gebhart/patrepeval huggingface dataset:
Development and clinical evaluation of a microarray for HLA‐A and ‐DRB1 genotyping (2008)

Microarray technology makes high-throughput genotyping possible by permitting the simultaneous analysis of large sets of genes on a small reaction slide. Human leukocyte antigen (HLA) loci showing high polymorphisms are suitable targets for microarray. In this study, we developed a microarray kit with newly designed oligonucleotide probes for the genotyping of HLA-A and -DRB1. In total, 42 probes were designed to hybridize to polymorphic sites for HLA-A and 36 for HLA-DRB1. Asymmetric polymerase chain reaction (PCR) using four primers was performed to amplify exon 2 of HLA-DRB1, whereas symmetric PCR was performed to amplify both exons 2 and 3 of HLA-A. Evaluation of performance using samples from 138 Koreans disclosed consistent microarray results with all sequence-based typing at the low-resolution level. Despite the occurrence of ambiguities in 35 HLA-A (25.4%) and 5 HLA-DRB1 (3.6%) cases, correct genotypes were assigned with high certainty by referring to allele distribution in Koreans. These data clearly indicate that our newly developed microarray kit is optimal in determining correct genotypes at the low-resolution level in Koreans.
SmartPill Capsule for Assessment of Gastric Emptying – Comparison with Simultaneous Gastric Emptying Scintigraphy (2006)

Purpose: Gastric emptying scintigraphy (GES) is used to measure gastric emptying. Recently, a wireless capsule (SmartPill), which measures pH and pressure, has been developed to measure GI transit. We have previously reported good correlation of the SmartPill to differentiate normal subjects from patients with gastroparesis. The aim of this analysis was to determine the ability of the SmartPill to differentiate subjects with normal and delayed gastric emptying. Methods: In a multicenter study, simultaneous SmartPill pH/pressure recording and GES were performed in 86 normal subjects and 60 patients with previously diagnosed gastroparesis. The SmartPill capsule was ingested after an overnight fast and GES was performed with imaging every 30 min for 4 hours after a 99mTc-SC Eggbeaters meal. After 6 hours, Ensure was given. The gastric residence time (GRT) of the SmartPill was determined as the duration after capsule/meal ingestion to a rapid rise in pH upon reaching the alkaline small intestine. Delayed GES was defined as >10% gastric retention at 4 hours. Results: Successful SmartPill recordings and GES were obtained in 77 normal subjects and 48 patients with previously diagnosed gastroparesis. In normal subjects, the median SmartPill GRT was 215 minutes with 95% confidence intervals (199, 225). In patients with a history of gastroparesis, the median SmartPill GRT was >360 minutes with 95% confidence intervals (322, >360). In patients with a history of gastroparesis, delayed GES on the study day was documented in 24 of 48 (50%). In normal subjects, GES was normal in 71 of 77 (92%). Using receiver operating characteristic (ROC) analysis, a 4 hour SmartPill GRT was best to identify subjects with gastroparesis or normal based on their history with sensitivity of 82% and specificity of 74%. A 5 hour SmartPill GRT was best to identify subjects with delayed or normal gastric emptying based on scintigraphy on the day of the test with sensitivity of 83% and specificity of 83%. Conclusions: The SmartPill gastric residence time is able to identify abnormal gastric emptying with good sensitivity and specificity. This study suggests the SmartPill can be used as a novel nonradioactive method for assessing gastric emptying in health and disease.
DIRAS3 regulates the autophagosome initiation complex in dormant ovarian cancer cells (2014)

