gebhart/patrepeval huggingface dataset:
Developmental and age‐related changes of peptidylarginine deiminase 2 in the mouse brain (2009)

Peptidylarginine deiminases (PADs) are a group of posttranslational modification enzymes that citrullinate (deiminate) protein arginine residues in a Ca(2+)-dependent manner. Enzymatic citrullination abolishes positive charges of native protein molecules, inevitably causing significant alterations in their structure and functions. Among the five isoforms of PADs, PAD2 and PAD4 are proved occupants of the central nervous system (CNS), and especially PAD2 is a main PAD enzyme expressed in the CNS. We previously reported that abnormal protein citrullination by PAD2 has been closely associated with the pathogenesis of neurodegenerative disorders such as Alzheimer's disease and prion disease. Protein citrullination in these patients is thought to play a role during the initiation and/or progression of disease. However, the contribution of changes in PAD2 levels, and consequent citrullination, during developmental and aging processes remained unclear. Therefore, we used quantitative real-time RT-PCR, Western blot analysis, and immunohistochemical methods to measure PAD2 expression and localization in the brain during those processes. PAD2 mRNA expression was detected in the brains of mice as early as embryonic day 15, and its expression in cerebral cortex, hippocampus, and cerebellum increased significantly as the animals aged from 3 to 30 months old. No citrullinated proteins were detected during that period. Moreover, we found here, for the first time, that PAD2 localized specifically in the neuronal cells of the cerebral cortex and Purkinje cells of the cerebellum. These findings indicate that, despite PAD2's normally inactive status, it becomes active and citrullinates cellular proteins, but only when the intracellular Ca(2+) balance is upset during neurodegenerative changes.
CCDs for the rotational velocity spectrometer on GAIA (2004)

The ESA cornerstone mission GAIA will perform astrometric, photometric and spectroscopic measurements and is due for launch in 2010 into L2 orbit. The astrometric telescope system will catalogue the position of over 10<sup>9</sup> objects down to 20<sup>th</sup> magnitude and perform broadband photometry. The spectroscopic telescope will provide narrow-band photometry and feed a Radial Velocity Spectrometer which will accurately determine the radial velocities of objects down to 17-18 magnitude. This paper discusses the characteristics of the detectors envisaged for the focal plane of the RVS instrument.
Phytochemicals as Dynamic Surface Ligands To Control Nanoparticle–Protein Interactions (2018)

The rapid formation of the protein corona on to the nanoparticle (NP) surface is the key that confers biological identity to NPs and subsequently dictates their fate both in vitro and in vivo. Despite significant efforts, the inability to control the spontaneous interaction of serum proteins with the administered NPs remains a major constraint in clinical translation of nanomedicines. The ligands present on the NP surface offer promise in controlling their biological interactions; however, their influence on the NP-protein interaction is not well-understood. The current study investigates the potential of phytochemical-capped silver nanoparticles (AgNPs) toward allowing a control over NP interactions with the human serum albumin (HSA), the most abundant protein in the biological fluids. Specifically, we demonstrate the ability of curcumin (Cur) and epigallocatechin-3-gallate (EGCG) to independently act as reducing agents to produce phytochemical-capped AgNPs that show biologically desirable interactions with HSA. The key finding of our study is that the phytochemical-capped AgNPs initially interact with HSA more strongly compared to the citrate-stabilized AgNPs; however, the resultant NP-HSA complexes are less stable in the case of the former, which causes a lesser degree of changes in the protein conformation during interactions. Further, the choice of the phytochemical allows control over NP-HSA interactions, such that Cur- and EGCG-capped AgNPs interacted with HSA in a static versus dynamic manner, respectively. The diversity of the functional groups present in natural phytochemicals and their potential as in situ capping ligands during synthesis offer new opportunities in controlling the interactions of NPs with complex biological fluids, with implications in nanodiagnostics and nanomedicine.
Imbalances in T Cell Subpopulations in Multiple Sclerosis Patients (1978)

Abnormal proportions of a distinct T cell subpopulation able to bind IgG immune complexes (T.G cells) were found in peripheral blood samples from patients with MS. About 50% of the patients examined had an overabundance of T.G cells. The possible role of these cells in the pathogenesis of MS is considered.
Denaturing Gradient Gel Electrophoresis for Detection of Bacterial Population and Diversity in Amniotic Fluids and Neonatal Gastric Fluids (2013)

