gebhart/patrepeval huggingface dataset:
Deep learning-based automated detection of retinal diseases using optical coherence tomography images (2019)

Retinal disease classification is a significant problem in computer-aided diagnosis (CAD) for medical applications. This paper is focused on a 4-class classification problem to automatically detect choroidal neovascularization (CNV), diabetic macular edema (DME), DRUSEN, and NORMAL in optical coherence tomography (OCT) images. The proposed classification algorithm adopted an ensemble of four classification model instances to identify retinal OCT images, each of which was based on an improved residual neural network (ResNet50). The experiment followed a patient-level 10-fold cross-validation process, on development retinal OCT image dataset. The proposed approach achieved 0.973 (95% confidence interval [CI], 0.971-0.975) classification accuracy, 0.963 (95% CI, 0.960-0.966) sensitivity, and 0.985 (95% CI, 0.983-0.987) specificity at the B-scan level, achieving a matching or exceeding performance to that of ophthalmologists with significant clinical experience. Other performance measures used in the study were the area under receiver operating characteristic curve (AUC) and kappa value. The observations of the study implied that multi-ResNet50 ensembling was a useful technique when the availability of medical images was limited. In addition, we performed qualitative evaluation of model predictions, and occlusion testing to understand the decision-making process of our model. The paper provided an analytical discussion on misclassification and pathology regions identified by the occlusion testing also. Finally, we explored the effect of the integration of retinal OCT images and medical history data from patients on model performance.
The design and implementation of an OGSA-based grid information service (2004)

The information service is a key component of a grid environment and critical to the operation of a computational grid. In this work, an OGSA (Open Grid Services Architecture) based information service that complies with OGSI (Open Grid Services Infrastructure) is presented. The main functionality of this information service is the provision of information essential for applications running on a computational grid such as resource information, job status, resource workload, service meta-information, and queue status. This OGSI-compliant information service is built on Globus Toolkit MDS-3, and it works with meta-scheduling services and local job scheduling systems to support resource discovery, job scheduling, and execution management. In this paper, the architecture of the Information Service and the models of information data organization are presented. Some implementation issues are discussed as well.
Cross-Regulation of the Bacillus subtilis glnRA and tnrA Genes Provides Evidence for DNA Binding Site Discrimination by GlnR and TnrA (2006)

Two Bacillus subtilis transcriptional factors, TnrA and GlnR, regulate gene expression in response to changes in nitrogen availability. These two proteins have similar amino acid sequences in their DNA binding domains and bind to DNA sites (GlnR/TnrA sites) that have the same consensus sequence. Expression of the tnrA gene was found to be activated by TnrA and repressed by GlnR. Mutational analysis demonstrated that a GlnR/TnrA site which lies immediately upstream of the -35 region of the tnrA promoter is required for regulation of tnrA expression by both GlnR and TnrA. Expression of the glnRA operon, which contains two GlnR/TnrA binding sites (glnRAo1 and glnRAo2) in its promoter region, is repressed by both GlnR and TnrA. The glnRAo2 site, which overlaps the -35 region of the glnRA promoter, was shown to be required for regulation by both GlnR and TnrA, while the glnRAo1 site which lies upstream of the -35 promoter region is only involved in GlnR-mediated regulation. Examination of TnrA binding to tnrA and glnRA promoter DNA in gel mobility shift experiments showed that TnrA bound with an equilibrium dissociation binding constant of 55 nM to the GlnR/TnrA site in the tnrA promoter region, while the affinities of TnrA for the two GlnR/TnrA sites in the glnRA promoter region were greater than 3 muM. These results demonstrate that GlnR and TnrA cross-regulate each other's expression and that there are differences in their DNA-binding specificities.
Low Loss Ferrite Y-Junction Circulator Based on Empty Substrate Integrated Coaxial Line at Ku-Band (2019)