DIRAS3 is an imprinted tumor suppressor gene that is downregulated in 60% of human ovarian cancers. Re-expression of DIRAS3 at physiological levels inhibits proliferation, decreases motility, induces autophagy, and regulates tumor dormancy. Functional inhibition of autophagy with choroquine in dormant xenografts that express DIRAS3 significantly delays tumor regrowth after DIRAS3 levels are reduced, suggesting that autophagy sustains dormant ovarian cancer cells. This study documents a newly discovered role for DIRAS3 in forming the autophagosome initiation complex (AIC) that contains BECN1, PIK3C3, PIK3R4, ATG14, and DIRAS3. Participation of BECN1 in the AIC is inhibited by binding of BECN1 homodimers to BCL2. DIRAS3 binds BECN1, disrupting BECN1 homodimers and displacing BCL2. Binding of DIRAS3 to BECN1 increases the association of BECN1 with PIK3C3 and ATG14, facilitating AIC activation. Amino acid starvation of cells induces DIRAS3 expression, reduces BECN1-BCL2 interaction and promotes autophagy, whereas DIRAS3 depletion blocks amino acid starvation-induced autophagy. In primary ovarian cancers, punctate expression of DIRAS3, BECN1, and the autophagic biomarker MAP1LC3 are highly correlated (P<0.0001), underlining the clinical relevance of these mechanistic studies. Punctate expression of DIRAS3 and MAP1LC3 was detected in only 21-23% of primary ovarian cancers but in 81-84% of tumor nodules found on the peritoneal surface at second-look operations following primary chemotherapy. This reflects a 4-fold increase (P<0.0001) in autophagy between primary disease and post-treatment recurrence. We suggest that DIRAS3 not only regulates the AIC, but induces autophagy in dormant, nutrient-deprived ovarian cancer cells that remain after conventional chemotherapy, facilitating their survival.
P422 Immunogenicity of a proposed adalimumab biosimilar, FKB327, and the reference product in patients with rheumatoid arthritis (2019)

The FKB327-002 double-blind (DB) study to compare the efficacy and safety of a candidate adalimumab biosimilar, FKB327, and the reference product (RP) in patients with rheumatoid arthritis also being treated with methotrexate (MTX)—the ARABESC trial—was presented previously. The FKB327-003 study, also known as the ARABESC-OLE trial, was a Phase 3 open-label extension (OLE) study to compare the long-term safety, efficacy, immunogenicity, and pharmacokinetics of FKB327 and RP. The immunogenicity of RP and FKB327 was examined across studies. In the DB study, patients were randomised 1:1 to receive FKB327 or RP (40 mg subcutaneously) every other week for 24 weeks, with continuing MTX. In the OLE study, patients completing the DB study with clinical response and no safety concerns were immediately re-randomised to FKB327 or RP, so that two-thirds of patients remained on the same treatment as in the DB study and one-third switched to the alternate treatment for weeks 0 through 28 (Part 1), then all received FKB327 through Week 78 (Part 2). A total of 645 patients (FKB327, n = 324; RP, n = 321) who entered the OLE study were evaluated for immunogenicity during continuous treatment and across switching sequences in the studies. Immunogenicity was assessed by evaluation of antidrug antibodies (ADAs; proportion of patients ADA-positive, ADA-titre, and neutralising ADAs) using validated, high-sensitivity electrochemiluminescence assay and competitive ligand-binding assay. The impact of ADAs on efficacy and safety was also evaluated. The proportion of patients with positive ADA status was highest prior to dosing at week 0 in the OLE study, at 61.7% and 60.0% for FKB327 and RP, respectively. The proportion of patients with positive ADA status did not increase over time to Week 30 (the end of Part 1) and was similar for FKB327 and RP at all time points. The majority of ADAs were neutralising. At Week 78, the proportion of patients with positive ADA status was lower in all treatment sequences, at 51.1%, 54.4%, 48.1%, and 42.5% for the FKB327–FKB327–FKB327, FKB327–RP–FKB327, RP–FKB327–FKB327, and RP–RP– FKB327 treatment sequences, respectively. The scale of negative impact of ADA on efficacy was higher in the ADA high-titre category in FKB327 and RP to a similar degree. Incidence of hypersensitivity and injection-site reactions was low in both FKB327 and RP, with no apparent relationship to ADA-titre category. The RP and FKB327 showed comparable immunogenicity in long-term administration. Treatment switching from RP to FKB327 or vice versa did not influence either immunogenicity or sustainability of efficacy or safety.
Mapping by Genetic Interaction (2001)

As many of the linked chromosome regions that predispose to type 1 diabetes in the NOD mouse have been dissected, it has become apparent that the initially observed effect is in fact attributable to several loci. One such cluster of loci on distal chromosome 3, originally described as Idd10, is now known to comprise three separate loci, Idd10, Idd17, and Idd18. Although these loci have a significant combined effect on diabetes development, their individual effects are barely detectable when diabetes is used as a read-out, which makes fine-mapping them by use of a conventional congenic approach impractical. In this study, we demonstrate that it is possible to map loci, with modest effects, to regions small enough for systematic gene identification by capitalizing on the fact that the combined loci provide more profound, measurable protection. We have mapped the Idd10 and Idd18 loci to 1.3- and 2.0-cM intervals, respectively, by holding the Idd3 allele constant. In addition, we have excluded Csf1 and Nras as candidates for both loci.
A Dual-Band Micromachined On-Wafer Probe with Integrated Diplexer for Ultra-Broadband Measurements to 220 GHz (2023)

