gebhart/patrepeval huggingface dataset:
Systems analysis-based assessment of post-treatment adverse events in lymphatic filariasis (2019)

This is the first global study of changes in gene expression associated with AEs after treatment of lymphatic filariasis. Changes in cytokines were consistent with prior studies and with the RNAseq data. These results suggest that Wolbachia lipoprotein is involved in AE development, because it activates TLR2-TLR6 and downstream NF-κB. Additionally, LPS Binding Protein (LBP, which shuttles lipoproteins to TLR2) increased post-treatment in individuals with AEs. Improved understanding of the pathogenesis of AEs may lead to improved management, increased MDA compliance, and accelerated LF elimination.
Adiponectin and leptin in overweight/obese and lean women with polycystic ovary syndrome (2014)

Adipose tissue might play an important role in the metabolic complications in women with PCOS. To study the impact of obesity biomarkers in women with PCOS, overweight/obese and lean women should be considered separately.
HER2/neu as a Potential Target for Immunotherapy in Gynecologic Carcinosarcomas (2012)

Carcinosarcomas of the female genital tract are rare tumors with an aggressive clinical behavior. Trastuzumab, a humanized monoclonal antibody, acts by binding to HER2/neu extracellular domain and exhibits therapeutic efficacy in HER2/neu-overexpressing cancers. Two uterine carcinosarcomas (UMMT-ARK-1, UMMT-ARK-2) and 2 ovarian carcinosarcomas (OMMT-ARK-1, OMMT-ARK-2) were established as primary tumor cell lines in vitro and evaluated for HER2/neu expression by immunohistochemistry, fluorescent in situ hybridization analysis, quantitative real-time polymerase chain reaction, and for membrane-bound complement regulatory proteins CD46, CD55, and CD59 by flow cytometry. Sensitivity to trastuzumab-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity was studied in 5-hr chromium release assays. HER2/neu expression was demonstrated in OMMT-ARK-1 and OMMT-ARK-2. OMMT-ARK-2 demonstrated an amplification of the c-erbB2 gene by fluorescent in situ hybridization analysis and a high sensitivity to ADCC (mean killing, 45.6%; range, 32.3%-72.6%). A lower level of killing was detected against the fluorescent in situ hybridization analysis-negative OMMT-ARK-1 cell line (mean, 26.5%; range, 21.0%-31.8%). CD46, CD55, and CD59 membrane-bound complement regulatory proteins were expressed at high levels in all primary mixed müllerian tumor cell lines, and all these tumors were found to be highly resistant to complement-dependent cytotoxicity with or without trastuzumab. Addition of untreated and heat-inactivated plasma did not significantly decrease ADCC against OMMT-ARK-2 cell line, suggesting that while the cell line is highly resistant to complement, irrelevant IgG does not significantly alter the ability of trastuzumab to mediate ADCC. Our results suggest that HER2/neu may represent a novel target for the immunotherapy of a subset of human carcinosarcomas refractory to salvage chemotherapy.
Ribosome loading, but not protein synthesis is required for estrogen stabilization ofXenopus laevisvitellogenin mRNA (1989)

We have examined the effect of protein synthesis and of ribosome loading on the estrogen-mediated stabilization of hepatic Xenopus laevis vitellogenin mRNA. Removal of estradiol-17 beta from the culture medium, which destabilizes vitellogenin mRNA, does not alter the density of ribosomes on polysomal vitellogenin mRNA, or change the proportion of vitellogenin mRNA associated with the endoplasmic reticulum. Cycloheximide, which inhibits elongation, without changing the density of ribosomes on vitellogenin mRNA, does not block estrogen-mediated stabilization. In contrast, 2-(4-methyl-2,6-dinitroanilino)-N-methylpropionamide, (MDMP), which inhibits initiation, greatly reduces the density of ribosomes on vitellogenin mRNA, and completely blocks estrogen-mediated stabilization. Vitellogenin mRNA in MDMP treated cells is degraded at a rate similar to that seen when untreated cells are transferred from medium containing estrogen to estrogen-free medium. This suggests that a ribosome-associated degradative system may not be responsible for vitellogenin mRNA degradation. The failure of estrogen to stabilize vitellogenin mRNA in MDMP-treated cells is not due to the release of vitellogenin mRNA from the endoplasmic reticulum. Vitellogenin mRNA in MDMP-treated cells remains associated with the endoplasmic reticulum in small polysomes containing 3-5 ribosomes. These data demonstrate that maintaining a high density of ribosomes on vitellogenin mRNA, but not continuing protein synthesis, is necessary for estrogen-mediated stabilization of vitellogenin mRNA.
S100A7 (psoriasin) inhibits human epidermal differentiation by enhanced IL‐6 secretion through IκB/NF‐κB signalling (2016)