A Y-junction circulator based on empty substrate integrated coaxial line (ESICL) technology is proposed in this paper. As ESICL is a novel transmission line, many of the common waveguide devices have not yet been developed in this technology, i.e., only filters, a power divider, a 90° hybrid directional coupler or transition structures have been presented but no nonreciprocal devices. In this paper, a ferrite-based circulator has been designed and fabricated to operate at a central frequency of 12 GHz. Measurements performed with the help of an electromagnet confirms the stability of the circulator response under different DC biasing fields. Also, measurements with magnets have been done to integrate the circulator in communication systems. In addition, different temperature tests from 20° C to 90°C have been carried out with the aim of checking the scattering parameters variations. The experimental results confirm the results obtained by the full wave simulations: insertion loss better than -1 dB isolation and return loss below -10 dB from 10 to 14 GHz.
Effects of carbonate and magnesium on calcium phosphate precipitation (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffects of carbonate and magnesium on calcium phosphate precipitationJohn F. Ferguson and Perry L. McCartyCite this: Environ. Sci. Technol. 1971, 5, 6, 534–540Publication Date (Print):June 1, 1971Publication History Published online1 May 2002Published inissue 1 June 1971https://pubs.acs.org/doi/10.1021/es60053a005https://doi.org/10.1021/es60053a005research-articleACS PublicationsRequest reuse permissionsArticle Views1106Altmetric-Citations66LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Lack of specificity of [35S]-ATP?S and [35S]-ADP?S as radioligands for ionotropic and metabotropic P2 receptor binding (1999)

Adenosine-5′-O-3-thio[35S]triphosphate ([35S]-ATPγS) has been reported to specifically bind several P2X receptor subtypes, including P2X1, P2X2, P2X3, and P2X4. Similarly, adenosine-5′-O-2-thio[35S]diphosphate ([35S]-ADPβS) has been reported to label putative P2Y receptors. To address whether these radioligands selectively label P2 receptors, the functional activity of various P2 ligands was compared with their ability to compete for [35S]-ATPγS and [35S]-ADPβS binding to cell membrane preparations from rat brain, HEK293 cells, and to native and P2X4 transfected 1321N1 astrocytoma cells. [35S]-ATPγS (0.2 nM) and [35S]-ADPβS (0.1 nM) displayed a high percentage of specific binding to membranes prepared from 1321N1 human astrocytoma cells, which were found to be devoid of detectable P2X and P2Y functional activity. [35S]-ATPγS and [35S]-ADPβS also exhibited equivalent high percentages of specific binding to HEK293 cell membranes, which endogenously express the P2Y1 and P2Y2 receptor subtypes, to 1321N1 cells stably transfected with the human P2X4 receptor, and to rat brain membranes, which have previously been shown to contain both P2X and P2Y receptor subtypes. The potency order of P2 agonists to compete for radioligand binding to these cell membrane preparations was significantly different from the functional rank order potencies determined in HEK293 cells and 1321N1 cells expressing the P2X4 receptor, as measured by cytosolic calcium flux. These data indicate that [35S]-ATPγS and [35S]-ADPβS appear to bind sites that do not correspond to known functional P2 receptor subtypes. The apparent lack of specificity of these radioligands for labeling P2 receptors is similar to that reported for other radiolabeled nucleotides and illustrates the need for caution in interpreting the apparent pharmacology of native P2 receptors on the basis of binding data alone. Drug Dev. Res. 48:84–93, 1999. © 1999 Wiley-Liss, Inc.
Use of DNA from Human Stools to Detect Aberrant CpG Island Methylation of Genes Implicated in Colorectal Cancer (2004)

Hypermethylation of cytosine residues in the CpG islands of tumor suppressor genes is a key mechanism of colorectal carcinogenesis. Detection and quantification of CpG island methylation in human DNA isolated from stools might provide a novel strategy for the detection and investigation of colorectal neoplasia. To explore the feasibility of this approach, colorectal biopsies and fecal samples were obtained from 32 patients attending for colonoscopy or surgery, who were found to have adenomatous polyps, colorectal cancer, or no evidence of neoplasia. A further 18 fecal samples were obtained from healthy volunteers, with no bowel symptoms. Isolated DNA was modified with sodium bisulfite and analyzed by methylation-specific PCR and combined bisulfite restriction analysis for CpG island methylation of ESR1, MGMT, HPP1, p16(INK4a), APC, and MLH1. CpG island methylation was readily detectable in both mucosal and fecal DNA with methylation-specific PCR. Using combined bisulfite restriction analysis, it was established that, in volunteers from whom biopsies were available, the levels of methylation at two CpG sites within ESR1 assayed using fecal DNA were significantly correlated with methylation in DNA from colorectal mucosa. Thus, noninvasive techniques can be used to obtain quantitative information about the level of CpG island methylation in human colorectal mucosa. The methods described here could be applied to a much expanded range of genes and may be valuable both for screening purposes and to provide greater insight into the functional consequences of epigenetic changes in the colorectal mucosa of free-living individuals.
A Utility Interactive PWM Sine-Wave Inverter Configured as a High Efficiency UPS (1982)

