gebhart/patrepeval huggingface dataset:
Repulsive charge mechanism serve to maintain lumens and cavities. An histochemical study of rat serosa and kidney. (2001)

The free surface of the rat peritoneum was covered with a rich negative-charged substance which is distinctly stained with cationic colloidal iron (pH 1.5). Neuraminidase digestion erased this iron stain. Treatment with Limax flavus agglutinin (LFA), which has specific affinity to sialic acid, interferred with iron staining on the serosal surface. Transmission electron microscopy of the peritoneal samples stained with colloidal iron showed that colloidal particles were deposited on the free surface of the mesothelial cells. At pH 1.5, the colloidal particles aggregated in a dotted fashion; in those stained at pH 7.0, the particles arranged in fine strands (100-300 nm in length). This difference may occur as a structural transformation due to pH level changes. The string like structure seemed to correspond well to membrane associated sialomucin. The urinary surface of the rat glomerular podocytes possessed negatively charged sites detectable with cationic colloidal iron even at pH 1.5. Neuraminidase and LFA treatments erased iron staining. Substance containing sialic acid such as podocalyxin on the podocyte surface may be stained. This study shows that negatively charged sites of the substance covering the free surface of these regions repulse each other to maintain the serosal cavities or the podocyte end-feet slits.
Photonic crystal waveguiding: mode solution and analysis in an envelope picture (2003)

Summary from only given. The envelope approximation formalism yields a direct picture of the waveguiding mechanism, allowing us to predict the frequency of the guided modes, the dispersion relations of waveguides and the shapes of the modes. It yields results that are in excellent agreement with a fully-vectorial computation of the field.
Critical role of mitochondrial dysfunction and impaired mitophagy in diabetic nephropathy (2019)

Mitochondrial dynamics play a critical role in deciding the fate of a cell under normal and diseased condition. Recent surge of studies indicate their regulatory role in meeting energy demands in renal cells making them critical entities in the progression of diabetic nephropathy. Diabetes is remarkably associated with abnormal fuel metabolism, a basis for free radical generation, which if left unchecked may devastate the mitochondria structurally and functionally. Impaired mitochondrial function and their aberrant accumulation have been known to be involved in the manifestation of diabetic nephropathy, indicating perturbed balance of mitochondrial dynamics, and mitochondrial turnover. Mitochondrial dynamics emphasize the critical role of mitochondrial fission proteins such as mitochondrial fission 1, dynamin-related protein 1 and mitochondrial fission factor and fusion proteins including mitofusin-1, mitofusin-2 and optic atrophy 1. Clearance of dysfunctional mitochondria is aided by translocation of autophagy machinery to the impaired mitochondria and subsequent activation of mitophagy regulating proteins PTEN-induced putative kinase 1 and Parkin, for which mitochondrial fission is a prior event. In this review, we discuss recent progression in our understanding of the molecular mechanisms targeting reactive oxygen species mediated alterations in mitochondrial energetics, mitophagy related disorders, impaired glucose transport, tubular atrophy, and renal cell death. The molecular cross talks linking autophagy and renoprotection through an intervention of 5'-AMP-activated protein kinase, mammalian target of rapamycin, and SIRT1 factors are also highlighted here, as in-depth exploration of these pathways may help in deriving therapeutic strategies for managing diabetes provoked end-stage renal disease.
Effect of varying material anisotropy on critical current anisotropy in vicinal YBa2Cu3O7−δ thin films (2003)

The high Tc cuprate superconductors are noted for their anisotropic layered structure, certain of these materials indeed tend toward the limit of a Lawrence–Doniach superconductor. However, YBa2Cu3O7−δ has a smaller anisotropy than would be expected from its interlayer spacing. This is due to the cuprate chains in the structure. To investigate the influence of the chain oxygen on transport properties critical current versus applied field angle measurements were performed on fully oxygenated and deoxygenated YBa2Cu3O7−δ thin films and optimally oxygenated Y0.75Ca0.25Ba2Cu3O7−δ thin films. The films were grown on 10° miscut SrTiO3 substrates to enable the intrinsic vortex channeling effect to be observed. The form of the vortex channeling minimum observed in field angle dependent critical current studies on the films was seen to depend on film oxygenation. The vortex channeling effect is dependent on a angular dependent crossover to a string-pancake flux line lattice. The results obtained appear to be consistent with the prediction of [G. Blatter, M. V. Feigelman, V. B. Geshkenbein, A. I. Larkin, and V. M. Vinokur, Rev. Mod. Phys. 66, 1125 (1994)] that increased superconducting anisotropy leads to the kinked string-pancake lattice existing over a smaller angular range.
EVALUATION OF THE METABOLIC PRODUCTION OF THE ENDOPHYTIC FUNGUS Phomopsis sp. (2020)