Purpose: Intra-amniotic infection (IAI) is often polymicrobial, and the 16S rDNA PCR assay has a major limitation that its interpretation is difficult in the presence of multiple 16S rDNAs. Denaturing gradient gel electrophoresis (DGGE) can overcome this limitation by separating PCR products based on sequence. We performed the DGGE analysis to investigate bacterial preva-lence and diversity in amniotic fluids from pregnant women with preterm births and gastric fluids from their newborns.
Polypeptide Modulators of Caspase Recruitment Domain (CARD)-CARD-mediated Protein-Protein Interactions (2011)

The caspase recruitment domain (CARD) is present in a large number of proteins. Initially, the CARD was recognized as part of the caspase activation machinery. CARD-CARD interactions play a role in apoptosis and are responsible for the Apaf-1-mediated activation of procaspase-9 in the apoptosome. CARD-containing proteins mediate the inflammasome-dependent activation of proinflammatory caspase-1. More recently, new roles for CARD-containing proteins have been reported in signaling pathways associated with immune responses. The functional role of CARD-containing proteins and CARDs in coordinating apoptosis and inflammatory and immune responses is not completely understood. We have explored the putative cross-talk between apoptosis and inflammation by analyzing the modulatory activity on both the Apaf-1/procaspase-9 interaction and the inflammasome-mediated procaspase-1 activation of CARD-derived polypeptides. To this end, we analyzed the activity of individual recombinant CARDs, rationally designed CARD-derived peptides, and peptides derived from phage display.
The ER function BiP is a master regulator of ER function. (2004)

The endoplasmic reticulum (ER) is a command center of the cell that is second only to the nucleus in terms of the breadth of its influence on other organelles and activities. It is a major site of protein synthesis, contains the cellular calcium stores that are an essential component of many signaling pathways, and is the proximal site of a signal transduction cascade that responds to cellular stress conditions and serves to maintain homeostasis of the cell. All eucaryotic cells possess an ER, which can comprise nearly 50% of the membranes of a cell. Its functions can be divided into those that occur on the cytosolic side of the membrane (where protein translation and signal transduction cascades occur) and the luminal space (where most other ER functions take place). Our studies during the past several years have revealed that the ER molecular chaperone BiP is a master regulator of ER function. It is responsible for maintaining the permeability barrier of the ER during protein translocation, directing protein folding and assembly, targeting misfolded proteins for retrograde translocation so they can be degraded by the proteasome, contributing to ER calcium stores, and sensing conditions of stress in this organelle, to activate the mammalian unfolded protein response.
Using an active temporal compensating system to achieve the super-Gaussian pulses in high-power lasers (2015)

In high-power solid-state laser, initiative pulse shaping can help improve the output laser’s performance. The evaluation for output laser pulse is also incomplete. In this paper, we propose a method of initiative pulse shaping by using arbitrary waveform generator (AWG), and establish a relatively complete evaluation system for the output pulses shape simultaneously. It achieves the super-Gaussian pulse output with high SNR (signal-to-noise ratio). As a consequence, a square laser pulse with pulse adjustable width ~5ns, rising time 197ps is obtained. The power imbalance of the output square pulse is 3.72%. The similarity between the eight-order super-Gaussian pulse and the one we get from experiment reached 99%.
Dynamic Sampling Meets Pooling (2019)

A team of six assessors used Dynamic Sampling (Cormack and Grossman 2018) and one hour of assessment effort per topic to form, without pooling, a test collection for the TREC 2018 Common Core Track. Later, official relevance assessments were rendered by NIST for documents selected by depth-10 pooling augmented by move-to-front (MTF) pooling (Cormack et al. 1998), as well as the documents selected by our Dynamic Sampling effort. MAP estimates rendered from dynamically sampled assessments using the xinfAP statistical evaluator are comparable to those rendered from the complete set of official assessments using the standard trec_eval tool. MAP estimates rendered using only documents selected by pooling, on the other hand, differ substantially. The results suggest that the use of Dynamic Sampling without pooling can, for an order of magnitude less assessment effort, yield information-retrieval effectiveness estimates that exhibit lower bias, lower error, and comparable ability to rank system effectiveness.
Digital 3D Brain MRI Arterial Territories Atlas (2021)

