gebhart/patrepeval huggingface dataset:
Best Entry Pages for the Topic Distillation Task (2013)

In a typical web search, users consider entry pages to rele-vant sites as more valuable than isolated pieces of relevant text. The Topic Distillation Task aims at identifying the page at the right level of site hierarchy considered to pro-vide optimal access, by browsing, to relevant pages within the site, i.e. its Best Entry Page. Our aim is to estimate a measure of how good a page is as an entry page to the site it belongs, by aggregating the page’s system-assessed relevance with that of its structurally related, Web pages belonging to the same site. To model this aggregation, we propose a framework which is expressed within Dempster-Shafer Theory of Evidence. Furthermore,we generalise our model by taking into account other system-assessed proper-ties of Web pages. Apart from their relevance, the authority and hub properties of Web pages are considered in the ag-gregation. We evaluate our approach by performing exper-iments using the.GOV test collection. The results of these experiments are promising.
Unusual N-Glycan Structures in α-Mannosidase II/IIx Double Null Embryos Identified by a Systematic Glycomics Approach Based on Two-dimensional LC Mapping and Matrix-dependent Selective Fragmentation Method in MALDI-TOF/TOF Mass Spectrometry (2006)

alpha-Mannosidase IIx (MX) is an enzyme closely related to alpha-mannosidase II (MII), a key enzyme in N-glycan biosynthesis that catalyzes the first step in conversion of hybrid- to complex-type N-glycans in Golgi apparatus. Recently we generated MII/MX double knock-out mice and found that double nulls completely lack the complex-type N-glycans (Akama, T. O., Nakagawa, H., Wong, N. K., Sutton-Smith, M., Dell, A., Morris, H. R., Nakayama, J., Nishimura, S.-I., Pai, A., Moremen, K. W., Marth, J. D., and Fukuda, M. N. (2006) Essential and mutually compensatory roles of alpha-mannosidase II and alpha-mannosidase IIx in N-glycan processing in vivo in mice. Proc. Natl. Acad. Sci. U. S. A. 103, 8983-8988). In the present study, we determined minor but unusual N-glycan structures found in MII/MX double knock-out mice. We identified such N-glycans by a systematic glycomics approach applying a two-dimensional LC mapping database and matrix-dependent selective fragmentation technique in MALDI-TOF/TOF MS, a highly sensitive and reliable technique that provides specific fragmentations enabling the determination of precise oligosaccharide structures including regioisomers (Kurogochi, M., and Nishimura, S.-I. (2004) Structural characterization of N-glycopeptides by matrix-dependent selective fragmentation of MALDI-TOF/TOF tandem mass spectrometry. Anal. Chem. 76, 6097-6101). Quantitative profiling of all N-glycan structures including minor components from MII/MX nulls, MII nulls, MX nulls, and wild-type mice at embryonic day 15.5 yielded a total of 37 species when structural heterogeneity was reduced by the removal of the sialic acids. Among six unusual N-glycan structures, two glycoforms were novel and were found only in MII/MX double nulls. We characterize such structure as pseudocomplex-type N-glycans. The present study demonstrated that use of the versatile matrix-dependent selective fragmentation method in MALDI-TOF/TOF MS greatly accelerates detailed structural analysis of a trace amount of N-glycans.
New high bandwidth single polarization fiber with elliptical central air hole (2005)

A new single polarization fiber with an elliptical central air hole is proposed. Effects of fiber design parameters on fiber performance are analyzed. Single polarization bandwidth as high as 240 nm is predicted.
A deep neural-network classifier for photograph-based estimation of hearing protection attenuation and fit (2021)

Occupational and recreational acoustic noise exposure is known to cause permanent hearing damage and reduced quality of life, which indicates the importance of noise controls including hearing protection devices (HPDs) in situations where high noise levels exist. While HPDs can provide adequate protection for many noise exposures, it is often a challenge to properly train HPD users and maintain compliance with usage guidelines. HPD fit-testing systems are commercially available to ensure proper attenuation is achieved, but they often require specific facilities designed for hearing testing (e.g., a quiet room or an audiometric booth) or special equipment (e.g., modified HPDs designed specifically for fit testing). In this study, we explored using visual information from a photograph of an HPD inserted into the ear to estimate hearing protector attenuation. Our dataset consists of 960 unique photographs from four types of hearing protectors across 160 individuals. We achieved 73% classification accuracy in predicting if the fit was greater or less than the median measured attenuation (29 dB at 1 kHz) using a deep neural network. Ultimately, the fit-test technique developed in this research could be used for training as well as for automated compliance monitoring in noisy environments to prevent hearing loss.
Author response: Cyclin D activates the Rb tumor suppressor by mono-phosphorylation (2014)

