a prelude to translating these findings to the clinic, we developed and evaluated a novel 2-step clinically compliant procedure for manipulating peripheral blood stem cells (PBSC) to remove TN, preserve CD34(+) hematopoietic stem cells, and provide for a fixed dose of memory T cells (TM) that includes T cells with specificity for common opportunistic pathogens encountered after HCT. Our studies demonstrate effective and reproducible performance of the immunomagnetic cell selection procedure for depleting TN. Moreover, after cell processing, the CD45RA-depleted PBSC products are enriched for CD4(+) and CD8(+) TM with a central memory phenotype and contain TM cells that are capable of proliferating and producing effector cytokines in response to opportunistic pathogens.
Natural communication with information systems (2000)

Pervasive networking and sophisticated computing open opportunities for collaborative information processing independent of time and space. In this instance the information system becomes an enhancer of human intellect, as well as a mediator for communication among participants. The human user favors the sensory dimensions of sight, sound, and touch as primary channels of communication. Machines that can accommodate these modes promise flexibilities and functionalities that transcend the traditional mouse and keyboard. The paper describes research to establish human-computer interfaces that capture attributes of natural face-to-face communication. An experimental multimodal system is developed to study several aspects of natural style human-computer communication. While as yet primitive, the technologies of image and gaze processing, hands-free conversation, and force feedback tactile transduction are combined and used simultaneously for manipulating objects in a shared workspace. Software agents fuse the sensory signals to estimate and interpret user intent. Current areas of experimental application include disaster relief/crisis management, telemedicine/rehabilitation, and mobile office/wearable computers.
Fabrication and Characterization of Polymer Hollow Microneedle Array Using UV Lithography Into Micromolds (2013)

Drug delivery through micromachined needles is an attractive alternative to intramuscular and subdermal injection by hypodermic needles, due to the potential for reduced pain caused by the micro-sized needles. In this paper, a polymer-based fabrication process using UV lithography into micromolds is developed, allowing the fabrication of microneedle (MN) shafts, tips, lumens, and substrate baseplate using lithography. Using UV lithography into micromolds allows complex three-dimensional structures to be defined, since both mask patterns and mold topography are available to define the structures. A hollow MN array and baseplate, in which the needle lumens extend through the thickness of the baseplate, are demonstrated. Fabricated SU-8 MNs are 825 μm in height and 400 μm in width, with a pyramidal tip; the needle lumen, 120 μm in diameter, intersects with one of the faces of the pyramidal tip. Mechanical characterization of the fabricated MNs shows that the fracture force of a single needle against a rigid surface is 12.0 N. The insertion force of a single needle into porcine skin is empirically determined to be 2.4 N. The fracture force of the needle against porcine skin is observed to be in excess of 90 N.
Ventilatory response to exercise in subjects breathing CO2 or HeO2 (1997)

To investigate the effects of mechanical ventilatory limitation on the ventilatory response to exercise, eight older subjects with normal lung function were studied. Each subject performed graded cycle ergometry to exhaustion once while breathing room air; once while breathing 3% CO2-21% O2-balance N2; and once while breathing HeO2 (79% He and 21% O2). Minute ventilation (VE) and respiratory mechanics were measured continuously during each 1-min increment in work rate (10 or 20 W). Data were analyzed at rest, at ventilatory threshold (VTh), and at maximal exercise. When the subjects were breathing 3% CO2, there was an increase (P < 0.001) in VE at rest and at VTh but not during maximal exercise. When the subjects were breathing HeO2, VE was increased (P < 0.05) only during maximal exercise (24 +/- 11%). The ventilatory response to exercise below VTh was greater only when the subjects were breathing 3% CO2 (P < 0.05). Above VTh, the ventilatory response when the subjects were breathing HeO2 was greater than when breathing 3% CO2 (P < 0.01). Flow limitation, as percent of tidal volume, during maximal exercise was greater (P < 0.01) when the subjects were breathing CO2 (22 +/- 12%) than when breathing room air (12 +/- 9%) or when breathing HeO2 (10 +/- 7%) (n = 7). End-expiratory lung volume during maximal exercise was lower when the subjects were breathing HeO2 than when breathing room air or when breathing CO2 (P < 0.01). These data indicate that older subjects have little reserve for accommodating an increase in ventilatory demand and suggest that mechanical ventilatory constraints influence both the magnitude of VE during maximal exercise and the regulation of VE and respiratory mechanics during heavy-to-maximal exercise.
Editorial (1992)