ABSTRACT The locus and extent of brain damage in the event of vascular insult can be quantitatively established quickly and easily with vascular atlases. Although highly anticipated by clinicians and clinical researchers, no digital MRI arterial atlas is readily available for automated data analyses. We created a digital arterial territory atlas based on lesion distributions in 1,298 patients with acute stroke. The lesions were manually traced in the diffusion-weighted MRIs, binary stroke masks were mapped to a common space, probability maps of lesions were generated and the boundaries for each arterial territory was defined based on the ratio between probabilistic maps. The atlas contains the definition of four major supra- and infra-tentorial arterial territories: Anterior, Middle, Posterior Cerebral Arteries and Vertebro-Basilar, and sub-territories (thalamoperforating, lenticulostriate, basilar and cerebellar arterial territories), in two hierarchical levels. This study provides the first publicly-available, digital, 3D deformable atlas of arterial brain territories, which may serve as a valuable resource for large-scale, reproducible processing and analysis of brain MRIs of patients with stroke and other conditions.
The viscosities of unbleached alkaline pulps. IV. The effect of alkali (1985)

Abstract An equation has been developed to relate the viscosity of unbleached pulp to the residual alkali in the spent liquor, and the time-temperature profile of the cook (expressed as the G-factor). The equation is applicable to kraft, kraft-AQ and soda-AQ pulping and to a variety of wood species.
Cavity solitons in a medium-size VCSEL (2014)

We consider a broad area vertical-cavity surface-emitting laser(VCSEL) subject to optical injection. We experimentally investigate the spontaneous formation of a Cavity Soliton (CS) in a medium size (80m diameter) VCSEL. CSs are generated and erased when sweeping optical injection power and a proper frequency detuning between the master laser and the VCSEL is set.
<title>Intralevel Hybrid Resist Process With Submicron Capability</title> (1982)

A hybrid lithographic process, utilizing both e-beam and conventional optical exposure techniques within the same device level, has been developed using a commercially available positive photoresist. Following E-beam exposure of the &lt; 3.0 micron geometries and optical exposure of the larger sized patterns, both sets of images are developed in a single development. Using this process, working CMOS devices have been fabricated with polysilicon gate lengths of 0.75 and 0.50 micron. The effect of E-beam dosage upon the submicron gate critical dimensions has been determined as well as other processing characteristics.
Anti-Mycobacterial Peroxides: A New Class of Agents for Development Against Tuberculosis (2019)

The incorporation of a pyrimidinyl residue adjacent to the peroxidic function in an organic peroxide results in anti-tubercular activity in an otherwise inactive peroxidic compound. This will be a useful approach for creating oxidative drugs to target tuberculosis.
Recent Advancement in Charge and Photo-Assisted Non-Contact Electrical Characterization of SiC, GaN, and AlGaN/GaN HEMT (2017)

The charge-based corona-Kelvin noncontact metrology, originally developed for Si IC fabrication, has recently been extended to wide energy gap semiconductors. We discuss principles of this extension and key applications, namely: high precision dopant measurement on SiC and GaN; two-dimensional electron gas characterization in AlGaN/GaN HEMT structures; interface and dielectric characterization on epi-layers with SiO2, SiN and Al2O3; comprehensive interfacial instability characterization of oxidized SiC; and whole wafer mapping of defects with a charge-assisted surface voltage technique. This powerful set of measurements is performed without fabrication of any test structures or electrical contact. Corresponding commercial tools are currently being introduced. Based on the historical example of silicon IC, we believe that this approach shall offer enhanced testing for research and for manufacturing process control with reduced cost and fast data feedback benefiting the wide-bandgap device technology.
L'inégalité des revenus primaires en France de 1962 à 1979 (1988)

Sollogoub Michel. L'inégalité des revenus primaires en France de 1962 à 1979. In: Revue économique, volume 39, n°3, 1988. pp. 545-572.
Synthesis and alkylation of 3,4‐dihydro‐1H‐1,3‐4‐benzotriazepine‐2,5‐diones and related systems (1996)

