gebhart/patrepeval huggingface dataset:
BKV Clearance Time Correlates With Exhaustion State and T-Cell Receptor Repertoire Shape of BKV-Specific T-Cells in Renal Transplant Patients (2019)

Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated a clear association between the resolution of BKV reactivation and reconstitution of BKV-specific CD4<sup>+</sup> T-cells. However, which factors determine the duration of viral infection clearance remains so far unclear. Here we apply a combination of in-depth multi-parametric flow cytometry and NGS-based CDR3 beta chain receptor repertoire analysis of BKV-specific T-cells to a cohort of 7 kidney transplant patients during the clinical course of BKV reactivation. This way we followed TCR repertoires at single clone levels and functional activity of BKV-specific T-cells during the resolution of BKV infection. The duration of BKV clearance did not depend on the number of peripheral blood BKV-specific T-cells nor on a few immunodominant BKV-specific T-cell clones. Rather, the T-cell receptor repertoire diversity and exhaustion status of BKV-specific T-cells affected the duration of viral clearance: high clonotype diversity and lack of PD1 and TIM3 exhaustion markers on BKV-specific T-cells was associated with short clearance time. Our data thus demonstrate how the diversity and the exhaustion state of the T-cells can determine the clinical course of BKV infection.
Edge-to-Face CH/"" Interaction between Ligand Phe-Phenyl and Receptor Aromatic Group in the Thrombin Receptor Activation (2000)

In the ligand/receptor interaction, the side chain phenyl group of phenylalanine (Phe) is involved in a so-called hydrophobic interaction, in which the Phe-phenyl group functions as a p element or merely as a hydrophobic element. The thrombin receptor-tethered ligand SFLLRNP consists of the Phe-2 residue essential for receptor activation. In order to explore the molecular characteristics of this Phe-2-phenyl group, a complete set of S/Phe/LLRNP peptides comprising six different difluorophenylalanine isomers [(F(2))Phe] was newly synthesized and assayed to evaluate their ability to induce the aggregation of human platelets. The assay results clarified several important structural elements to conclude that Phe-2-phenyl of S/Phe/LLRNP is in the edge-to-face CH/pi interaction with the receptor aromatic group, utilizing the Phe-phenyl edge along with adjacent benzene hydrogens at positions (2-3) or (5-6). It was also found that the fluorine atom at position 4 increases the acidity of the hydrogen mainly at its ortho position, resulting in a reinforcement of the CH/pi interaction and thus in an enhancement of biological activity. The H-->F replacement in the benzene ring was found to provide an effective structural examination to the Phe residue; i.e., to identify the hydrogens in the CH/pi interaction, and to strengthen the CH/pi interaction.
A protocol extension to HiperLAN/2 to support single-relay networks (2002)

The use of ad-hoc-based multi-hop relaying has been advocated as a means to increase the capacity and energy-efficiency of wireless networks. It is one of the goals of the IBMS project to investigate the potential of such ad-hoc relaying, using HiperLAN/2 as a case study. To realize relaying in a HiperLAN/2 network, the HiperLAN/2 protocol needs to be extended. This paper describes a standard-conform extension to HiperLAN/2 that enables terminals to relay data traffic within a single HiperLAN/2 cell. This extension is flexible, imposes little overhead, and work on the time scale of a single HiperLAN/2 MAC frame. Keywords: Wireless LAN, multi-hop wireless relaying, HiperLAN/2 1
Genetic and Epigenetic Alterations of the NF2 Gene in Sporadic Vestibular Schwannomas (2012)

The molecular genetic changes in sporadic VS identified here included mutations and allelic loss, but no aberrant hypermethylation of the NF2 gene was detected. In addition, no clear genotype/phenotype correlation was identified. Therefore, it is likely that other factors contribute to tumor formation and growth.
Anomalous non-ergodic scaling in adiabatic multicritical quantum quenches (2009)

We investigate non-equilibrium dynamical scaling in adiabatic quench processes across quantum multicritical points. Our analysis shows that the resulting power-law scaling depends sensitively on the control path, and that anomalous critical exponents may emerge depending on the universality class. We argue that the observed anomalous behavior originates in the fact that the dynamical excitation process takes place asymmetrically with respect to the static multicritical point, and that non-critical energy modes may play a dominant role. As a consequence, dynamical scaling requires introducing new non-static exponents.
Selective repartition of in situ generated silica produced during the evolution of an epoxide network from a homogeneous precursors mixture and effects on properties (2004)