Endophytic microorganisms have been shown to be an important source of bioactive compounds, and much has been studied about their metabolites. For example, compounds with different biological activities have been isolated from Phomopsis sp. The metabolic study of this genus may lead to a better understanding of the routes of production of metabolites of interest. The aim of this study was to map the metabolic profile of Phomopsis sp., isolated as an endophyte of Syzygium jambolanum DC, using culture filtrate. The fungus was cultivated for six weeks in potato dextrose medium under hypoxia and at room temperature. The filtrate was collected weekly, and the analyses were performed using proton nuclear magnetic resonance ( 1 H NMR) spectroscopy by applying NOESY1D with suppression of the water signal. The occurrence of reductive routes was verified: alcoholic fermentation throughout cultivation and reductive tricarboxylic acid cycle in the cytosol until the third week of cultivation were observed.
Supplementary Data from Lymphatic PD-L1 Expression Restricts Tumor-Specific CD8<sup>+</sup> T-cell Responses (2023)

Supplementary Data from Lymphatic PD-L1 Expression Restricts Tumor-Specific CD8&lt;sup&gt;+&lt;/sup&gt; T-cell Responses
An experimental comparison of conventional two-bank and novel four-bank dynamic MLC tracking (2013)

The AccuLeaf mMLC featuring four multileaf-collimator (MLC) banks has been used for the first time for an experimental comparison of conventional two-bank with novel four-bank dynamic MLC tracking of a two-dimensional sinusoidal respiratory motion. This comparison was performed for a square aperture, and for three conformal treatment apertures from clinical radiotherapy lung cancer patients. The system latency of this prototype tracking system was evaluated and found to be 1.0 s and the frequency at which MLC positions could be updated, 1 Hz, and therefore accurate MLC tracking of irregular patient motion would be difficult with the system in its current form. The MLC leaf velocity required for two-bank-MLC and four-bank-MLC tracking was evaluated for the apertures studied and a substantial decrease was found in the maximum MLC velocity required when four-banks were used for tracking rather than two. A dosimetric comparison of the two techniques was also performed and minimal difference was found between two-bank-MLC and four-bank-MLC tracking. The use of four MLC banks for dynamic MLC tracking is shown to be potentially advantageous for increasing the delivery efficiency compared with two-bank-MLC tracking where difficulties are encountered if large leaf shifts are required to track motion perpendicular to the direction of leaf travel.
Applicability of oxide superconductor to magnetic shielding (1989)

Magnetic shielding capability has been investigated on the Y-B-Cu-O oxide superconductor, aiming at a practical use of oxide superconductors. Critical-transport-current density and magnetization were measured using the four-terminal and electromagnetic methods at temperatures of 77 K and 4.2 K. The results indicated that the critical-current density by the transport measurement was two orders of magnitude lower than that by the magnetization. This means that the larger shielding currents were found to be induced in the grain. The magnetic field behind the disk-shaped specimen was measured using a magnetic sensor. The shielding capability does not depend upon the critical-current density derived from magnetization but the critical-transport-current density. The applicability of oxide superconductors to magnetic shielding is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comopact image representation using wavelet lifting along arbitrary trees (2008)

In this work, we present a method for achieving a compact image representation by applying wavelet lifting along an arbitrary combination of trees. This is done by extending a lifting transform along a single tree to a series of lifting transforms along a number of different trees, each of which exploits directionality differently. The trees are constructed in ways that force tree edges to follow the geometric flows inherent in images. In particular, we propose a method for constructing trees that trace out geometric flows using edges in the image. Our preliminary results demonstrate promising performance in terms of PSNR as a function of the percentage of retained coefficients, motivating its potential for image coding.
Optical properties and electronic structures of synthetic melanins (1995)