Cells go through a tightly controlled, multi-step procedure before they divide. This cell division program—the cell cycle—is necessary for preventing unrestrained cellular growth, which may lead to cancer. Proteins called cyclins control the progression through each of the phases of the cell cycle, with different cyclins working during different phases. During the G1 phase of the cell cycle, cells grow in size and produce the proteins that are required to copy DNA. Once a cell passes a checkpoint called the 'restriction point' at the end of the G1 phase, it is committed to dividing. It is therefore particularly important to keep events during G1 phase in check. The Retinoblastoma tumor suppresor protein (Rb) is a key player in regulating the G1 phase. Rb sequesters transcription factors that are essential for the cell cycle to progress. Previously, it was thought that a complex called cyclin D added more and more phosphates to the Rb protein during the G1 phase. This process predicted a slow release of transcription factors, which attach to DNA and start the process of DNA replication. While many studies have presented data that is consistent with this model, direct biochemical evidence of these events is lacking. Narasimha, Kaulich, Shapiro et al. now present biochemical analyses of Rb proteins that show—completely unexpectedly—that the cyclin D complex adds just one phosphate group to Rb during the G1 phase, although this group can be added to one of fourteen different sites. The resulting 'mono-phosphorylated' Rb varieties can each sequester different transcription factors and stop them working. At the restriction point, many more phosphate groups are then rapidly added, and the Rb protein is inactivated by a different cyclin. This cyclin—called Cyclin E—then drives cells into the next phase of the cell cycle. Establishing how cyclin E is activated is a priority for future research.
Experimentally Tractable, Pseudo-elastic Constitutive Law for Biomembranes: II. Application (2003)

This is the second paper of a 2 part series. In the first, a theoretical framework is developed that provides 3 enhancements for the constitutive theory of biomembranes. 1) Covariance amongst response terms is minimized, 2) the pseudo-strain-energy potential is redefined so as to be measurable, and 3) the stress response is decomposed into 2 parts--a hyperelastic part plus a hypoelastic-stress-residual. This paper illustrates the experimental advantages of this novel constitutive theory via analysis of biaxial test data obtained from chemically treated bovine pericardium.
Premature ventricular extrastimulus without His or ventricular capture: An unexpected response during AV nodal reentrant tachycardia (2018)

A 52-year-old male was referred to our center for catheter ablation of recurrent episodes of paroxysmal supraventricular tachycardia. No relevant abnormalities were observed at his basal ECG and echocar- diogram. Electrophysiological study was performed, and multipolar diagnostic catheters were introduced via the femoral veins. Typical atrioventricular (AV) nodal reentrant tachycardia with a medium rate of 200 bpm was reproducibly induced and diagnosed according to the standard criteria. During ventricular resetting maneuver using the His catheter, an expected phenomenon was observed after applying an early premature ventricular extrastimulus (PVE) (Figure 1). At a first look, the stimulus occurred during the ventricular refractory period without any capture. However, a phase of right bundle branch block (RBBB) occurred immediately after this apparently noncapturing PVE and without any subsequent change in the tachycardia cycle length making rate-dependent RBBB unlikely as a mechanism. The PVE did not capture ventricular myocardium, nor the His bundle (H-H intervals remained unchanged), and the tachycardia was not reset (Figure 1A). The induced RBBB was likely due to local concealed capture of the proximal RBB during its relative refractory period by the applied PVE. The stimulus could generate only an attenuated action potential with slow conduction in the RBB (the asterisk, Figure 1B) unable to advance the next QRS. Nevertheless, the local capture of proximal RBB rendered it unexcitable by the antegrade activation of the ongoing tachycardia. Another possible mechanism is local electrotonus after PVE causing local loss of membrane potential adjacent to the distal RBB and resulting in conduction block of the advancing wave coming down the RBB. Subsequently, RBBB was likely maintained through a linking effect and repetitive retrograde penetration of the RBB by impulses propagating antegradely over the contralateral left bundle (Figure 1C). This case highlights intriguing electrophysiological phenomena that can still be observed during a classical pacing maneuver of a common reentry circuit including concealed capture of the His-Purkinje system, electrotonus, linking effect, and functional aberrancy.
Measuring assurance case confidence using Baconian probabilities (2013)

