gebhart/patrepeval huggingface dataset:
Dysfunction of Delayed Rectifier Potassium Channels in an Inherited Cardiac Arrhythmia (1999)

The rapid (IKr) and slow (IKs) delayed rectifier K+ currents are key regulators of cardiac repolarization. HERG encodes the Kr channel, and KVLQT1 and hminK encode subunits that coassemble to form Ks channels. Mutations in any one of these genes cause Romano-Ward syndrome, an autosomal dominant form of long QT syndrome (LQT). Mutations in KVLQT1 and HERG are the most common cause of LQT. Not all missense mutations of HERG or KVLQT1 have the same effect on K+ channel function. Most mutations result in a dominant-negative effect, but the severity of the resulting phenotype varies widely, as judged by reduction of current induced by coexpression of wild-type and mutant subunits in heterologous expression systems. Mutations in hminK (S74L, D76N) reduce IKs by shifting the voltage dependence of activation and accelerating channel deactivation. A recessive form of LQT is caused by mutations in either KVLQT1 or hminK. The functional consequences of mutations in delayed rectifier K+ channel subunits are delayed cardiac repolarization, lengthened QT interval, and an increased risk of torsade de pointes and sudden death.
Clinical and imaging assessment of acute combat mild traumatic brain injury in Afghanistan (2015)

Somatic, behavioral, and cognitive symptoms and performance deficits are substantially elevated in acute blast-related mTBI. Postconcussive symptoms and performance on measures of posttraumatic stress disorder, depression, and neurocognitive performance at initial presentation correlate with return-to-duty time. Although changes in fractional anisotropy are uncommon and subtle, DTI is more sensitive than conventional MRI in imaging white matter integrity in blast-related mTBI acutely.
Reproducible Floating-Point Aggregation in RDBMSs: Extended version (2018)

Industry-grade database systems are expected to produce the same result if the same query is repeatedly run on the same input. However, the numerous sources of non-determinism in modern systems make reproducible results difficult to achieve. This is particularly true if floating-point numbers are involved, where the order of the operations affects the final result.&#13;\nAs part of a larger effort to extend database engines with data representations more suitable for machine learning and scientific applications, in this paper we explore the problem of making relational GroupBy over floating-point formats bit-reproducible, i.e., ensuring any execution of the operator produces the same result up to every single bit. To that aim, we first propose a numeric data type that can be used as drop-in replacement for other number formats and is---unlike standard floating-point formats---associative. We use this data type to make state-of-the-art GroupBy operators reproducible, but this approach incurs a slowdown between 4x and 12x compared to the same operator using conventional database number formats. We thus explore how to modify existing GroupBy algorithms to make them bit-reproducible and efficient. By using vectorized summation on batches and carefully balancing batch size, cache footprint, and preprocessing costs, we are able to reduce the slowdown due to reproducibility to a factor between 1.9x and 2.4x of aggregation in isolation and to a mere 2.7% of end-to-end query performance even on aggregation-intensive queries in MonetDB. We thereby provide a solid basis for supporting more reproducible operations directly in relational engines.&#13;\nThis document is an extended version of an article currently in print for the proceedings of ICDE'18 with the same title and by the same authors. The main additions are more implementation details and experiments.
Urinary Stone Disease: Advancing Knowledge, Patient Care, and Population Health (2016)

Expanding epidemiologic and physiologic data suggest that urinary stone disease is best conceptualized as a chronic metabolic condition punctuated by symptomatic, preventable stone events. These acute events herald substantial future chronic morbidity, including decreased bone mineral density, cardiovascular disease, and CKD. Urinary stone disease imposes a large and growing public health burden. In the United States, 1 in 11 individuals will experience a urinary stone in their lifetime. Given this high incidence and prevalence, urinary stone disease is one of the most expensive urologic conditions, with health care charges exceeding $10 billion annually. Patient care focuses on management of symptomatic stones rather than prevention; after three decades of innovation, procedural interventions are almost exclusively minimally invasive or noninvasive, and mortality is rare. Despite these advances, the prevalence of stone disease has nearly doubled over the past 15 years, likely secondary to dietary and health trends. The NIDDK recently convened a symposium to assess knowledge and treatment gaps to inform future urinary stone disease research. Reducing the public health burden of urinary stone disease will require key advances in understanding environmental, genetic, and other individual disease determinants; improving secondary prevention; and optimal population health strategies in an increasingly cost-conscious care environment.
III-Y on silicon DFB laser arrays (2016)

