gebhart/patrepeval huggingface dataset:
Anephrogenic phenotype induced by SALL1 gene knockout in pigs (2019)

To combat organ shortage in transplantation medicine, a novel strategy has been proposed to generate human organs from exogenous pluripotent stem cells utilizing the developmental mechanisms of pig embryos/foetuses. Genetically modified pigs missing specific organs are key elements in this strategy. In this study, we demonstrate the feasibility of using a genome-editing approach to generate anephrogenic foetuses in a genetically engineered pig model. SALL1 knockout (KO) was successfully induced by injecting genome-editing molecules into the cytoplasm of pig zygotes, which generated the anephrogenic phenotype. Extinguished SALL1 expression and marked dysgenesis of nephron structures were observed in the rudimentary kidney tissue of SALL1-KO foetuses. Biallelic KO mutations of the target gene induced nephrogenic defects; however, biallelic mutations involving small in-frame deletions did not induce the anephrogenic phenotype. Through production of F1 progeny from mutant founder pigs, we identified mutations that could reliably induce the anephrogenic phenotype and hence established a line of fertile SALL1-mutant pigs. Our study lays important technical groundwork for the realization of human kidney regeneration through the use of an empty developmental niche in pig foetuses.
Real-Time Investigation of Tuberculosis Transmission: Developing the Respiratory Aerosol Sampling Chamber (RASC) (2016)

Knowledge of the airborne nature of respiratory disease transmission owes much to the pioneering experiments of Wells and Riley over half a century ago. However, the mechanical, physiological, and immunopathological processes which drive the production of infectious aerosols by a diseased host remain poorly understood. Similarly, very little is known about the specific physiological, metabolic and morphological adaptations which enable pathogens such as Mycobacterium tuberculosis (Mtb) to exit the infected host, survive exposure to the external environment during airborne carriage, and adopt a form that is able to enter the respiratory tract of a new host, avoiding innate immune and physical defenses to establish a nascent infection. As a first step towards addressing these fundamental knowledge gaps which are central to any efforts to interrupt disease transmission, we developed and characterized a small personal clean room comprising an array of sampling devices which enable isolation and representative sampling of airborne particles and organic matter from tuberculosis (TB) patients. The complete unit, termed the Respiratory Aerosol Sampling Chamber (RASC), is instrumented to provide real-time information about the particulate output of a single patient, and to capture samples via a suite of particulate impingers, impactors and filters. Applying the RASC in a clinical setting, we demonstrate that a combination of molecular and microbiological assays, as well as imaging by fluorescence and scanning electron microscopy, can be applied to investigate the identity, viability, and morphology of isolated aerosolized particles. Importantly, from a preliminary panel of active TB patients, we observed the real-time production of large numbers of airborne particles including Mtb, as confirmed by microbiological culture and polymerase chain reaction (PCR) genotyping. Moreover, direct imaging of captured samples revealed the presence of multiple rod-like Mtb organisms whose physical dimensions suggested the capacity for travel deep into the alveolar spaces of the human lung.
Automatic Steering of Manually Inserted Needles (2013)

Bevel-tipped flexible needles can be robotically steered to reach clinical targets along curvilinear paths in 3D. Manual needle insertion allows the clinician to control the insertion speed, ensuring patient safety. This paper presents a control law for automatic 3D steering of manually inserted flexible needles, enabling path-following control. A look-ahead proportional controller for position and orientation is presented. The look-ahead distance is a linear function of insertion speed. Simulations in a 3D brain-like environment demonstrate the performance of the proposed controller. Experimental results also show the feasibility of this technique in 2D and 3D environments.
Fine tuning of Piezo1 Expression and Activity Ensures Efficient Myoblast Fusion during Skeletal Myogenesis (2020)

Abstract Mechanical stimuli such as stretch and resistance training are essential to regulate growth and function of skeletal muscle. However, the molecular mechanisms involved in sensing mechanical stress during muscle formation remain unclear. Here, we investigate the role of the mechano-sensitive ion channel Piezo1 during myogenic progression. Direct manipulation of Piezo1 in muscle stem cells alters their myogenic progression. Indeed, Piezo1 knockdown suppresses myoblast fusion leading to smaller myotubes. Such event is accompanied by significant downregulation of the fusogenic protein Myomaker . In parallel, while Piezo1 knockdown also lowers Ca 2+ influx in response to stretch, Piezo1 activation increases Ca 2+ influx in response to stretch and enhances myoblasts fusion. We believe these findings may help understand molecular defects present in some muscle diseases. Altogether our study shows that Piezo1 is essential for terminal muscle differentiation acting on myoblast fusion, suggesting that Piezo1 deregulation may have implications in muscle aging and degenerative diseases including muscular dystrophies.
Spectral polarimetry with a differential group delay bias (2004)