1Dipartimento di Scienze Biochimiche, Università di Roma ‘La Sapienza’, p.le A. Moro, 5, 00185 Rome, Italy; 2Dipartimento di Ingegneria Elettronica, Terza Università di Roma, Rome, Italy
FIT: A Flexible, Lightweight, and Real-Time Scheduling System for Wireless Sensor Platforms (2009)

We propose FIT, a flexible, lightweight, and real-time scheduling system for wireless sensor platforms. There are three salient features of FIT. First, its two-tier hierarchical framework supports customizable application-specific scheduling policies, hence, FIT is very flexible. Second, FIT is lightweight in terms of minimizing the thread number to reduce preemptions and memory consumption while at the same time ensuring system schedulability. We propose a novel Minimum Thread Scheduling Policy (MTSP) exploration algorithm within FIT to achieve this goal. Finally, FIT provides a detailed real-time schedulability analysis method to help check if application's temporal requirements can be met. We implemented FIT on MicaZ motes and carried out extensive evaluations. Results demonstrate that FIT is indeed flexible and lightweight for implementing real-time applications, at the same time, the schedulability analysis provided can predict the real-time behavior. FIT is a promising scheduling system for implementing complex real-time applications in sensor networks.
Long-Distance Movement, Virulence, and RNA Silencing Suppression Controlled by a Single Protein in Hordei- and Potyviruses: Complementary Functions between Virus Families (2002)

RNA silencing is a natural defense mechanism against genetic stress factors, including viruses. A mutant hordeivirus (Barley stripe mosaic virus [BSMV]) lacking the gammab gene was confined to inoculated leaves in Nicotiana benthamiana, but systemic infection was observed in transgenic N. benthamiana expressing the potyviral silencing suppressor protein HCpro, suggesting that the gammab protein may be a long-distance movement factor and have antisilencing activity. This was shown for gammab proteins of both BSMV and Poa semilatent virus (PSLV), a related hordeivirus. Besides the functions in RNA silencing suppression, gammab and HCpro had analogous effects on symptoms induced by the hordeiviruses. Severe BSMV-induced symptoms were correlated with high HCpro concentrations in the HCpro-transgenic plants, and substitution of the gammab cistron of BSMV with that of PSLV led to greatly increased symptom severity and an altered pattern of viral gene expression. The efficient systemic infection with the chimera was followed by the development of dark green islands (localized recovery from infection) in leaves and exemption of new developing leaves from infection. Recovery and the accumulation of short RNAs diagnostic of RNA silencing in the recovered tissues in wild-type N. benthamiana were suppressed in HCpro-transgenic plants. These results provide evidence that potyviral HCpro and hordeivirus gammab proteins contribute to systemic viral infection, symptom severity, and RNA silencing suppression. HCpro's ability to suppress the recovery of plants from viral infection emphasizes recovery as a manifestation of RNA silencing.
(Tetrafluorovinylphenyl)carbazole as a Multifunctional Material for OLED Applications (2023)

The multifunctional materials for application in organic light-emitting devices (OLEDs) based on a single structural motif are very desired but quite rare species. Such structures allow simplifying the chemical variety within OLED heterostructures and thus reducing their cost, manufacturing time, and logistic efforts. In this paper, we report the 9-(2,3,5,6-tetrafluoro-4-vinylphenyl)carbazole molecule (Cz4FS) utilized as a fluorescent emitter, host material for quantum dot based OLEDs (QLEDs), acceptor part of the exciplex active layer, and monomer that can be used for the preparation of emissive polymers and copolymers. The external quantum efficiency (EQE) of the corresponding fluorescent OLED based on a Cz4FS single emitter doped into a 1,3-bis(carbazol-9-yl)benzene matrix is 4.2%, which is close to the theoretical limit and maximum brightness at the level of 3600 cd/m2. An OLED based on exciplex emission obtained utilizing Cz4FS as an acceptor demonstrates higher efficiency (5.3%) and much higher brightness near 25 000 cd/m2. A QLED based on Cz4FS as a host for CdSeS/ZnS core–shell quantum dots demonstrates excellent energy transfer from the Cz4FS matrix that results in a clear spectrum of quantum dots with an EQE of 2.3%, maximum of 19 000 cd/m2, and narrow spectral distribution. An OLED based on a Cz4FS-based polymer and copolymer demonstrates not extraordinary efficiency but low-efficiency roll-off in a wide range of current densities.
F-1307 Reduciotn of Windage of Head Suspenison Assemblies and Arm for Hard Disk Drives (2001)