Conventional UPS equipment employs a tandem charger, battery, and inverter to isolate critical loads from utility disturbances and failures. Since two distinct stages of power conversion -- charger and inverter -- are required, this method is both inefficient and expensive. This paper describes a new circuit topology and operating method that uses a single four-quadrant PWM sine-wave inverter to both regulate the critical load and charge the standby battery. The complete power system consists of an inverter coupled to the utility through an inductor. The critical load is connected directly across the inverter output. This allows the inverter complete control of the load voltage and waveform. When the inverter is operated synchronously with the utility, power flow is regulated by varying the phase angle between the inverter and the utility. The phase angle is automatically adjusted using an 8-bit microprocessor to meet the load and battery charge current requirements. The microprocessor also performs housekeeping and display functions. Since the system requires only one power conversion stage, throughput efficiencies exceeding 90% have been achieved at the 3kW power level. Power densities also have been improved because of its "chargerless" construction. General principles of operation with phasor diagrams including actual system waveforms are presented as well as advantages and disadvantages of this approach with respect to conventional UPS equipment.
Understanding the Switching Mechanisms of the Antiferromagnet/Ferromagnet Heterojunction (2020)

Electric-field-driven spintronic devices are considered promising candidates for beyond CMOS logic and memory applications thanks to their potential for ultralow energy switching and nonvolatility. In this work, we have developed a comprehensive modeling framework to understand the fundamental physics of the switching mechanisms of the antiferromagnet/ferromagnet heterojunction by taking BiFeO<sub>3</sub>/CoFe heterojunctions as an example. The models are calibrated with experimental results and demonstrate that the switching of the ferromagnet in the antiferromagnet/ferromagnet heterojunction is caused by the rotation of the Neel vector in the antiferromagnet and is not driven by the unidirectional exchange bias at the interface as was previously speculated. Additionally, we demonstrate that the fundamental limit of the switching time of the ferromagnet is in the subnanosecond regime. The geometric dependence and the thermal stability of the antiferromagnet/ferromagnet heterojunction are also explored. Our simulation results provide the critical metrics for designing magnetoelectric devices.
The Normal Risk Ovarian Screening Study (NROSS): Twenty-one year update. (2023)

5522 Background: The Normal Risk Ovarian Screening Study (NROSS) tested a two-stage screening strategy in post-menopausal women at conventional hereditary risk where significantly rising CA125 prompted transvaginal sonography (TVS) and abnormal TVS prompted surgery to detect ovarian cancer. Methods: A total of 7,856 healthy postmenopausal women were screened annually for a total of 50,596 women-years in a single arm study ( NCT00539162 ). Serum CA125 was analyzed with the Risk of Ovarian Cancer Algorithm (ROCA) each year. If risk was normal ( &lt; 1:2000), women returned in a year. If risk was elevated ( &gt; 1:500), TVS was undertaken immediately and if risk was intermediate, CA125 was repeated in 3 months, risk recalculated, and the participant re-triaged. An average of 2% of participants were referred to TVS annually. Results: Thirty-four patients were referred for operations detecting 15 ovarian cancers and 2 borderline tumors with 12 in early stage (I-II). In addition, 7 endometrial cancers were detected with 6 in early stage. Thus, the positive predictive value (PPV) of the NROSS trial was 50% (17/34) for detecting ovarian cancer and 74% (25/34) for any cancer, far exceeding the minimum acceptable study endpoint of 10% PPV. As 4 ovarian cancers and 2 borderline tumors were diagnosed within a year of each participant’s last normal risk, the sensitivity for detecting ovarian and borderline cancer was 74% (17/23) and 70% of ROCA-detected cases (12/17) were in stage I-II. NROSS screening reduced incidence of late stage (III-IV) disease by 34% compared to the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) control arm and by 30% compared to US SEER values. Results of our NROSS trial contrast dramatically with those of the recently reported UKCTOCS that showed only a modest 14% early-stage shift, underlying a lack of reduction in mortality. Across multiple randomized trials of mammography, those trials that demonstrated at least a 20% late-stage incidence reduction had a significant mortality reduction, whereas those with less of a stage shift did not. Conclusions: An elevated ROCA, characterized by a significantly rising CA125, prompted referral of 2% of participants to TVS each year and required only 2 operations to detect each case of ovarian cancer, indicating that CA125 used in this way is adequately specific for effective screening. While the NROSS trial was not powered to detect reduced mortality, the high specificity, PPV and marked stage shift support further development of this strategy. Clinical trial information: NCT00539162 .
357. A Mouse Model of Cobalamin A (cblA) Class Isolated Methymalonic Academy (MMA) Provides Unique Platform for Testing Gene and Cell Therapies (2016)