We show that the addition of a polarization controller and bias differential group delay to a spectral polarimeter increases the amount of polarization information that can be extracted from a Stokes spectrum measurement. We use this biased spectral polarimetry on 40-Gbit/s signals to measure the polarization mode dispersion of the optical fiber through which they propagate. Our measurements do not require any control of the polarization at the fiber input. Averaging measurements from several settings of the polarization controller yields improved accuracy, and, after data rejection is applied, both the accuracy and the number of valid data points is increased when using several measurements.
Improved upper bounds for the number of points on curves over finite\n fields (2002)

We give new arguments that improve the known upper bounds on the maximal\nnumber N_q(g) of rational points of a curve of genus g over a finite field F_q\nfor a number of pairs (q,g). Given a pair (q,g) and an integer N, we determine\nthe possible zeta functions of genus-g curves over F_q with N points, and then\ndeduce properties of the curves from their zeta functions. In many cases we can\nshow that a genus-g curve over F_q with N points must have a low-degree map to\nanother curve over F_q, and often this is enough to give us a contradiction. In\nparticular, we able to provide eight previously unknown values of N_q(g),\nnamely: N_4(5) = 17, N_4(10) = 27, N_8(9) = 45, N_{16}(4) = 45, N_{128}(4) =\n215, N_3(6) = 14, N_9(10) = 54, and N_{27}(4) = 64. Our arguments also allow us\nto give a non-computer-intensive proof of the recent result of Savitt that\nthere are no genus-4 curves over F_8 having exactly 27 rational points.\nFurthermore, we show that there is an infinite sequence of q's such that for\nevery g with 0 &lt; g &lt; log_2 q, the difference between the Weil-Serre bound on\nN_q(g) and the actual value of N_q(g) is at least g/2.\n
Deriving User- and Content-specific Rewards for Contextual Bandits (2019)

Bandit algorithms have gained increased attention in recommender systems, as they provide effective and scalable recommendations. These algorithms use reward functions, usually based on a numeric variable such as click-through rates, as the basis for optimization. On a popular music streaming service, a contextual bandit algorithm is used to decide which content to recommend to users, where the reward function is a binarization of a numeric variable that defines success based on a static threshold of user streaming time: 1 if the user streamed for at least 30 seconds and 0 otherwise. We explore alternative methods to provide a more informed reward function, based on the assumptions that streaming time distribution heavily depends on the type of user and the type of content being streamed. To automatically extract user and content groups from streaming data, we employ ”co-clustering”, an unsupervised learning technique to simultaneously extract clusters of rows and columns from a co-occurrence matrix. The streaming distributions within the co-clusters are then used to define rewards specific to each co-cluster. Our proposed co-clustered based reward functions lead to improvement of over 25% in expected stream rate, compared to the standard binarized rewards.
PW1/Peg3 expression regulates key properties that determine mesoangioblast stem cell competence (2015)

Mesoangioblasts are vessel-associated progenitor cells that show therapeutic promise for the treatment of muscular dystrophy. Mesoangioblasts have the ability to undergo skeletal muscle differentiation and cross the blood vessel wall regardless of the developmental stage at which they are isolated. Here we show that PW1/Peg3 is expressed at high levels in mesoangioblasts obtained from mouse, dog and human tissues and its level of expression correlates with their myogenic competence. Silencing PW1/Peg3 markedly inhibits myogenic potential of mesoangioblasts in vitro through MyoD degradation. Moreover, lack of PW1/Peg3 abrogates mesoangioblast ability to cross the vessel wall and to engraft into damaged myofibres through the modulation of the junctional adhesion molecule-A. We conclude that PW1/Peg3 function is essential for conferring proper mesoangioblast competence and that the determination of PW1/Peg3 levels in human mesoangioblasts may serve as a biomarker to identify the best donor populations for therapeutic application in muscular dystrophies.
A Hybrid Electrochemical/Chemical Synthesis of Supported, Luminescent Cadmium Sulfide Nanocrystals (1997)