We will present our work on epitaxially grown III-V on silicon DFB laser arrays, including results of pure InP-based lasers emitting around 900nm and InGaAs-on-InP lasers emitting around 1300nm.
Outcomes with Anti-Tumour Necrosis Factor-Alpha Therapy and Serology in Patients withDenovoCrohn’s Disease After Ileal Pouch Anal Anastomosis (2016)

I2 serology may possibly help identify patients who have developed or are at risk for developing denovo CD. Anti-TNFα therapy for denovo CD after IPAA can help prevent permanent ileostomy in almost 75% of cases, even in patients who previously failed anti-TNFα treatment before surgery.
Infection After Total Knee Arthroplasty. A Retrospective Study of the Treatment of Eighty-One Infections* (1999)

Our treatment protocols, which were based on the clinical setting of the infection, were successful for most patients. A major factor associated with treatment failure was a compromised immune status. Bone loss and necrosis of the soft tissues around the joint also complicated the treatment of these infections.
Electrochemical Triggering of Reflectin Protein Assembly (2021)

In this work, we demonstrate electrochemical triggering and assembly of reflectin, the protein that mediates neuronal fine-tuning of color reflected from skin cells used for camouflage and communication in squids. Electrochemical reduction of histidine residues in the protein acts as an in vitro surrogate for phosphorylation in vivo , driving the assembly previously shown to regulate its function. Using micro-drop voltammetry and in situ dynamic light scattering, we demonstrate selective reduction of the imidazolium sidechains of histidine in monomers, oligopeptides and reflectin in acidic solution. The formal reduction potential of imidazolium proves readily distinguishable from those of hydronium and primary amines, allowing unequivocal confirmation of the direct and energetically-selective deprotonation of histidine in reflectin. The resulting “electro-assembly” methodology provides a new approach to probe, understand, and control the mechanisms that dynamically tune protein structure and function. Figure 1
Rapid Evaporative Ionisation Mass Spectrometry (REIMS) Provides Accurate Direct from Culture Species Identification within the Genus Candida (2016)

Members of the genus Candida, such as C. albicans and C. parapsilosis, are important human pathogens. Other members of this genus, previously believed to carry minimal disease risk, are increasingly recognised as important human pathogens, particularly because of variations in susceptibilities to widely used anti-fungal agents. Thus, rapid and accurate identification of clinical Candida isolates is fundamental in ensuring timely and effective treatments are delivered. Rapid Evaporative Ionisation Mass Spectrometry (REIMS) has previously been shown to provide a high-throughput platform for the rapid and accurate identification of bacterial and fungal isolates. In comparison to commercially available matrix assisted laser desorption ionisation time of flight mass spectrometry (MALDI-ToF), REIMS based methods require no preparative steps nor time-consuming cell extractions. Here, we report on the ability of REIMS-based analysis to rapidly and accurately identify 153 clinical Candida isolates to species level. Both handheld bipolar REIMS and high-throughput REIMS platforms showed high levels of species classification accuracy, with 96% and 100% of isolates classified correctly to species level respectively. In addition, significantly different (FDR corrected P value < 0.05) lipids within the 600 to 1000 m/z mass range were identified, which could act as species-specific biomarkers in complex microbial communities.
Fibroblast Growth Factor Receptor-Mediated Rescue of x-Ephrin B1-Induced Cell Dissociation in XenopusEmbryos (2000)