Psoriasin (S100A7), a member of the S100 protein family, is a well-known antimicrobial peptide and a signalling molecule which regulates cellular function and is highly expressed in hyperproliferative skin conditions such as atopic dermatitis (AD) and psoriasis with disrupted skin barrier function. However, its role in epidermal differentiation remains unknown. We examined the effect of S100A7 on epidermal differentiation in normal human keratinocytes (NHKs) and on a reconstituted human epidermis model. When NHKs were exposed to disruptive stimuli such as Staphylococcus aureus, ultraviolet irradiation and retinoic acid, the secretion of S100A7 into the culture medium increased and the expression of epidermal differentiation markers decreased. Treatment of NHKs with S100A7 significantly inhibited epidermal differentiation by reducing the expression of keratin 1, keratin 10, involucrin and loricrin and by increasing the expression of abnormal differentiation markers (keratin 6 and keratin 16). We verified that the MyD88-IκB/NF-κB signal cascade was activated via RAGE after S100A7 treatment, resulting in the upregulation of interleukin-6. Finally, we confirmed that S100A7 is a negative regulator of epidermal differentiation using a reconstituted human epidermis model. This study suggests that S100A7-related signalling molecules could be potent targets for recovering skin barrier function in AD and psoriasis where S100A7 is accumulated excessively.
Automatic Defect Classification Using Boosting (2006)

This paper deals with automatic defect classification (ADC) in semiconductor fabrication. The defects such as particle and scratch are automatically classified using a boosting approach. The boosting scheme is based on the Kullback-Leibler distance and linear projection along feature vectors. The paper generates the linear features which discriminate the defects maximally. The features are the linear combinations of Haar-like patterns in the frequency domain. By learning in a boosting manner, the particle and scratch are recognized out of the other defects. And, we propose another feature in the spatial domain which is based on the orientation histogram in the local region. The spatial feature is combined with frequency domain features in a boosting manner. According to the experiments with various defect samples, the accuracy of defect classification is larger than 92% on the average, and scratch is especially recognized with 98% purity. More improvement is expected by the new spatial features such as defect colors, shapes, textures, and so on.
Modeling Border Traffic Flow Using Cell Phone Header Packets (2013)

This research in progress paper describes a novel approach for improving resource allocation decision-making at ports of entry along a border. The approach involves the collection of cell phone header packets to estimate density of a population around a port of entry, and proposes that such data, if collected in real-time, could allow border agents to more effectively respond to random increases or decreases in border traffic. It is further suggested that such data could be incorporated continuously to update border flow models and help identify trends in traffic flow. The overall result of these advantages could lead to decision-makers at ports of entry being able to reduce queue times and thereby use resources more efficiently.
Tofacitinib for Maintenance Therapy in Patients With Active Ulcerative Colitis in the Phase 3 OCTAVE Sustain Trial: Results by Local and Central Endoscopic Assessments (2017)