Reduction of windage, or vibration of the slider in the off track direction induced by airflow, is very important issue to increase the track density of hard disk drives (HDDs). New head suspension assembly which is designed to increase the stiffness and natural frequencies to improve the windage and to be used for ramp load/unload 10-krpm 3.5type HDD has been developed. The windage of the new suspension was measured by using laser Doppler vibrometer in the spin stand. The windage peaks were mainly located from 9 to 12 kHz, since those of the former head suspension assembly were from 6 to 9 kHz. Total windage from 1 kHz to 15kHz of the new one was reduced to 68% of the old one. The windage of the suspensions with carriage arm was also measured. Total widage of the new one was reduced to 73% of the old one. By increasing the natural frequency and decoupling from the carriage arm mode, the windage of the new suspension was improved.
Damp heat versus field reliability for crystalline silicon (2012)

This paper demonstrates a multi-stress time-to-failure analysis of selected silicon PV cells due to metallic corrosion. This work indicates that the time-to-failure is a system effect and the kinetics of the reactions are different for different cells.
Blockade of NF-κB improves cardiac function and survival after myocardial infarction (2006)

NF-kappaB is a key transcription factor that regulates inflammatory processes. In the present study, we tested the hypothesis that blockade of NF-kappaB ameliorates cardiac remodeling and failure after myocardial infarction (MI). Knockout mice with targeted disruption of the p50 subunit of NF-kappaB (KO) were used to block the activation of NF-kappaB. MI was induced by ligation of the left coronary artery in male KO and age-matched wild-type (WT) mice. NF-kappaB was activated in noninfarct as well as infarct myocardium in WT+MI mice, while the activity was completely abolished in KO mice. Blockade of NF-kappaB significantly reduced early ventricular rupture after MI and improved survival by ameliorating congestive heart failure. Echocardiographic and pressure measurements revealed that left ventricular fractional shortening and maximum rate of rise of left ventricular pressure were significantly increased and end-diastolic pressure was significantly decreased in KO+MI mice compared with WT+MI mice. Histological analysis demonstrated significant suppression of myocyte hypertrophy as well as interstitial fibrosis in the noninfarct myocardium of KO+MI mice. Blockade of NF-kappaB did not ameliorate expression of proinflammatory cytokines in infarct or noninfarct myocardium. In contrast, phosphorylation of c-Jun NH2-terminal kinase was almost completely abolished in KO+MI mice. The present study demonstrates that targeted disruption of the p50 subunit of NF-kappaB reduces ventricular rupture as well as improves cardiac function and survival after MI. Blockade of NF-kappaB might be a new therapeutic strategy to attenuate cardiac remodeling and failure after MI.
Neuromodulation for tinnitus treatment: an overview of invasive and non-invasive techniques (2018)

Tinnitus is defined as a perception of sound without any external sound source. Chronic tinnitus is a frequent condition that can affect the quality of life. So far, no causal cure for tinnitus has been documented, and most pharmacologic and psychosomatic treatment modalities aim to diminish tinnitus' impact on the quality of life. Neuromodulation, a novel therapeutic modality, which aims at alternating nerve activity through a targeted delivery of a stimulus, has emerged as a potential option in tinnitus treatment. This review provides a brief overview of the current neuromodulation techniques as tinnitus treatment options. The main intention is to provide updated knowledge especially for medical professionals counselling tinnitus patients in this emerging field of medicine. Non-invasive methods such as repetitive transcranial magnetic stimulation, transcranial electrical stimulation, neurofeedback, and transcutaneous vagus nerve stimulation were included, as well as invasive methods such as implanted vagus nerve stimulation and invasive brain stimulation. Some of these neuromodulation techniques revealed promising results; nevertheless, further research is needed, especially regarding the pathophysiological principle as to how these neuromodulation techniques work and what neuronal change they induce. Various studies suggest that individually different brain states and networks are involved in the generation and perception of tinnitus. Therefore, in the future, individually tailored neuromodulation strategies could be a promising approach in tinnitus treatment for achieving a more substantial and longer lasting improvement of complaints.
A Practical Synthesis of a PI3K Inhibitor under Noncryogenic Conditions via Functionalization of a Lithium Triarylmagnesiate Intermediate (2012)