No AccessJournal of Urology1 Nov 1992Editorial John T. Grayhack John T. GrayhackJohn T. Grayhack More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)36968-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Editorial." The Journal of Urology, 148(5 Part 1), p. 1564 © 1992 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 148 Issue 5 Part 1 November 1992 Page: 1564 Advertisement Copyright & Permissions© 1992 by The American Urological Association Education and Research, Inc.Metrics Author Information John T. Grayhack More articles by this author Expand All Advertisement PDF downloadLoading ...
Selecting Appropriate Dose Regimens for AM-101 in the Intratympanic Treatment of Acute Inner Ear Tinnitus (2015)

Inhibition of cochlear N-methyl-D-aspartate (NMDA) receptors with AM-101, a small molecule antagonist delivered by intratympanic injection, represents a novel approach to treat acute tinnitus triggered by glutamate excitotoxicity. An earlier double-blind, randomized, placebo-controlled phase II clinical trial (TACTT0) had demonstrated a significant and dose-dependent improvement in tinnitus triggered by acute acoustic trauma or otitis media from baseline to day 90. A second phase II trial (TACTT1) now sought to evaluate the most appropriate dose regimen for this treatment. Outcomes from the TACTT1 trial showed no significant difference in tinnitus improvement between a single-dose treatment and a dose regimen comprising three doses over 2 weeks. Taken together, three injections over 3 consecutive days showed the best results in the two phase II trials, suggesting that repeated and concentrated inhibition of cochlear NMDA receptors provides best treatment effects, while keeping the procedural impact on patients short.
Keratinocyte Apoptosis on Type I Collagen Fibrils is Prevented by Erk1/2 Activation under High Calcium Condition (2007)

Keratinocytes adhere and proliferate well on collagen-coated surfaces, but they undergo apoptosis without differentiation on collagen gels according to our past research. In the current studies, we investigated the necessary conditions for keratinocyte survival on fibrous collagen gels. We found that keratinocytes survived on collagen gels when the medium contains elevated levels (1.8 mM) of calcium. Under this high calcium condition, cells formed multicellular colonies and differentiated. Akt was not activated in cells cultured on collagen gels regardless of the calcium concentration, whereas it was activated in cells cultured on nonfibrous collagen. On the other hand, Erk1/2, key kinases of MAPK pathway, were phosphorylated in cells cultured under high calcium condition but not in cells cultured on collagen gels under low calcium condition. The necessity of Erk1/2 activation for keratinocyte survival on collagen gel was confirmed with experiment using U0126, an inhibitor for Erk1/2. These studies show that activation of Akt depends on collagen assembly, whereas activation of Erk1/2 is induced by increased extracellular calcium concentration. Thus, activation of the Erk1/2 by increasing calcium concentration in the incubation medium may compensate for the loss of Akt activation, allowing keratinocyte survival on collagen gels.
Delayed Onset of Nonthermal Melting in Single-Crystal Silicon Pumped with Hard X Rays (2018)

In this work, we monitor the onset of nonthermal melting in single-crystal silicon by implementing an x-ray pump-x-ray probe scheme. Using the ultrashort pulses provided by the Linac Coherent Light Source (SLAC) and a custom-built split-and-delay line for hard x rays, we achieve the temporal resolution needed to detect the onset of the transition. Our data show no loss of long-range order up to 150±40 fs from photoabsorption, which we interpret as the time needed for the electronic system to equilibrate at or above the critical nonthermal melting temperature. Once such equilibration is reached, the loss of long-range atomic order proceeds inertially and is completed within 315±40 fs from photoabsorption.
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (2020)

(Cell 179, 964–983.e1–e31; October 31, 2019) In the originally published version of this article, Daniel Geiszler's last name was misspelled. This error has now been corrected in the article online. Integrated Proteogenomic Characterization of Clear Cell Renal Cell CarcinomaClark et al.CellOctober 31, 2019In BriefComprehensive proteogenomic characterization in 103 treatment-naive clear cell renal cell carcinoma patient samples highlights tumor-specific alterations at the proteomic level that are unrevealed by transcriptomic profiling and proposes a revised subtyping scheme based on integrated omics analysis. Full-Text PDF Open Access