A hybrid electrochemical/chemical (E/C) method is employed to synthesize epitaxially oriented CdS nanocrystallitessize selectivelyon graphite surfaces. The E/C synthesis involves three steps: (1) cadmium metal nanocrystals (NCs) are electrochemically deposited on the graphite basal plane surface; (2) cadmium NCs are oxidized at high pH to Cd(OH)2; (3) upon immersion of the Cd(OH)2 NCs in an aqueous sulfide solution, displacement of OH- by S2- occurs yielding wurtzite phase NCs of the semiconducting salt, cadmium sulfide. Dispersions of E/C-synthesized CdS nanocrystallites having mean diameters ranging from 20 to 80 Å were prepared and characterized using noncontact scanning force microscopy, transmission and high-resolution electron microscopy, selected area electron diffraction, and micrometer-scale spatially resolved photoluminescence spectroscopy. It is demonstrated that individual CdS nanocrystals are oriented with the c-axis of the crystallite perpendicular to basal plane (i.e. (0001)), and NCs located within the boundaries of a single grain on the graphite basal plane possess identical azimuthal orientations. Photoluminescence spectra reveal transitions that are assigned to band gap and surface trap states.
Nonparametric Signal Extraction and Measurement Error in the Analysis of Electroencephalographic Activity During Sleep (2009)

We introduce methods for signal and associated variability estimation based on hierarchical nonparametric smoothing with application to the Sleep Heart Health Study (SHHS). SHHS is the largest electroencephalographic (EEG) collection of sleep-related data, which contains, at each visit, two quasi-continuous EEG signals for each subject. The signal features extracted from EEG data are then used in second level analyses to investigate the relation between health, behavioral, or biometric outcomes and sleep. Using subject specific signals estimated with known variability in a second level regression becomes a nonstandard measurement error problem. We propose and implement methods that take into account cross-sectional and longitudinal measurement error. The research presented here forms the basis for EEG signal processing for the SHHS.
Interfacial Behavior of Anionically Synthesized Amphiphilic Star Block Copolymers Based on Polybutadiene and Poly(ethylene oxide) at the Air/Water Interface (2005)

We describe the preparation and the surface properties of monolayers of a new set of (PB-b-PEO)4 amphiphilic four-arm star block copolymers. A divergent anionic polymerization method yielded copolymers with well-defined molecular weights, block volume fractions, and architecture. Initially, tri- and tetracarbanionic initiators were used to initiate the polymerization of butadiene followed by end-capping of living chains with ethylene oxide. The tri- and tetrafunctionalities of the resulting hydroxyl-terminated star polydienes were confirmed by 1H NMR spectroscopy. The four-arm star polymeric alcohols were then titrated with diphenylmethylpotassium to yield the analogous potassium alkoxides. The resulting macroinitiators were used to polymerize corona blocks of ethylene oxide. Different samples of well-defined (PB-b-PEO)4 amphiphilic star block copolymers exhibiting narrow molar mass distribution were prepared with poly(ethylene oxide) over a range of volume fractions. Isotherm experiments at the air/water interface showed the following three characteristic regions: a compact brush region, a pseudoplateau at a pressure of ca. 10 mN/m, and a pancake region where the observed surface area depended on the amount of PEO present. The elasticity properties of the monolayer were examined by repetative compression/expansion cycles and resulted in reproducible hysteresis at different pressures. The monolayers were also transferred as Langmuir−Blodgett films on mica at various surface pressures and analyzed by atomic force microscopy (AFM), demonstrating different morphologies from analogous (PS-b-PEO)4 star copolymers.
Characteristics of 5-eV absorption band in sputter deposited GeO2-SiO2 thin glass films (1994)

Thin films (4.6 μm thick) of 5 GeO2-95 SiO2 and 55 GeO2-45 SiO2 (mol %) glasses were prepared by rf sputtering method in an Ar-O2 atmosphere. An intense absorption band at around 5 eV was distinctly observed in both films after the as-deposited films were annealed at 350 °C for 30 min in a vacuum. A part of this 5-eV band was gradually decreased by UV irradiation. Saturated absorptivity changes (−Δα∞) of the UV bleached component, which is considered to be the origin of Hill gratings [K. O. Hill, Y. Fujii, and B. S. Kawasaki, Appl. Phys. Lett. 32, 647 (1978)] and second-harmonic generation in SiO2 glass fibers doped with GeO2, after a prolonged irradiation were 50 cm−1 for 5 GeO2-95 SiO2 films and 400 cm−1 for 55 GeO2-45 SiO2 films. These values are greater by one or two orders of magnitude than those (∼2 cm−1) of bulk germanosilicate glasses prepared by the vapor axial deposition method.
Old and new prognostic factors in a series of 910 patients with malignant pleural mesothelioma (MPM). (2014)