This work presents a micromachined dual-band probe for ultra-broadband single-sweep measurements to 220 GHz. The probe features both WR-5.1 waveguide and 1.0 mm coaxial inputs that are combined in an integrated passive diplexer. The probe shows a maximum loss in the crossover region of 6-7 dB and a minimum output return loss of 10 dB.
Retracted: Does the technique of cardiopulmonary bypass affect lung water content? (1991)

Several efforts have been made to improve the technique of cardiopulmonary bypass (CPB), including the use of pulsatile flow and the modification of cannulation technique. The present study focused upon extravascular lung water (EVLW) in 60 aortocoronary bypass patients subjected to four different perfusion techniques during CPB: group 1 (n = 15): non-pulsatile flow and standard cannulation; group 2 (n = 15); pulsatile flow and standard cannulation; group 3 (n = 15): nonpulsatile flow and monoatrial cannulation (i.e., always "partial" bypass during CPB); group 4 (n = 15): pulsatile flow and monoatrial cannulation. EVLW content was measured using the double-indicator dilution technique with indocyanine green; in addition, various hemodynamic and laboratory variables were measured. Lung water content rose above normal values (mean: 5.79 +/- 0.33 ml/kg) only in the groups submitted to the standard cannulation technique, irrespective of whether the perfusion flow was pulsatile or not (group 1: + 27.4%; group 2: + 25.5%). Pulmonary gas exchange, too, was compromised only in these patients (PaO2 in group 1 -19% and in group 2 -17%; Qs/Qt in group 1 + 36 rel. % and in group 2 + 29 rel. %), whereas all patients with monoatrial cannulation and partial bypass throughout the CPB period showed no rise in EVLW content or Qs/Qt and no drop in PaO2. From the results of this study we conclude that pulsatile perfusion during open heart surgical procedure has no advantages in regard to lung water content. Monoatrial cannulation with partial bypass at all times during CPB, however, seems to be beneficial, probably owing to the maintenance of pulmonary circulation during the bypass period.
Study of functional properties of thermally irreversible photochromic diarylethenes in various aggregate states (2011)

Abstract One of problems for a development of multilayer recording media for 3D bitwise working optical memory is making thin photochromic layers containing maximal concentration of photochromic compounds in the layer and developing a high efficiency of photochromic transformations. In this connection, the comparative spectral‐kinetic study of photochromism for certain thermally irreversible diarylethenes in solution, a polymer matrix and a solid film without the polymer binder was carried out for the first time. As a photochromic compounds 1,2‐bis(3‐benzothienyl‐6‐carboxyl‐2‐methyl)cyclopentene and 1,2‐bis(3‐benzothienyl‐2‐methyl‐6‐phenyl‐carbonyl)cyclopentene synthesized by the reaction of 1,2‐bis(3‐benzothienyl‐2‐methyl) cyclo‐pentene with corresponding acylation agents were used. Polymethylmethacrylate and polycarbonate (both in granulated form and thin film) were selected as polymer binders. Differences in the structure of diarylethene not lead to any fundamental changes in the photochromic properties, in the applicable state of matter, as it was detected. The dependences of the efficiency for processes such as photocoloration, photobleaching and photodegradation from the aggregate state, the nature of the polymer binder and the structure of photochromic compounds have been revealed. The obtained results indicate that photochromic films both polymeric and thin solid are characterized by comparable photosensitivity and can be used for making a multilayer recording media for 3D bitwise working optical memory. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana (2017)

Albugo sp. alter tryptophan-derived metabolites and suppress elements of the responses to salicylic acid in Arabidopsis. Albugo sp. imposed alterations in tryptophan-derived metabolites may play a role in Arabidopsis non-host resistance to P. infestans. Understanding the basis of non-host resistance to pathogens such as P. infestans could assist in development of strategies to elevate food security.
Queue-aware optimal resource allocation for the LTE downlink (2013)

We address the problem of optimal downlink resource allocation in an OFDMA system, in a scenario where very limited channel quality information (CQI) is available at the base-station. Our work is particularly applicable in the context of the LTE downlink, since the feedback mechanism we consider closely resembles one of the CQI reporting modes in LTE. Specifically, the users only report the indices of their best M sub-bands and an effective CQI corresponding to these best M bands. Our policy simultaneously performs optimal sub-band assignment and rate allocation, by taking into account channel quality as well as the queue backlogs of each user. The technical novelty of our work lies in exploiting a limit theorem on the best SNRs reported by the users, and combining it within a Lyapunov stability framework. We show that our policy is throughput maximizing among all policies which are constrained to the CQI mechanism considered. Numerical results indicate that in terms of throughput and average delay, our policy compares favorably to existing resource allocation policies such as proportional fair.
Alemtuzumab Therapy for Leukemic Cutaneous T-Cell Lymphoma (2014)