Introduction: Tofacitinib is an oral, small molecule JAK inhibitor that is being investigated for ulcerative colitis (UC). A Phase 3, randomized, double-blind, placebo-controlled maintenance study (OCTAVE Sustain, NCT01458574) demonstrated the efficacy of tofacitinib 5 and 10 mg twice daily (BID) vs placebo (PBO) in patients (pts) with moderate to severe UC.1 Methods: We describe clinical efficacy endpoints assessed by local endoscopy readings and previously reported results assessed by central readings, to compare local vs central readings in the assessment of tofacitinib efficacy. Pts who completed OCTAVE Induction 1 (NCT01465763) or OCTAVE Induction 2 (NCT01458951) studies and achieved clinical response (decrease of baseline Mayo score ≥3 points and ≥30%, with decrease in rectal bleeding subscore ≥1 or absolute rectal bleeding subscore ≤1) were eligible to participate in OCTAVE Sustain. 593 pts were randomized (1:1:1) to PBO, tofacitinib 5 or 10 mg BID for 53 weeks (wks). Pts' eligibility was assessed based on central endoscopic reading. Pts were permitted concomitant treatment with oral corticosteroids; tapering was mandatory from baseline. Concomitant treatment with immunosuppressants and biologics was prohibited. Efficacy endpoints at Wk 52 included remission (primary endpoint: Mayo score ≤2, no subscore >1 and rectal bleeding subscore of 0), mucosal healing (Mayo endoscopic subscore ≤1) and clinical response. Results: At Wk 52, remission was achieved by significantly more pts with both tofacitinib doses vs PBO, as demonstrated by both central and local endoscopic readings, and similar results were observed with mucosal healing, clinical response and sustained steroid-free remission among pts in remission at baseline. Efficacy assessed by local endoscopic readings was numerically greater than central readings, except for clinical response. There was good agreement between locally and centrally read endoscopic subscores (kappa=0.6 [95% CI 0.5, 0.6]). Conclusion: Efficacy assessed by local endoscopic readings was numerically greater than efficacy assessed by central readings for tofacitinib 5 and 10 mg BID vs PBO. Overall, local endoscopic readings were consistent with central readings. Both methods demonstrated that both tofacitinib doses were more effective than PBO for maintenance therapy in pts with moderately to severely active UC. Funded by Pfizer Inc.Table: Table. Summary of efficacy endpoints at Wk 52, determined by local and central reading
Reconstituting the NLRP1 Inflammasome In Vitro (2013)

Nucleotide-binding domain leucine-rich-repeat containing receptors; NOD-Like Receptors (NLRs) were originally described as microbial sensors involved in host defense against pathogens that comprise an important component of the innate immune system. Recently, their cellular functions have expanded beyond classical pathogen detection, to danger sensors that may contribute to the pathophysiology of a wide range of inflammation-driven human illnesses such as metabolic diseases (atherosclerosis, obesity, type 2 diabetes, gout, age-related macular degeneration) and neurological disorders (Alzheimer's disease). Pathogen-stimulated NLRs such as NLR family Pyrin domain-containing protein 1 (NLRP1) assemble into molecular platforms called "inflammasomes" to activate inflammatory protease caspase-1, which processes pro-IL-1β and pro-IL-18 into active cytokines. We describe methods for reconstituting the human NLRP1 inflammasome in vitro. Protocols are provided for: (a) expression and purification of inflammasome core components (NLRP1 and pro-caspase-1 proteins) using the baculovirus/insect cell expression system, and (b) functional monitoring of NLRP1-mediated caspase-1 activation in response to NLRP1 ligand muramyl dipeptide (MDP) and ATP.
Modeling and analysis of real-time issues in rehabilitation robotic systems using coloured Petri nets (2003)

In this paper, we discuss some of the real-time issues that must be addressed in the design of rehabilitation robotic systems. A Coloured Petri Net (CPN) model is developed to analyze critical timing and resource requirements for achieving reliable and safe performance. A CPU scheduling problem is introduced and analyzed. An example of a robotic system treating injured or impaired limbs is used as a study case. This work shows the advantages of using CPN to model and simulate the robot-control system in real-time. This work is part of a research and development project to design and build an intelligent robot for physical and occupational therapy to help limb recovery. It is assumed that both the position and velocity of the patient's limb are measurable and controllable in real-time. The therapy process duration and frequency of limb movement are also controlled by the robot-control system. A time concept is introduced to the design to investigate the performance of the control system. Compact and extendable system design is achieved by utilizing the hierarchical aspect of CPN. This paper presents simulation results that demonstrate satisfactory mission critical performance of the system.
Limiting order of amino acids in a low-protein corn-soybean meal-whey-based diet for nursery pigs. (1998)