The basis for assessing the validity of an assurance case is an active area of study. In this paper, we discuss how to assess confidence in a case by considering the doubts eliminated by the claims and evidence in a case. This is an application of eliminative induction and the notion of Baconian probability as put forward by L. Jonathan Cohen.
Physical and Molecular Landscapes of Mouse Glioma Extracellular Vesicles Define Heterogeneity (2019)

Cancer extracellular vesicles (EVs) are highly heterogeneous, which impedes our understanding of their function as intercellular communication agents and biomarkers. To deconstruct this heterogeneity, we analyzed extracellular RNAs (exRNAs) and extracellular proteins (exPTNs) from size fractionation of large, medium, and small EVs and ribonucleoprotein complexes (RNPs) from mouse glioblastoma cells by RNA sequencing and quantitative proteomics. mRNA from medium-sized EVs most closely reflects the cellular transcriptome, whereas small EV exRNA is enriched in small non-coding RNAs and RNPs contain precisely processed tRNA fragments. The exPTN composition of EVs and RNPs reveals that they are closely related by vesicle type, independent of their cellular origin, and single EV analysis reveals that small EVs are less heterogeneous in their protein content than larger ones. We provide a foundation for better understanding of segregation of macromolecules in glioma EVs through a catalog of diverse exRNAs and exPTNs.
Coverage-Dependent Adsorption of Bifunctional Molecules: Detailed Insights into Interactions between Adsorbates (2014)

Adsorption of bifunctional molecules is important for chemical modification of semiconductor surfaces, since such molecules can be used to alter the terminal functionality. In this work, the effect of coverage in the reaction of catechol (1,2-benzenediol) and resorcinol (1,3-benzenediol) with the (100) surface of germanium is investigated by surface spectroscopy experiments and theoretical methods. The benzenediols are site-specifically adsorbed on the Ge surface dimers through dissociative adsorption of either one or two of the −OH groups. Infrared spectroscopy and density functional theory results suggest that the dually tethered products selectively assume certain geometrical configurations at the surface. Infrared and X-ray photoelectron spectroscopies reveal that singly tethered species become increasingly prevalent as the coverage approaches saturation. Monte Carlo simulations that account for specific binding configurations and interadsorbate interactions, identified through density functional theory calculations, quantitatively reproduce the experimentally observed coverage-dependence of singly and dually tethered adsorbates for both benzenediols. Our results indicate that the singly bound adsorbates with unreacted hydroxyls appear on the reactive pristine Ge surface due to a limitation of available adjacent reaction sites, and show that interadsorbate interactions play a major role in determining reaction product distributions.
Phase I Study of Ipilimumab (Neutralizing Monoclonal Anti-CTLA4 Antibody) To Treat Relapse of Malignancy after Allogeneic Hematopoietic Stem Cell Transplantation: Evidence of Tumor Regression without Induction of GVHD. (2006)