Abstract Phase separation of organic networks derived from mixtures of reactive monomers and/or oligomers can take place through the formation of IPNs or precipitation of particles. The latter systems are widely used as a means of increasing the fracture toughness of thermosetting resins, and particularly for products obtained from mixtures of epoxy resins and functionalized aliphatic oligomers. In the present work several mixtures comprised of difunctional epoxy resins, silane functionalized perfluoroether oligomers, prehydrolyzed tetraethoxysilane, and an aromatic amine hardener were examined in a variety of compositions and preparative procedures. The aims were to control the kinetics of phase separation and the repartition of the different components in the two phases, so that the silica domains could be preferentially located within the precipitated soft particles. It was found that the silane functionalization of the perfluoroether oligomer provided an effective mechanism for the localization of the siloxane networks within the precipitated particles. However, phase separation by the precipitation of particles would only take place for systems in which the perfluoroether oligomer could be reacted with an excess of epoxy resin prior to adding the alkoxysilane solution and the hardener. Moreover, it was difficult to achieve the total localization of the siloxane component into the perfluoroether network. The siloxane species remaining dissolved in the resin gave rise to severe embrittlement of the products through reactions with the epoxy chains. Using mixtures of suitably functionalized perfluoroether oligomers it was possible to produce the conditions by which the localization of the silica domains into the precipitated particles could be maximized. This has resulted also in the formation of graded interphase regions and to a global improvement in mechanical properties, manifested as a concomitant increase in modulus, strength, and toughness. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 94: 1279–1290, 2004
A Stereoselective Hydroamination Transform To Access Polysubstituted Indolizidines (2012)

Stereoselective, intramolecular, formal hydroamination of dienamines via directed hydroboration is reported. Four stereocenters are set in the process. Natural and unnatural indolizidine alkaloids can be synthesized from simple unsaturated amines using the title process.
Characterization and quantitation of the epidermal growth factor receptor in invasive and superficial bladder tumors. (1989)

Epidermal growth factor receptors (EGFr) have been measured on primary human bladder tumor membranes by 125I-EGF ligand binding. High affinity receptors were detected on both superficial (Kd 0.2-1.45 nM; mean, 0.86 nM; median, 0.88 nM) and invasive tumors (Kd 0.19-2.38 nM; mean, 0.9 nM, median, 0.79 nM). There was one class of binding sites and EGFr concentration was quantified by competitive binding and Scatchard analysis. The EGFr was further characterized and shown to be cleaved at the major autophosphorylation site by a calcium-activated mechanism. Thus the EGFr from primary bladder tumors exhibits similar biochemical characteristics to those in established cell lines. Tumors classified as invasive on the basis of muscle invasion had higher EGFr levels [EGF binding, 99 +/- 252 (SD) fmol/mg protein; median, 21; n = 24] than superficial tumors (12 +/- 12 fmol/mg protein; median, 11; n = 23) or normal bladder mucosa (9 +/- 12 fmol/mg protein; median, 6; n = 6) (P = 0.05). When the two largest subgroups of superficial and invasive tumors were compared (15 pTa, 16 T3), the invasive tumors had significantly higher EGFr levels (P less than 0.05). EGFr may therefore be involved in mechanisms of tumor progression. EGFr may be a target for selective therapy with EGF-linked drugs in a subset of invasive bladder cancers.
Primary study of the mathematization of traditional Chinese medicine (2015)

The article aims to expound the necessity, historical inevitability and research status of the mathematization of traditional Chinese medicine. It is necessary to introduce the modern mathematics tool to the researches of traditional Chinese medicine. The present studies are scattered and have no unified standard, which is not good for the overall development of the mathematization of traditional Chinese medicine. It is suggested here to establish uniform standard.
ENCRUSTED CYSTITIS AND PYELITIS (1998)

Early clinical and bacterial diagnosis of encrusted cystitis and pyelitis could improve the prognosis of these infectious diseases.
ChemInform Abstract: Enantiomerically Pure 7‐Oxabicyclo(2.2.1)hept‐5‐en‐2‐yl Derivatives (“ Naked Sugars”) as Synthetic Intermediates. Part 20. Total Asymmetric Syntheses of D‐Lividosamine and 2‐Acetamido‐2,3‐dideoxy‐D‐arabino‐ Hexose Derivatives. (1993)

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.
The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (2020)

Summary Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotency. To investigate the dynamics of this process under spatial confinement, we used either polydimethylsiloxane (PDMS) pillars or micro-contact printing of vitronectin. There was a progressive upregulation of OCT4, E-cadherin, and NANOG within 70 µm from the outer rim of iPSC colonies. Single- cell RNA-sequencing demonstrated that OCT4 high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interactions were found to be relevant for the self-organization. Interestingly, after 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.
Modeling and optimization of high-frequency ultrasound transducers (1994)