Three trials were carried out with pigs between 5 and 8 wk of age to determine the limiting order of amino acids in a 13.5% CP corn-soybean meal-based diet containing 8% dried whey. The positive-control diet was a 19.2% CP corn-soybean meal-based diet (1.15% lysine), also with 8% dried whey. Amino acid additions to the low-protein, negative-control diet were based on levels needed to accomplish 110% of ideal ratios (to lysine, set at 1.15%). In Exp. 1, the addition of an amino acid mixture containing Lys, Trp, Thr, Met, Ile, and Val to the low-protein diet increased (P<.05) gain and gain: feed ratio, and these response traits were not different from those of pigs fed the 19.2% CP positive-control diet. Single deletion of Lys from the supplemental amino acid mixture depressed performance to a greater (P<.05) extent than single deletion of any of the other amino acids. Single deletions of Trp, Thr, Met, or Val decreased (P<.05) performance in a similar but lesser magnitude than the decrease caused by Lys deletion, whereas Ile deletion was without effect. Experiments 2 and 3 were designed to evaluate the limiting order of AA beyond Lys in the low-protein diet. Neither His nor Glu were found to be deficient, and, as in Exp. 1, deletion of Trp, Thr, Met, or Val from the supplemental amino acid mixture resulted in performance depressions (P<.05) that were similar. The results suggest that Lys is first-limiting and Trp, Thr, Met, and Val are equally second-limiting in a reduced protein (13.5% CP) corn-soybean meal-based diet with 8% whey for 10-kg pigs.
Aggressive vertebral hemangioma masquerading as neurological disease in a pediatric patient (2021)

Aggressive hemangioma is a rare vertebral lesion in pediatric patients which can present with deteriorating neurological function. It can mimic malignancy on imaging, particularly as it regularly has an extrasosseous soft tissue component. We present a case of a 13-year-old male who presented with a three month history of lower extremity weakness that was found to have an infiltrative mass at T10 with associated cord compression from epidural extension of the lesion. In this report we review the characteristic imaging findings associated with aggressive hemangioma, including its appearance on read-out segmented diffusion-weighted images. It is imperative that radiologists who interpret studies of children be aware that this lesion exists and what it looks like, as it can be associated with massive hemorrhage if encountered unexpectedly during surgery.
The Effects of Supercritical Propane on the Alkylation of Toluene with Ethylene over USY and Sulfated Zirconia Catalysts (2002)

The alkylation of toluene with ethylene over microporous USY zeolite and mesoporous sulfated zirconia (S/ZrO2) catalysts was explored at liquid, near-critical liquid, and supercritical conditions using propane as the supercritical cosolvent. Liquid, near-critical liquid, and supercritical conditions were examined for their effects on product selectivity and catalyst activity maintenance. The S/ZrO2 catalyst demonstrated alkylation activity almost exclusively, whereas the USY catalyst demonstrated both alkylation and cracking/disproportionation activities. Near-critical and supercritical reaction conditions improved product selectivity with the USY catalyst through the suppression of disproportionation reactions and enhanced ortho- and para-ethyltoluene selectivity. However, the addition of the supercritical cosolvent resulted in increased deactivation for both the S/ZrO2 and USY catalysts, with deactivation increasing with propane mole fraction.
Kappa-on-Heavy (KoH) bodies are a distinct class of fully-human antibody-like therapeutic agents with antigen-binding properties (2019)

We describe a Kappa-on-Heavy (KoH) mouse that produces a class of highly diverse, fully human, antibody-like agents. This mouse was made by replacing the germline variable sequences of both the Ig heavy-chain (IgH) and Ig kappa (IgK) loci with the human IgK germline variable sequences, producing antibody-like molecules with an antigen binding site made up of 2 kappa variable domains. These molecules, named KoH bodies, structurally mimic naturally existing Bence-Jones light-chain dimers in their variable domains and remain wild-type in their antibody constant domains. Unlike artificially diversified, nonimmunoglobulin alternative scaffolds (e.g., DARPins), KoH bodies consist of a configuration of normal Ig scaffolds that undergo natural diversification in B cells. Monoclonal KoH bodies have properties similar to those of conventional antibodies but exhibit an enhanced ability to bind small molecules such as the endogenous cardiotonic steroid marinobufagenin (MBG) and nicotine. A comparison of crystal structures of MBG bound to a KoH Fab versus a conventional Fab showed that the KoH body has a much deeper binding pocket, allowing MBG to be held 4 Å further down into the combining site between the 2 variable domains.
Compartmentalization of cerebrospinal fluid inflammation across the spectrum of untreated HIV-1 infection, central nervous system injury and viral suppression (2021)