Abstract Failure of adoptive cellular immunotherapy is an important cause of relapse of malignancy (RM) and death following allogeneic hematopoietic stem cell transplantation (allo-HCT). CTLA-4 is a negative regulator of activated T-cells. Therapeutic blockade of CTLA-4 has demonstrated potent anti-cancer effects in animal models, and in patients with some solid tumors. Although CTLA-4 blockade may augment graft-versus-malignancy following allo-HCT, GVHD and other immune complications may also be increased. We report the results of a completed phase I dose-escalation trial of a neutralizing human monoclonal anti-CTLA-4 antibody (ipilimumab) in patients with RM following allo-HCT. Eligibility criteria included allo-HCT ≥90 days previously, &amp;gt; 50% donor T-cell chimerism, no prior grade 3/4 GVHD, no prophylaxis/therapy for GVHD for ≥ 6 weeks. Patients received a single dose of ipilimumab over 90 min. (Donor lymphocyte infusion (DLI) at a dose of 5 x 10e6 CD3 cells/kg was allowed 8 weeks following ipilimumab if no GVHD occurred and malignancy was present. Seventeen patients (13M, 4F; median age 42 (21–64); Hodgkin’s disease [HD] =7 Myeloma [MM]=3, CML=2, CLL=1, AML=1, NHL=1, Renal Ca =1, Breast Ca=1; 14 related donors, 3 unrelated; 5 myeloablative, 12 RICT) were treated at three centers (4 at dose-level 1 [DL1] 0.1 mg/kg, 3 at 0.33 mg/kg [DL2], 4 at 0.66 mg/kg [DL3], 3 at 1.0 mg/kg [DL4] and 3 at 3.0 mg/kg [DL5]). Six patients had failed prior DLI. Median time between BMT and ipilimumab was 374 d (125–2368). Seven patients received additional DLI. Ipilimumab was well tolerated in this setting. No DLT was seen at levels up to DL5. No infusional toxicity was seen. No patient developed clinically significant GVHD within 90 days following ipilimumab. One patient developed grade II acute GVHD of the skin 12 weeks following DLI. Two possible immune breakthrough events were documented: grade 3 polyarthropathy 14 weeks following ipilimumab, but also 6 weeks post DLI, which resolved with corticosteroid therapy, (AML, DL1, RhF+ pre- ipilimumab); grade 1 chemical hyperthyroidism with thyroid-stimulating antibody 6 weeks post ipilimumab (CLL, DL3). Two patients developed objective evidence of disease response after ipilimumab alone: regression of refractory lymphadenopathy in a patient with mantle cell NHL lasting 3m [DL4]; CR in a patient with HD ongoing at 2m [DL5].Both patients had failed prior DLI. Two additional patients demonstrated possible anti-cancer effects (reduction of PB and BM blasts in AML, DL1; maintenance of molecular remission in a CML patient given ipilimumab alone for 2.5 yrs despite stopping imatinib, DL1). PK data will be presented. This study shows that clinically active doses of ipilimumab (up to 3.0 mg/kg) can safely be administered to patients with RM following allo-HCT without inducing/exacerbating GVHD. Organ specific immune breakthrough events can be seen as in non-allo-HCT patients.
Waves in Distributed Systems (2017)

The movement of waves down the basilar membrane is analogous to the propagation of light waves in a medium of continuously changing index of refraction. While the velocity of light varies as it travels through the substance, substantial reflections will not occur as long as the index of refraction changes slowly enough.—“The cochlear compromise,” Zweig, Lipes, and Pierce (1976)
Combined scanning probe electronic and thermal characterization of an indium arsenide nanowire (2018)

As electronic devices are downsized, physical processes at the interface to electrodes may dominate and limit device performance. A crucial step towards device optimization is being able to separate such contact effects from intrinsic device properties. Likewise, an increased local temperature due to Joule heating at contacts and the formation of hot spots may put limits on device integration. Therefore, being able to observe profiles of both electronic and thermal device properties at the nanoscale is important. Here, we show measurements by scanning thermal and Kelvin probe force microscopy of the same 60 nm diameter indium arsenide nanowire in operation. The observed temperature along the wire is substantially elevated near the contacts and deviates from the bell-shaped temperature profile one would expect from homogeneous heating. Voltage profiles acquired by Kelvin probe force microscopy not only allow us to determine the electrical nanowire conductivity, but also to identify and quantify sizable and non-linear contact resistances at the buried nanowire-electrode interfaces. Complementing these data with thermal measurements, we obtain a device model further permitting separate extraction of the local thermal nanowire and interface conductivities.
Fabrication Development of a Large Area Grating for Out of Plane Beam Coupling (2020)

We develop a single-layer waveguide surface grating structure to vertically couple near infrared (NIR) light at ~1.55 um wavelength from a large area (~100 um length scale) Si waveguide on a Silicon-On-Insulator (SOI) substrates to free-space for high-power laser applications. Our design approach is based on the optimization of local emission angles and the out-coupling intensities. Simulation results show that a focal spot with a 1/e2 width of 3.82 um can be achieved at the desired focal position, with 33% (-4.81 dB) simulated source to free-space focusing efficiency, while initial measurements show an efficiency of 22% (-6.58 dB).
Developing High Medical Technology, a Challenge for Developing Countries: The Percutaneous Closure of Atrial Septal Defects Using Nit-Occlud ASD-R: Early and Mid-term Results (2019)