Obtaining an accurate transducer model for a high-frequency transducer can be troublesome using traditional models, such as the KLM model, since it is often difficult to measure precisely the piezoelectric, dielectric, and mechanical properties of the transducer. This paper describes an alternative method of modeling transducers using network theory. The network theory model for a transducer is determined from a measurement of the transducer impedance in water and the pulse-echo response of the system for a given electrical source and load. A discussion of how this model can be used to optimize the design of an electrical matching circuit is given. This method is illustrated by designing a two-element transmission line matching circuit for a miniature 53 MHz transducer. Excellent agreement between the network model prediction and the experimental response is obtained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The role of the headgear timer in extraoral co-operation (2004)

The aim of this research was to study headgear co-operation using an objective measuring instrument, the Compliance Science System (CSS). Forty-six patients were included in the investigation, 32 girls and 14 boys (10-15 years of age; mean 13 years). The patients, who were not informed that they were being monitored, were instructed to wear the headgear, with an electronic module timer attached to the neckstrap, for 16 hours per day. At the end of 2 months (T1), the time for which the headgear was worn was measured. At this stage the patients were divided into two groups: group 1 (unco-operative patients) who wore the headgear for less than 16 hours per day, and group 2 (co-operative patients) who wore the headgear for at least 16 hours per day. Only the unco-operative patients were informed that they had been monitored, and a subsequent 4 month treatment period was initiated for both groups. The time was also measured at the end of the second (T2) and third (T3) 2 month treatment periods. The unco-operative patients increased their use of the headgear to approximately 4.5 to 6 hours per day (P < 0.05). All of the co-operative patients also used their headgear as recommended during the 4 month period.
A Complete System for High-Speed Navigation of Prescribed Routes (2006)

This paper presents an approach that achieves robust high-speed navigation of prescribed routes. We present the mechatronic and software considerations that resulted in two robots that have completed over 4000 km of autonomous navigation of trails and off-road terrain at an average speed of approximately 30 km/h, with sustained top speeds of 55 km/h
Thyroid hormone and dietary carbohydrate induce different hepatic zonation of both "spot 14" and acetyl-coenzyme-A carboxylase: a novel mechanism of coregulation. (1993)

The S14 gene encodes a protein found in the nuclei of lipogenic tissues that is induced synergistically by thyroid hormone (T3) and dietary carbohydrate, as are several lipogenic enzymes. In hyperthyroid rats, hepatic expression of S14 protein is zonated. The established association of S14 gene expression with lipogenesis, therefore, prompted a comparison of the zonal distribution of induction of S14 and acetyl-coenzyme-A-carboxylase (ACC), a rate-determining enzyme of fatty acid synthesis, by T3, dietary carbohydrate, and both stimuli together. As determined by immunohistochemistry, liver from chow-fed hypothyroid or euthyroid fasted rats showed essentially no reactivity for either S14 or ACC. Sections from hyperthyroid rats exhibited nuclear staining with anti-S14 antibodies and cytoplasmic reactivity for ACC that was primarily perivenous in both cases. In contrast, sections from euthyroid-fasted animals refed a high carbohydrate, fat-free diet for 3 days exhibited panlobular expression of both antigens. Animals receiving both T3 and high carbohydrate diet refeeding showed increased intensity of staining, compared to the refed group, for both S14 and ACC across the entire lobule. Therefore, in rats consuming normal chow, T3 induced S14 and ACC only in the perivenous zone of the acinus, whereas it further induced these proteins across the entire lobule in the presence of increased carbohydrate intake. Modulation, by the carbohydrate content of the diet, of the fraction of the liver that may express S14 and ACC in response to T3 provides a mechanism for coregulation of the genes involved in hepatic lipid formation. Moreover, the observed cozonation of S14 and ACC as well as the quantitatively similar effects of T3 and dietary carbohydrate on S14, ACC, fatty acid synthetase, and ATP-citrate lyase protein abundance prompt the speculation that S14 acts in the nucleus to promote expression of the genes involved in the lipogenic pathway.
Association of Initial Disease-Modifying Therapy With Later Conversion to Secondary Progressive Multiple Sclerosis (2019)

Among patients with relapsing-remitting MS, initial treatment with fingolimod, alemtuzumab, or natalizumab was associated with a lower risk of conversion to secondary progressive MS vs initial treatment with glatiramer acetate or interferon beta. These findings, considered along with these therapies' risks, may help inform decisions about DMT selection.
Comparison of Cerebral Volume in Children Aged 18-22 and 36-47 Months Born Preterm and Term (2011)