Abstract A synthesis of the 1,3,4‐benzotriazepine‐2,5‐dione 2a and its 2‐thio analog 11 is described. The key step was the mild and efficient cyclization of the o ‐(aminobenzoyl)hydrazine 10 , obtained from the reaction of a protected hydrazine derivative with the o ‐nitrobenzoyl chloride 3 . Alkylation of 2a takes place exclusively at N ‐3 while alkylation of 11 takes place on sulfur. Cyclization of the o ‐(aminobenzoyl)hydrazine 14 gave the 2,4(1 H ,3 H )‐quinazolinedione 15 as the sole product.
Afferent influences on brain stem auditory nuclei of the chicken: presynaptic action potentials regulate protein synthesis in nucleus magnocellularis neurons (1988)

Studies of the avian auditory system indicate that neurons in nucleus magnocellularis (NM) and nucleus laminaris of young animals are dramatically altered by changes in the auditory receptor. We examined the role of presynaptic activity on these transneuronal regulatory events. TTX was used to block action potentials in the auditory nerve. TTX injections into the perilymph reliably blocked all neuronal activity in the cochlear nerve and NM. Far-field recordings of sound-evoked potentials revealed that responses returned within 6-12 hr after a single TTX injection. Changes in protein synthesis by NM neurons were measured by determining the incorporation of 3H-leucine using autoradiography. NM neurons on the side of the brain ipsilateral to the TTX injection were compared to normally active cells on the other side of the same tissue section. Grain counts over individual neurons revealed that a single injection of TTX produced a 40% decrease in grain density in ipsilateral NM neurons within 1.5 hr after the TTX injection. However, by 24 hr after a single TTX injection, grain densities were not different on the 2 sides of the brain. Continuous activity blockade for 6 hr caused the cessation of amino acid incorporation in a portion of NM neurons and a 15-20% decrease in the remaining neurons. These changes in amino acid incorporation are comparable to those following complete removal of the cochlea (Steward and Rubel, 1985). We also examined NM for neuron loss and soma shrinkage after blocking eighth nerve action potentials. TTX injected every 12 hr for 48 hr caused a 20% neuron loss and an 8% shrinkage of the remaining neurons. Similar reductions were found following cochlea removal (Born and Rubel, 1985). It is concluded that neuronal activity plays a major role in the maintenance of normal NM neurons. Furthermore, these results suggest that transneuronal morphological changes seen in neurons following deafferentation or alterations of sensory experience are a result of changes in the level of presynaptic activity.
Prognostic significance of pre-operative body composition in early stage NSCLC patients. (2020)

Body composition of NSCLC patients remains poorly characterized in regard to NSCLC clinical characteristics. This study analysed muscle and adipose tissue compartments in respect to outcome in a large cohort of early stage NSCLC patients treated surgically within the prospective TRACERx trial. <b>Methods:</b> Preoperative weight and height were used to compute BMI in 375 patients with stage I-III NSCLC (8th TNM). Computed tomography (CT) scans at the 3rd lumbar vertebra were used to estimate skeletal muscle tissue compartment and provide muscle index (MI), i.e. area of the muscle (cm2)/height (m2). Associations with RNA-seq data were performed. <b>Results:</b> According to pre-operative BMI measures, 38% and 23% of patients were overweight or obese, respectively. There were no differences in BMI in regard to NSCLC histology, stage or gender (p&gt;0.05). There were 44% of patients with sarcopenia, i.e. MI &lt; 38.5 for women and &lt; 52 for men. Gender-specific MI values indicative of sarcopenia were not associated with recurrence-free survival (RFS) (p=0.53) or overall survival (p=0.48). MI moderately correlated BMI, r=0.52 (p&lt;0.001). In multivariate Cox model for RFS including BMI, statin use, pack-years, age, gender, histology and stage, increasing BMI values significantly correlated with longer RFS (HR=0.93, 95%CI: 0.87-0.96, p=0.009). Patients with the lowest quartile of BMI had shortest lung-cancer specific survival, with median of 40 mo. vs. not reached for other quartiles (log-rank, p=0.002). Associations with RNA-seq data from primary tumours revealed enrichment for genes involved in lipid metabolism and immune functions. <b>Conclusion:</b> Sarcopenia does not influence the survival of early stage NSCLC patients. Increasing BMI is associated with less aggressive course of early stage NSCLC.
An Efficient Procedure for Synthesis of Phosphopeptides through the Benzyl Phosphate-Protection by the Boc Mode Solid-Phase Method (1993)