The Nit-Occlud ASD-R device is safe and effective with very good closure rates.
Supplementary Figure 1 from Vascular Endothelial Growth Factor Receptor 3 Is Involved in Tumor Angiogenesis and Growth (2023)

Supplementary Figure 1 from Vascular Endothelial Growth Factor Receptor 3 Is Involved in Tumor Angiogenesis and Growth
Head‐to‐Head Comparison of Selected Extra‐ and Intracellular CO‐Releasing Molecules on Their CO‐Releasing and Anti‐Inflammatory Properties (2021)

Over the past decade, a variety of carbon monoxide releasing molecules (CORMs) have been developed and tested. Some CORMs spontaneously release CO once in solution, while others require a trigger mechanism to release the bound CO from its molecular complex. The modulation of biological systems by CORMs depends largely on the spatiotemporal release of CO, which likely differs among the different types of CORMs. In spontaneously releasing CORMs, CO is released extracellularly and crosses the cell membrane to interact with intracellular targets. Other CORMs can directly release CO intracellularly, which may be a more efficient method to modulate biological systems. In the present study, we compared the efficacy of extracellular and intracellular CO-releasing CORMs that either release CO spontaneously or require an enzymatic trigger. The efficacy of such CORMs to modulate HO-1 and VCAM-1 expression in TNF-α-stimulated human umbilical vein endothelial cells (HUVEC) was evaluated.
Efficient induction of apoptosis by ONYX-015 adenovirus in human colon cancer cell lines regardless of p53 status (2002)

The ONYX-015 virus is a mutated adenovirus that in theory selectively replicates and induces cytolysis in tumor cells lacking functional p53. The present study investigated whether ONYX-015 viral infection alone or in combination with conventional chemotherapeutic agents could significantly increase apoptosis in human colon cancer cell lines, regardless of p53 status, compared to untreated cells. A pair of colon cancer cell lines that differ only in their p53 status (RKO with wild-type p53 and RKOp53 with deficient p53) was tested. Two chemotherapeutic agents, 5-fluorouracil (5-FU) and CPT-11, were tested in combination with ONYX-015. Final concentrations of these agents corresponded to peak plasma levels achievable in patients. ONYX-015 concentration was 10 p.f.u./cell. In RKO and RKOp53 cell lines, ONYX-015 viral infection alone or in combination with 5-FU or CPT-11 induced a significant increase in apoptosis compared to chemotherapeutic agents alone, regardless of p53 status. Moreover, the combination of ONYX-015 and chemotherapeutics induced more apoptosis than chemotherapeutics alone in the two colon cancer cell lines independently of their p53 status. We conclude that ONYX-015 virus infection alone or in combination with 5-FU or CPT-11 induced apoptosis in human colon cancer cell lines, independently of p53 status.
Health Effects Associated With Kratom (Mitragyna speciosa) and Polysubstance Use: A Narrative Review (2022)

Increasing medical awareness of this herb is vital to ensuring prompt administration of best-practice medical advice or treatment for people seeking information related to kratom use or for patients experiencing an adverse health effect that may be associated with using or withdrawing from kratom. Knowledge gained from continued surveillance and study of kratom and its associated health effects may assist in guiding clinical decision-making and preventing development of adverse health effects among people using kratom.
Electrodeposition-enabled, electrically-transduced sensors and biosensors (2022)

Electrodeposition and electropolymerization have emerged as versatile tools for the fabrication of chemical and biosensors. The literature in this area, published since 2017, is the main focus of this review. Electropolymerization has played a particularly prominent role in sensor development since its discovery in 1980 by Diaz at IBM. The ability to entrain receptors such as antibodies, engineered virus particles, and metal chelating agents into a conductive polymer sensing element during electropolymerization has proven to be a powerful means of preparing chemiresistors for a variety of analyses. Electrodeposition has also been used to prepare nanostructured metal indicator microelectrodes, enabling of a new modality for transducing biosensors. Electrodeposited metal nanowires have formed the basis for rapid and sensitive sensors for hydrogen gas. Electrodeposition has also been exploited as a powerful means for amplifying weak biosensor signals, extending their dynamic range. Opportunities for the application of electrodeposition and electropolymerization for chemical and biological sensor fabrication and function are discussed.