Isolated Methylmalonic Acidemia (MMA) comprises a relatively common and heterogeneous group of inborn errors of metabolism. Most affected individuals display severe multisystemic disease with episodes of metabolic instability, chronic renal disease, and neurological complications. The most severe clinical presentations are typically associated with complete loss of methylmalonyl-CoA mutase (MUT) enzymatic activity. MUT converts methylmalonyl-CoA to succinyl-CoA within mitochondria but defects in the transport or synthesis of its cobalamin co-factor also variably impair MUT activity. Previous mouse models of Mut MMA generated by our group have been critical to developing gene therapy for MMA but have either displayed neonatal lethality or required concomitant transgenesis for viability. Thus, the need for ameliorated models to further investigate disease-associated pathophysiology and facilitate gene therapy studies exists. We have therefore constructed a mouse model of an attenuated form of isolated MMA, the cblA subtype, by using homologous recombination to create a deletion allele of Mmaa, the enzyme that performs the gated transfer of adenosylcobalamin to Mut and protects Mut from oxidative inactivation. Patients with the cblA subtype of MMA can have variable presentations, spanning the full spectrum of MMA associated symptoms and pathology, yet always harbor an element of clinical and biochemical responsiveness to injectable B12. Mmaa-/- mice were born in mendelian proportions, exhibited decreased survival after weaning (P<0.0001), weighed 50% less than littermates at 6 months (P<0.0001), lacked immunoreactive Mmaa and Mmaa mRNA in multiple tissues, including the liver, and manifested severe metabolic perturbations. Plasma methylmalonic acid concentrations ranged between 63.88-1641.91 µM, representing a 62-fold or more elevation over age matched littermates. Mmaa-/- mice also display diminished 1-C-13 propionate oxidative capacity (P<0.0001) and hepatic complex IV activity (P=0.002). Electron microscopy confirmed the presence of hepatic megamitochondria and abnormal proximal renal tubular mitochondria. The glomerular filtration rate, measured using FITC-sinistrin decay, showed that Mmaa-/- mice have diminished kidney function compared to heterozygous littermates. Following hydroxycobalamin administration, Mmaa-/- mice had improved survival and increased weight (P=0.0003), which was associated with improved 1-13C-propionate oxidative capacity. This new mouse model fully recapitulates the clinical and biochemical features seen in cblA patients, and provides a robust platform for testing gene and cell therapies for MMA because affected mice are relatively severe but survive until weaning. These animals also offer the opportunity to longitudinally examine disease biomarkers and more easily assay vectors across a wide age range.
The clinical efficacy and safety of neoadjuvant chemoradiation therapy with immunotherapy for the organ preservation of ultra low rectal cancer: A single arm and open label exploratory study. (2022)