A energy exposure from commercial 5 nail polish drying devices would fall within the estimated range determined to be potentially carcinogenic. 1,2,4 However, considering the low UV-A energy exposure in an average manicure visit, multiple visits would be required to reach the threshold for potential DNA damage.Although the in vivo risk from multiple manicure visits remains untested, our data suggest that, even with numerous exposures, the risk for carcinogenesis remains small.That said, we concur with previous authors in recommending use of physical blocking sunscreens or UV-A protective gloves to limit the risk of carcinogenesis and photoaging.
Fast NMR Methods for Measuring in the Direct and/or Competition Mode the Dissociation Constants of Chemical Fragments Interacting with a Receptor (2019)

Ligand-based NMR screening represents a powerful method in fragment-based drug discovery for the identification of chemical matter interacting with the receptor of interest. The large dynamic range of these methods allows the detection of weakly binding ligands. However, the methodology has not been extensively used for quantifying the strength of these interactions. This knowledge is important for ranking fragments according to their binding strength and for prioritizing structure-based and medicinal chemistry activities. Rapid NMR methods for measuring the dissociation constant in direct and competition modes are presented here. The theory underpinning these methods are presented, along with their application to the measurement of the binding affinities of several ligands of the heat shock protein 90.
Dynorphin-Processing Endopeptidase in the Rat Anterior Pituitary Lactotrophic Cell Line, GH4C1 (1992)

Several peptide hormones and neurotransmitters are produced by cleavage at the monobasic processing sites. An endoprotease capable of cleaving a dynorphin peptide at the monobasic processing site is secreted from the rat anterior pituitary lactotrophic cell line, GH4C1. When characterized by fast protein liquid chromatography using an ion exchange column, the majority of the endoprotease activity elutes as a single symmetrical peak around 0.3 M NaCl. The protease inhibitor profile suggests that the activity is due to putative thiol protease. These enzymatic properties are similar to a monobasic processing enzyme previously found in bovine pituitary and in the rat brain. The secretory pathway which contains the enzyme activity in GH4C1 cells was characterized by stimulation of secretion by thyrotropin releasing hormone, forskolin, phorbol ester, or potassium chloride. The secretion of the enzyme activity was substantially increased by these compounds suggesting that the GH4C1 cells secrete the activity via the regulated pathway. A hormonal treatment of the GH4C1 cells which has been previously shown to produce a substantial increase in the number of secretory granules and ir-prolactin has been found in this study to elevate this enzyme activity 2-fold. This increase is similar to that seen in the carboxypeptidase E activity, another putative peptide hormone processing enzyme activity. These data suggest that the peptide processing activity is regulated to a small but significant extent and is coordinately regulated with carboxypeptidase E activity.
The Metallographical Characteristics and the Formation Mechanism of Longitudinal Surface Cracks in CC Slabs (1982)

A plant experiment was carried out the copper mould of a continuous slab caster was artificially grooved and thus longitudinal mid-face cracks were formed. The obtained cast samples were metallographically examined. Local segregation of C, Mn, P and S existed in front of longitudinal cracks in both directions of thickness and length and the cracks propagated along these segregated regions. This feature was common in cracks appeared differently. The very vicinity to the crack entry showed the deformation of ferrite and pearlite structure. This means that the opening of cracks to the surface occurred when the surface temperature decreased below Ar3 point, possibly in the secondary cooling zone. A formation mechanism of longitudinal surface cracks was proposed based on these findings.
Hydrothermal Preparation of Porous Hydroxyapatite Ceramics. (1998)

Porous ceramics of calcium hydroxyapatite with non-stoichiometric composition were prepared hydrothermally. The hydroxyapatite ceramics prepared at 105°C under the saturated vapor pressure for 20h were composed of rod-shaped crystals with about 10μm in length with the mean aspect ratio of 40. The porous ceramics of calcium deficient hydroxyapatite had about 50% porosity with the inter-connecting pore structure. This porous ceramics had compressive strength of about 10MPa. According to the in vitro test, this calcium deficient hydroxyapatite must be the bio-active material.