The Eph family of receptor tyrosine kinases and their membrane-bound ligands, the ephrins, have been implicated in regulating cell adhesion and migration during development by mediating cell-to-cell signaling events. Genetic evidence suggests that ephrins may transduce signals and become tyrosine phosphorylated during embryogenesis. However, the induction and functional significance of ephrin phosphorylation is not yet clear. Here, we report that when we used ectopically expressed proteins, we found that an activated fibroblast growth factor (FGF) receptor associated with and induced the phosphorylation of ephrin B1 on tyrosine. Moreover, this phosphorylation reduced the ability of overexpressed ephrin B1 to reduce cell adhesion. In addition, we identified a region in the cytoplasmic tail of ephrin B1 that is critical for interaction with the FGF receptor; we also report FGF-induced phosphorylation of ephrins in a neural tissue. This is the first demonstration of communication between the FGF receptor family and the Eph ligand family and implicates cross talk between these two cell surface molecules in regulating cell adhesion.
Data on cardiac and vascular functionality in ex vivo and in vivo models following acute administration of trimethylamine N-oxide (2023)

This dataset describes in detail the outcomes of acute trimethylamine N-oxide (TMAO) administration on cardiac, vascular and mitochondrial functionality in <i>ex vivo</i> and <i>in vivo</i> models. The accumulation of TMAO in target tissues was assessed after performing heart perfusion or by incubating aortic tissue in a solution containing TMAO. To evaluate the impact of TMAO on mitochondrial function, the aortic rings and heart homogenates of Wistar rats were incubated in a solution containing [9,10-<sup>3</sup>H] palmitate (5 µCi/ml) or D-[U-<sup>14</sup>C] glucose (0.625 µCi/ml) in the presence or absence of TMAO with subsequent measurement of substrate oxidation and uptake. The effects of TMAO on the vascular reactivity of isolated conductance and resistance vessels were tested by measuring their response to acetylcholine and sodium nitroprusside. The impact of elevated TMAO levels on cardiac function and infarct size caused by ischemia-reperfusion injury was evaluated in Langendorff perfused heart model. Normal and forced heart functioning was analyzed by echocardiography in CD-1 mouse acute cardiac stress model induced by isoproterenol (10 µg/mouse) upon single and 7 repeated daily administrations of TMAO (120 mg/kg). The data presented in the manuscript provide valuable information on measurements performed under conditions of acutely elevated TMAO levels in experimental models of cardiac and vascular function and energy metabolism. Furthermore, the data have high reuse potential as they could be applied in the planning of future <i>in vitro, ex vivo</i>, and <i>in vivo</i> studies addressing the molecular mechanisms targeted by elevated levels of TMAO.
Data from A Phase I, First-in-Human Study of AMG 780, an Angiopoietin-1 and -2 Inhibitor, in Patients with Advanced Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To assess the toxicity, pharmacokinetics, tumor vascular response, tumor response, and pharmacodynamics of AMG 780, a mAb designed to inhibit the interaction between angiopoietin-1 and -2 and the Tie2 receptor.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; This was a phase I dose-escalation study of patients with advanced solid tumors refractory to standard treatment without previous antiangiogenic treatment. AMG 780 was administered by intravenous infusion every 2 weeks in doses from 0.1 to 30 mg/kg. The primary endpoints were incidences of dose-limiting toxicity (DLT) and adverse events (AE), and pharmacokinetics. Secondary endpoints included tumor response, changes in tumor volume and vascularity, and anti-AMG 780 antibody formation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Forty-five patients were enrolled across nine dose cohorts. Three patients had DLTs (0.6, 10, and 30 mg/kg), none of which prevented dose escalation. At 30 mg/kg, no MTD was reached. Pharmacokinetics of AMG 780 were dose proportional; median terminal elimination half-life was 8 to 13 days. No anti-AMG 780 antibodies were detected. At week 5, 6 of 16 evaluable patients had a &gt;20% decrease in volume transfer constant (&lt;i&gt;K&lt;/i&gt;&lt;sup&gt;trans&lt;/sup&gt;), suggesting reduced capillary blood flow/permeability. The most frequent AEs were hypoalbuminemia (33%), peripheral edema (29%), decreased appetite (27%), and fatigue (27%). Among 35 evaluable patients, none had an objective response; 8 achieved stable disease.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; AMG 780 could be administered at doses up to 30 mg/kg every 2 weeks in patients with advanced solid tumors. AMG 780 treatment resulted in tumor vascular effects in some patients. AEs were in line with toxicity associated with antiangiopoietin treatment. &lt;i&gt;Clin Cancer Res; 22(18); 4574–84. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
A Survey of Wireless Power Transfer and a Critical Comparison of Inductive and Capacitive Coupling for Small Gap Applications (2015)