HIV-1 infection was associated with a broad compartmentalized CSF inflammatory response that developed early in its course and changed with systemic disease progression, development of neurological injury, and viral suppression. CSF inflammation in untreated individuals without overt HAD exhibited at least two overall patterns of inflammation as blood CD4+ T lymphocytes decreased: one that peaked at 200-350 blood CD4+ T cells/μL and associated with lymphocytic CSF inflammation and HIV-1 RNA concentrations; and a second that steadily increased through the full range of CD4+ T cell decline and associated with macrophage responses and increasing CNS injury. Subacute HAD was distinguished by a third inflammatory profile with increased blood-brain barrier permeability and robust combined lymphocytic and macrophage CSF inflammation. Suppression of CSF and blood HIV-1 infections by antiretroviral treatment and elite viral control were associated with reduced CSF inflammation, though not fully to levels found in HIV-1 seronegative controls.
PERPENDICULAR MAGNETIC ANISOTROPY AND MAGNETO-OPTICAL PROPERTIES IN Fe(Co)/Pt MULTILAYER FILMS (1993)

A systematic study on structure, magnetic and magneto-optical properties of Fe/Pt and FeCo/Pt multilayer films has been performed. It is found that the microstructure observed by cross-sectional TEM as well as the effective perpendicular anisotropy Keff varied according as substrate-deposition-temperature. In Fe/Pt multilayer film deposited on the substrate above room temperature, a fine columnar structure were discerned and the perpendicular anisotropy was fairly large. In the sample grown on a cooling substrate, however, the structure with irregular small crystal grains appeared instead of a columnar structure and the Keff reduced. This result implies that the columnar microstructure contributes to the perpendicular anisotropy of multilayer films.
Effectiveness of Mechanical Aeration in Floating Aquatic Macrophyte‐Based Wastewater Treatment Systems (1989)

Abstract Outdoor tanks containing the floating aquatic macrophyte water hyacinth [ Eichhornia crassipes (Mart) Solms] were provided with diffuse aeration to evaluate its effect on wastewater treatment efficiency and plant growth. Light aeration (0.003 and 0.021 L m −2 min −1 ) had no effect on the treatment of primary domestic effluent in the batch‐fed water hyacinth tanks. Heavy aeration (1.03 and 3.53 L m −2 min −1 ) raised wastewater dissolved oxygen (DO) concentrations, but did not improve biochemical oxygen demand (BOD 5 ) removal efficiency or increase plant growth rates during 21‐d experiments. Heavy aeration slightly increased wastewater N removal, but the effectiveness of aeration for nutrient removal was not consistent among experiments. In continuous‐flow raceways fed primary domestic effluent, vigorous aeration (6.1 L m −2 min −1 ) improved effluent quality, with contaminant removal rates averaging 77% (BOD 5 ) and 76% (suspended solids [SS]) in nonaerated raceways, and 94% (BOD 5 ) and 89% (SS) in aerated raceways. Results of this study suggest that the high aeration requirement for enhanced contaminant removal in floating aquatic macrophyte systems (FAMS) is due not only to poor O 2 transfer efficiencies (1.6–4.0%), but also to the inefficient utilization of O 2 for BOD 5 removal. The primary benefit of moderate aeration (0.1–1.0 L m −2 min −1 ) in FAMS appears to be the elevation of wastewater DO concentrations (from 0.5 to 2.5 mg L −1 ), which may be useful for controlling odors and mosquito proliferation.
Nonlinear distortion and DSP-based compensation in metro and access networks using discrete multi-tone (2014)

The nonlinear distortion caused by the interaction between chromatic dispersion and direct detection reduces the capacity of optical discrete multi-tone system beyond dozens of kilometers. The proposed nonlinear equalizer compensated the distortion and increased the capacity by up to 50%.
Whole grain oats, more than just a fiber: Role of unique phytochemicals (2017)

Oats are a good source of soluble dietary fiber, especially β-glucan, which has outstanding functional and nutritional properties. β-Glucan is considered to be the major active component of oats because of its cholesterol-lowering and antidiabetic effects. However, the nutritional benefits of oats appear to go beyond fiber to bioactive phytochemicals with strong antioxidant and anti-inflammatory effects. In this review, we summarize current knowledge on the chemistry, stability, bioavailability, and health effects of two unique phytochemicals in oats, avenanthramides, and avenacosides A and B. We conclude that studies on the beneficial effects of avenanthramides and avenacosides A and B are still in their infancy, and additional health benefits of these unique oat components may yet be identified.
On demagnetization induced boosting of the short-wavelength in perpendicular recording (1985)

It is shown that the presence of a permeable underlayer in the medium enhances the short-wavelength response in perpendicular recording.