e15603 Background: Neoadjuvant chemoradiotherapy (nCRT) not only could bring tumor downsizing and downstaging but also could achieve clinical complete response (cCR) or pathological complete response (pCR). Although immunotherapy benefits MSI-H/dMMR rectal cancer patients, little response is observed in MSS/pMMR patients. Several clinical trials including VOLTAGE trial demonstrated that a combination of PD-1 inhibitor and nCRT could result in a promising pathological response even in MSS/pMMR patients. But the elucidation regarding organ preservation after treatment is lacking. Watch and Wait (W&amp;W) is an effective strategy in rectal cancer patients showing cCR after nCRT to preserve organs. This study was designed to explore the efficacy, safety, and organ preservation rate of a combination of nCRT and PD-1 inhibitor(sintilimab) in MSS/pMMR patients with ultra-low rectal cancers. Methods: This was a single-arm, phase II trial. Patients with ultra-low rectal cancer that was confirmed as MSS/pMMR T 1- 3a N 0-1 M 0 and received 50 Gy (25×2 Gy) chemoradiotherapy and 2 cycles of sintilimab, followed by 6 cycles of capecitabine or CAPOX regimen plus 2 cycles of sintilimab as consolidation therapy. Patients with cCR were managed using the W&amp;W strategy, patients with ncCR were given local excision. The primary outcome was cCR rate and secondary outcomes were anal preservation rate, organ preservation rate, tumor regression grade (TRG), and safety profile. Results: From 2021 January to 2021 December, a total of 23 patients were enrolled. The median age was 55 y (range; 38 to 75). Male patients were 61%. cT2 was 56.5% (13/23), cT3 was 43.5% (10/23), cN0 was 69.6% (16/23), and cN1 was 30.4% (7/23). All patients completed 50Gy chemoradiotherapy. Nineteen patients received 4 cycles of sintilimab treatment, 3 patients received 3 cycles of sintilimab, and 1 patient received 1 cycle of sintilimab. cCR was 43.5% (10/23), ncCR was 26.1% (6/23), and cPR was 30.4% (7/23). The anal preservation rate was not assessed in 1 patient due to cerebral ischemic stroke. The anal preservation rate was 95.5% (21/22), rectal preservation rate was 59.1% (13/22). Ten patients underwent surgery. Among them, two patients achieved pCR, and the major pathologic response rate (TRG0-1) was 60.0% (6/10). The overall CR(cCR+pCR) rate was 52.2% (12/23). Grade 3/4 treatment-related adverse events occurred in 17.4% (4/23) of patients. No unexpected adverse events or deaths were observed. Conclusions: Given the favorable tolerability and encouraging cCR rate, nCRT plus sintilimab could be a feasible and safe option for patients with pMMR/MSS, ultra-low rectal cancer who have a strong desire to preserve the anus. Based on these results, a prospective, randomized, controlled, multicenter, phase III study is currently in progress (NCT05215379). Clinical trial information: ChiCTR2100042785.
The MemSQL query optimizer (2016)

Real-time analytics on massive datasets has become a very common need in many enterprises. These applications require not only rapid data ingest, but also quick answers to analytical queries operating on the latest data. MemSQL is a distributed SQL database designed to exploit memory-optimized, scale-out architecture to enable real-time transactional and analytical workloads which are fast, highly concurrent, and extremely scalable. Many analytical queries in MemSQL's customer workloads are complex queries involving joins, aggregations, sub-queries, etc. over star and snowflake schemas, often ad-hoc or produced interactively by business intelligence tools. These queries often require latencies of seconds or less, and therefore require the optimizer to not only produce a high quality distributed execution plan, but also produce it fast enough so that optimization time does not become a bottleneck. In this paper, we describe the architecture of the MemSQL Query Optimizer and the design choices and innovations which enable it quickly produce highly efficient execution plans for complex distributed queries. We discuss how query rewrite decisions oblivious of distribution cost can lead to poor distributed execution plans, and argue that to choose high-quality plans in a distributed database, the optimizer needs to be distribution-aware in choosing join plans, applying query rewrites, and costing plans. We discuss methods to make join enumeration faster and more effective, such as a rewrite-based approach to exploit bushy joins in queries involving multiple star schemas without sacrificing optimization time. We demonstrate the effectiveness of the MemSQL optimizer over queries from the TPC-H benchmark and a real customer workload.