Inductive power transfer (IPT) and capacitive power transfer (CPT) are the two most pervasive methods of wireless power transfer (WPT). IPT is the most common and is applicable to many power levels and gap distances. Conversely, CPT is only applicable for power transfer applications with inherently small gap distances due to constraints on the developed voltage. Despite limitations on gap distance, CPT has been shown to be viable in kilowatt power level applications. This paper provides a critical comparison of IPT and CPT for small gap applications, wherein the theoretical and empirical limitations of each approach are established. A survey of empirical WPT data across diverse applications in the last decade using IPT and CPT technology graphically compares the two approaches in power level, gap distance, operational frequency, and efficiency, among other aspects. The coupler volumetric power density constrained to small gap sizes is analytically established through theoretical physical limitations of IPT and CPT. Finally, guidelines for selecting IPT or CPT in small gap systems are presented.
Bisebromoamide, an extract from Lyngbya species, induces apoptosis through ERK and mTOR inhibitions in renal cancer cells (2013)

Advanced renal cell carcinoma (RCC) remains an incurable disease, and newer anticancer drugs are needed. Bisebromoamide, a novel cytotoxic peptide, was isolated from the marine cyanobacterium Lyngbya species at our laboratory in 2009. This compound specifically inhibited the phosphorylation of ERK in platelet-derived growth factor-activated normal rat kidney cells. The aim of this study was to evaluate the effect and elucidate the potential mechanism of Bisebromoamide actions on human RCC cells. Two renal cancer cell lines, 769-P and 786-O, were used. The effects of Bisebromoamide were analyzed employing assays for water-soluble Tetrazolium-1 salts. Apoptosis was determined by flow cytometric TUNEL analysis. Cell-cycle distributions were analyzed by flow cytometry using BrdU/propidium iodide (PI) staining. Kinases of the phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of Rapamycin (mTOR) pathway and Raf/MEK/ERK pathway were analyzed by Western blotting. After Bisebromoamide treatment for 48 and 72 h, cell viability was significantly decreased in both cell lines at 1 and 10 μmol/L. After treatment with 1 μmol/L Bisebromoamide for 72 h, apoptosis and the increased percentage of cells in the sub-G1 phase were observed in both cell lines. Bisebromoamide inhibited the phosphorylation of ERK and Akt in both cell lines tested. Similar effects were demonstrated for phosphorylation of mTOR and p70 S6. Bisebromoamide is a promising potential agent against RCC due to its ability to inhibit both the Raf/MEK/ERK and PI3K/Akt/mTOR pathways.
Enacting responsibility assignment in software development environments (2008)

In this paper we present the concept of responsibility assignment and its use as a governance mechanism in a software development environment. We review common representations of responsibility assignments, their relationship to the operational model of software engineering and the semantics required to automate their enactment in development tools. We also present a vision for enactment scenarios in tools and compare with the process extensibility mechanisms currently implemented in the Jazz Team Platform.
Inversion Of Travel Time For Velocity (1983)

Common source velocities and borehole compensated (BC) estimates have been used to obtain formation velocity estimates from full waveform acoustic logs (Willis and Toksoz, 1982). With both of these methods the receiver separation of the tool dictates the depth resolution of the velocities determined. This paper presents a method to 1) increase the depth resolution of the velocity estimates, and 2) remove the effects of a changIng borehole radius upon the velocity estimates through formal inversion of arrival times and travel time moveouts. Results obtained by the inversion of full waveform acoustic log travel times appear quite promising. The velocity estimates on synthetic arrival times are slightly more noisy than those obtained using the standard BC technique. The most significant aspect of synthetic arrival times is that they generally appear to be unbiased. The BC technique is biased around formation boundaries and is especially biased for thin layers.
Offline Policy Evaluation for Learning-based Deep Brain Stimulation Controllers (2022)