Abstract The benzyl phosphate-protection for phosphoamino acid is very useful for Boc mode solid-phase synthesis of phosphopeptides. A phosphothreonine-containing peptide related to the EGF receptor protein was synthesized by use of this methodology.
Percutaneous ethanol injection therapy for hepatocellular carcinoma. A histopathologic study (1991)

Histopathologic examination was done on 18 cases after percutaneous ethanol injection therapy (PEIT) for hepatocellular carcinoma. In eight cases, the lesion was treated by PEIT alone; in the other ten cases, PEIT was combined with transcatheter arterial embolization. The lesion was completely necrotic in 13 cases, 90% necrotic in four cases, and 70% necrotic in the rest. In addition, PEIT seemed to be effective against intercapsular, extracapsular, and vascular invasions. In the four cases of incomplete necrosis, the viable cancer tissue remained in small tumor nodules around the main tumor, in portions isolated by septa, or along the edge of the lesion. Therefore, ethanol should be injected not only into the center of the lesion, but also into sites close to its edge. Ethanol did not damage noncancerous liver parenchyma distant from injected sites. Local dissemination of the cancer cells was not found in any case. Therefore, PEIT seems to be a valuable therapy and may be an alternative to surgery in some cases.
Effects of hydroxyurea on polyoma virus replication. (1968)

Summary Hydroxyurea inhibits DNA synthesis and growth of mouse embryonic and kidney cells. It is also an effective inhibitor of polyoma virus synthesis in these cells. Uninfected embryo cells are more sensitive to hydroxyurea than infected ones. Several different parameters of polyoma infection, i.e., DNA synthesis, infectivity, and capsid protein formation are affected similarly by hydroxyurea.
Scanning tunneling microscope tip structures (1988)

Studies of electrochemically etched tungsten scanning tunneling microscope tips, using scanning electron microscopy, show that (i) the tips are often convolved or bent if the mass of the tungsten wire submerged in the etchant is large (an effect ascribed to surface plastic flow), (ii) bent tips nevertheless often produce good quality scanning tunneling microscopy images of Au films in air, but (iii) tips, once crashed clumsily into the Au films, no longer produce images.
Acupuncture, Connective Tissue, and Peripheral Sensory Modulation (2014)

Although considerable controversy surrounds the legitimacy of acupuncture as a treatment, a growing literature on the physiological effects of acupuncture needling in animals and humans is providing new insights into basic cellular mechanisms including connective tissue mechanotransduction and purinergic signaling. This review summarizes these findings and proposes a model combining connective tissue plasticity and peripheral sensory modulation in response to the sustained stretching of tissue that results from acupuncture needle manipulation.
The role of soluble factors in bleomycin-induced pulmonary fibrosis. (1982)

Endotracheal administration of bleomycin causes pulmonary fibrosis characterized by increased collagen synthesis and deposition. Incubation of normal lung mince with neutral salt soluble extracts of lungs from normal and bleomycin-treated rats caused a dose-dependent inhibition of collagen and noncollagenous protein synthesis. Bleomycin-treated lung extracts, however, were significantly less effective in such inhibition when compared with normal lung extracts. This inhibitory activity was not diminished by dialysis in tubing with nominal molecular weight cutoff of 10,000 but was destroyed by heat (70 C) and trypsin digestion. This inhibitory activity could not be ascribed to residual serum or bleomycin in the lung extracts. Fractionation on Sephacryl S-200 (Pharmacia, Piscataway, NJ) showed inhibitory activity to be heterogeneous with Mr (apparent molecular weight) greater than 100,000. Extracts from spleen showed similar inhibitory activity but showed no difference in intensity between normal and bleomycin-treated spleen. These data suggest that loss or decrease in production of lung inhibitory regulatory factors is partly responsible for the noted increase in collagen production and deposition in bleomycin-induced pulmonary fibrosis.