Studies investigating differences in regional brain volumes in children born preterm and term during early childhood are limited. Neuroimaging could help understand patterns of deficit in children born preterm and target areas of development associated with these regions. The goal of this study was to identify differences in regional brain volume at 2 different ages using magnetic resonance imaging in preterm and term children. Magnetic resonance imaging and developmental testing occurred in children 18 to 22 months old (16 preterm and 10 term children) and 36 to 47 month old (12 preterm and 10 term children). There were significant differences between the 4 groups in the parietal region, cerebral white matter, third ventricle, and lateral ventricle. Correlations between regional cerebral volume and developmental testing were explored for the third and lateral ventricles. Our findings indicate that in young children differences in regional cerebral volume are due to both maturation and prematurity.
Smooth muscle relaxation and local hydraulic impedance properties of the aorta (2001)

Smooth muscle relaxation is expected to yield beneficial effects on hydraulic impedance properties of large vessels. We investigated the effects of intravenous diltiazem infusion on aortic wall stiffness and local hydraulic impedance properties. In seven anesthetized, closed-chest dogs, instantaneous cross-sectional area and pressure of the descending thoracic aorta were measured using transesophageal echocardiography combined with acoustic quantification and a micromanometer, respectively. Data were acquired during a vena caval balloon inflation, both at the control condition and with diltiazem infusion. At the operating point, diltiazem reduced blood pressure in all dogs but did not alter aortic dimensions or wall stiffness. Over the observed pressure range, aortic area-pressure relationships were linear. Whereas diltiazem affected the slope of this relationship variably (no change in 3 dogs, increase in 1 dog, decrease in 3 dogs), the zero-pressure area intercept was significantly increased in every case such that higher area was observed at any given pressure. When comparisons were made at a common level of wall stress, wall stiffness was either increased or unchanged during diltiazem infusion. In contrast, diltiazem decreased wall stiffness in every case when comparisons were made at a common level of aortic midwall radius. Aortic characteristic impedance and pulse wave velocity, components of left ventricular hydraulic load that are determined by aortic elastic and geometric properties, were affected variably. A comparison of wall stiffness at matched wall stress appears inappropriate for assessing changes in smooth muscle tone. Because of the competing effects of changes in vessel diameter and wall stiffness, smooth muscle relaxation is not necessarily accompanied by the expected beneficial changes in local aortic hydraulic impedance. These results can be reconciled by recognizing that components other than vascular smooth muscle (e.g., elastin, collagen) contribute to aortic wall stiffness.
Mycobacterium xenopi IS1395, a novel insertion sequence expanding the IS256 family (1996)

An insertion sequence (IS) of Mycobacterium xenopi has been isolated and sequenced. This 1323 bp element, designated IS1395, is present in up to 18 copies in the M. xenopi genome and may be harboured in an M. xenopi extrachromosomal element. It encodes a putative transposase of 415 amino acids which displays sequence homology to the Staphylococcus aureus IS256 family. Members of this class of elements have been described in the genus Mycobacterium-for example IS1081 is present in the M. tuberculosis complex, IS1245-IS1311 in M. avium, and IS6120 in M. smegmatis; these elements exhibit an 89%, 45% and 16% amino acid identity with IS1395, respectively. Investigation of the host range of IS1395 by Southern blot analysis revealed additional IS1395-related repeated sequences in M. gordonae and M. celatum. Moreover, IS1395 represents a useful epidemiological tool for M. xenopi strain typing as it provides a diversity of restriction fragment length polymorphism patterns.
Detection of Protein-DNA Interactions at β-Globin Gene Cluster in Intact Human Cells Utilizing Hedamycin as DNA-Damaging Agent (1998)

The DNA sequence specificity of hedamycin (HDM) damage was investigated in the single-copy human beta-globin gene cluster in an erythroid cell line, a nonerythroid cell line, and purified genomic DNA. The target DNA sequences for this study were the beta-globin gene locus control region (LCR) hypersensitive site 2 (HS-2) and the beta-globin gene promoter. The DNA fragments produced by HDM damage in these target sequences were selectively amplified by the ligation-mediated polymerase chain reaction (LMPCR) and analyzed at nucleotide resolution by DNA-sequencing gel electrophoresis. The DNA sequences damaged by HDM in the cellular environment were found to be similar to that observed in the purified genomic DNA. However, substantial differences did occur between the intensity of cellular and purified genomic DNA reaction products at discrete regions corresponding to transcription factor-binding motifs. This was most apparent in the LCR HS-2 at the tandem NF-E2/AP-1 motif, where the DNA damage activity of HDM was severely impaired. This motif has been shown to bind to the erythroid-specific nuclear factor-erythroid 2 (NF-E2) and the widely distributed activator protein-1 (AP-1). The HDM damage protection patterns or "genomic footprints" observed at this motif were probably caused by protein-DNA interactions with one or both of these transcription factors. This result indicates that the DNA damaging activity of HDM in cells is sensitive to bound nuclear factors. Because HDM can enter intact cells, where its DNA damaging activity is modulated by protein-DNA interactions, it may have application in genomic footprinting experiments.