Deep brain stimulation (DBS) is an effective procedure to treat motor symptoms caused by nervous system disorders such as Parkinson's disease (PD). Although existing implantable DBS devices can suppress PD symptoms by delivering fixed periodic stimuli to the Basal Ganglia (BG) region of the brain, they are considered inefficient in terms of energy and could cause side-effects. Recently, reinforcement learning (RL)-based DBS controllers have been developed to achieve both stimulation efficacy and energy efficiency, by adapting stimulation parameters (e.g., pattern and frequency of stimulation pulses) to the changes in neuronal activity. However, RL methods usually provide limited safety and performance guarantees, and directly deploying them on patients may be hindered due to clinical regulations. Thus, in this work, we introduce a model-based offline policy evaluation (OPE) methodology to estimate the performance of RL policies using historical data. As a first step, the BG region of the brain is modeled as a Markov decision process (MDP). Then, a deep latent MDP (DL-MDP) model is learned using variational inference and previously collected control trajectories. The performance of RL controllers is then evaluated on the DL-MDP models instead of patients directly, ensuring safety of the evaluation process. Further, we show that our method can be integrated into offline RL frameworks, improving control performance when limited training data are available. We illustrate the use of our methodology on a computational Basal Ganglia model (BGM); we show that it accurately estimates the expected returns of controllers trained following state-of-the-art RL frameworks, outperforming existing OPE methods designed for general applications.
Schemaless Queries over Document Tables with Dependencies (2019)

Unstructured enterprise data such as reports, manuals and guidelines often contain tables. The traditional way of integrating data from these tables is through a two-step process of table detection/extraction and mapping the table layouts to an appropriate schema. This can be an expensive process. In this paper we show that by using semantic technologies (RDF/SPARQL and database dependencies) paired with a simple but powerful way to transform tables with non-relational layouts, it is possible to offer query answering services over these tables with minimal manual work or domain-specific mappings. Our method enables users to exploit data in tables embedded in documents with little effort, not only for simple retrieval queries, but also for structured queries that require joining multiple interrelated tables.
HLA-Matched Allogeneic iPS Cells-Derived RPE Transplantation for Macular Degeneration (2020)

Immune attacks are key issues for cell transplantation. To assess the safety and the immune reactions after iPS cells-derived retinal pigment epithelium (iPS-RPE) transplantation, we transplanted HLA homozygote iPS-RPE cells established at an iPS bank in HLA-matched patients with exudative age-related macular degeneration. In addition, local steroids without immunosuppressive medications were administered. We monitored immune rejections by routine ocular examinations as well as by lymphocytes-graft cells immune reaction (LGIR) tests using graft RPE and the patient's blood cells. In all five of the cases that underwent iPS-RPE transplantation, the presence of graft cells was indicated by clumps or an area of increased pigmentation at 6 months, which became stable with no further abnormal growth in the graft during the 1-year observation period. Adverse events observed included corneal erosion, epiretinal membrane, retinal edema due to epiretinal membrane, elevated intraocular pressure, endophthalmitis, and mild immune rejection in the eye. In the one case exhibiting positive LGIR tests along with a slight fluid recurrence, we administrated local steroid therapy that subsequently resolved the suspected immune attacks. Although the cell delivery strategy must be further optimized, the present results suggest that it is possible to achieve stable survival and safety of iPS-RPE cell transplantation for a year.
An efficient wideband numerical simulation technique for nanostructures comprised of DCP media (2017)

This work presents an efficient time domain numerical approach to simulate the wideband response of Drude-critical point (DCP) media. Based on previous research and development of the Discontinuous Galerkin Time Domain (DGTD) method, this approach applies the collocated E-J scheme to discretize the electric fields and polarization currents. A hybridization of the Runge-Kutta and Newmark methods is also proposed to solve the associated first-order and second-order temporal auxiliary differential equations. The effectiveness and efficiency of this new approach is validated through comparison with commercial software.
Supplementary Figure 2 from Toll-like Receptor 9 Agonist IMO Cooperates with Cetuximab in <i>K</i>-<i>Ras</i> Mutant Colorectal and Pancreatic Cancers (2023)

&lt;p&gt;PDF file - 1498KB&lt;/p&gt;