We report a practical synthesis of PI3K inhibitor GDC-0941. The synthesis was achieved using a convergent approach starting from a thienopyrimidine intermediate through a sequence of formylation and reductive amination followed by Suzuki-Miyaura cross-coupling. Metalation of the thienopyrimidine intermediate involving the intermediacy of triarylmagnesiates allowed formylation under noncryogenic conditions to produce the corresponding aldehyde. We also investigated aminoalkylation via a benzotriazolyl-piperazine substrate as an alternative to the reductive amination route. We evaluated both palladium and nickel catalyzed processes for the borylation and Suzuki-Miyaura cross-coupling. Final deprotection and salt formation afforded the API.
The BRUCE‐ATR Signaling Axis Is Required for Accurate DNA Replication and Suppression of Liver Cancer Development (2019)

Replication fork stability during DNA replication is vital for maintenance of genomic stability and suppression of cancer development in mammals. ATR (ataxia-telangiectasia mutated [ATM] and RAD3-related) is a master regulatory kinase that activates the replication stress response to overcome replication barriers. Although many downstream effectors of ATR have been established, the upstream regulators of ATR and the effect of such regulation on liver cancer remain unclear. The ubiquitin conjugase BRUCE (BIR Repeat containing Ubiquitin-Conjugating Enzyme) is a guardian of chromosome integrity and activator of ATM signaling, which promotes DNA double-strand break repair through homologous recombination. Here we demonstrate the functions for BRUCE in ATR activation in vitro and liver tumor suppression in vivo. BRUCE is recruited to induced DNA damage sites. Depletion of BRUCE inhibited multiple ATR-dependent signaling events during replication stress, including activation of ATR itself, phosphorylation of its downstream targets CHK1 and RPA, and the mono-ubiquitination of FANCD2. Consequently, BRUCE deficiency resulted in stalled DNA replication forks and increased firing of new replication origins. The in vivo impact of BRUCE loss on liver tumorigenesis was determined using the hepatocellular carcinoma model induced by genotoxin diethylnitrosamine. Liver-specific knockout of murine Bruce impaired ATR activation and exacerbated inflammation, fibrosis and hepatocellular carcinoma, which exhibited a trabecular architecture, closely resembling human hepatocellular carcinoma (HCC). In humans, the clinical relevance of BRUCE down-regulation in liver disease was found in hepatitis, cirrhosis, and HCC specimens, and deleterious somatic mutations of the Bruce gene was found in human hepatocellular carcinoma in the Cancer Genome Atlas database. Conclusion: These findings establish a BRUCE-ATR signaling axis in accurate DNA replication and suppression of liver cancer in mice and humans and provides a clinically relevant HCC mouse model.
Replication timing of the human genome (2003)

We have developed a directly quantitative method utilizing genomic clone DNA microarrays to assess the replication timing of sequences during the S phase of the cell cycle. The genomic resolution of the replication timing measurements is limited only by the genomic clone size and density. We demonstrate the power of this approach by constructing a genome-wide map of replication timing in human lymphoblastoid cells using an array with clones spaced at 1 Mb intervals and a high-resolution replication timing map of 22q with an array utilizing overlapping sequencing tile path clones. We show a positive correlation, both genome-wide and at a high resolution, between replication timing and a range of genome parameters including GC content, gene density and transcriptional activity.
Clinical Factors That Predict Noncirrhotic Portal Hypertension in HIV-Infected Patients: A Proposed Diagnostic Algorithm (2013)

Noncirrhotic portal hypertension (NCPH) is a rare but important clinical entity in human immunodeficiency virus (HIV) populations. The purpose of this study was to describe the clinical factors associated with the condition in an effort to formulate a diagnostic algorithm for easy and early diagnosis. We performed a multicenter, retrospective case-control study of 34 patients with NCPH and 68 control HIV patients. The study found that thrombocytopenia, splenomegaly, didanosine use, elevated aminotransferases, and an elevated alkaline phosphatase level were all significantly more prevalent in the NCPH cohort. Using these easily available clinical parameters, we developed an algorithm for early diagnosis of NCPH in HIV.