7586 Background: Whilst the prognosis of most MPM patients is poor, a small proportion demonstrate long term survival. We investigate patient and treatment factors associated with survival and the impact of chemotherapy (CT) and surgery in a large patient series. Methods: Data sets of patients registered with the NSW Dust Diseases Board (2002-2009) were reviewed and prognostic factors such as age, gender, histological subtype and stage evaluated using Kaplan-Meier and Cox regression analysis. The impact of treatment, smoking and asbestos exposure were evaluated and subgroup analyses explored long(er) (>20 months) vs. short(er) (< 20 months) survivors. Results: We identified 910 patients: 90% male; median age 72 yrs; histological subtype (epithelioid 60%; biphasic 13%; sarcomatoid 17%; unknown 10%); stage (Tx-I-II 48%; III-IV 52%); calretinin expression (74.8%). Treatment: CT 41%, extrapleural pneumonectomy (EPP) 6%. Median age of first occupational asbestos exposure was 18 yrs; cumulative exposure 24 yrs. Median overall survival (OS) was 10.1 mo. Longer OS (p<0.001) was associated with: age <70yrs (13.5 vs. 8.5 mo.); female gender (12.0 vs. 9.9 mo.); epithelioid subtype (13.4 vs. 6.2 mo.); calretinin expression (11.0 vs. 5.5 mo.); NLR (neutrophil lymphocyte ratio) <5 (12.0 vs. 7.5 mo.); platelets <400 (11.6 vs. 7.1 mo.); and normal hemoglobin (16.6 vs 8.8). Patients undergoing CT (15.6 vs. 6.6 months; p<0.001) and EPP (24.8 vs. 9.5 months; p<0.001) had improved survival. Smoking history and cumulative asbestos exposure did not affect survival. On multivariate analysis, all variables remained significant, including EPP and CT use (time dependent analysis). 24% of patients survived >20 months: 16% underwent EPP, 61% received CT; but 31% received neither. Epithelioid histology, calretinin expression, age, stage and hemoglobin levels were independently associated with survival >20 months. Conclusions: In this large, population-based series, we validated calretinin expression, age, gender, histological subtype, stage and NLR as significant prognostic factors. Patients undergoing EPP/CT demonstrated better survival but 84% and 39% of long survivors respectively did not receive EPP or chemotherapy.
Applications of Wide-Band-Gap Materials for Optoelectronic Functional Devices Fabricated by a Pair of Interfering Femtosecond Laser Pulses (2005)

A pair of interfering near-IR femtosecond pulses from a mode-locked Ti:sapphire laser with a regenerative amplifier have been applied to wide-band-gap materials such a lithium fluoride (LiF) to create laser-active F 2 and F 3 + color centers and to encode nonerasable periodic gratings with fine fringe spacings of submicrometer size simultaneously. Using such a photon-written microstructure, a distributed-feedback LiF laser oscillation based on F 2 color centers has been realized at room temperature. A lasing output performance with a linewidth of less than 1 nm, slope efficiency of ∼10%, and beam divergence of ∼20 mrad was obtained at 710 nm.
ChemInform Abstract: Ethenesulfonamide Derivatives, a Novel Class of Orally Active Endothelin‐A Receptor Antagonists. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Luderitz Port expansion plans - an innovative approach (2011)

Luderitz Port is the second major port of Namibia. The main berth of the port is a 500m long concrete quay with alongside depth of 8.15m to 4.70m at LAT. The present throughput of the port is about 350,000 tonnes per annum. The main commodities being handled at the port are diesel oil, sulphur, zinc ingot, frozen and wet fish, ice and containers. The port is surrounded by dense population and has very limited area for landside expansion. At present the port doesn't have rail connectivity. A light railway link with a capacity of 1 million tonnes per annum (Mtpa) is under construction which is expected to be completed by 2014. The trade analysis revealed that throughput of the port could be increased substantially, if required equipment, storage and a heavy haul rail linkage is provided. The port has a potential of being developed as a major resource export centre. The throughput of the port could increase to 775,000 tonnes per annum if the port could provide additional equipment, cold storage and container, reefer and break bulk cargo handling facilities. After the light railway is commissioned, the port could get up to 1 Mtpa (limited by railway capacity) of manganese for export. However if a heavy haul railway linkage could be established the port could achieve solid bulk export of up to 50 Mtpa. Considering the trade forecast and limitation of the finances, a three phase expansion plan has been developed for the port. The Phase I and Phase II port development plans are seamless plans, aimed at increasing the utilisation of existing assets at Robert Harbour. In Phase II transhipment facilities for export of manganese in bulk has been introduced as a low cost solution to increase the throughput of the port. In Phase III, major solid bulk material handling facilities are proposed to be built at Angra Point (a new site).
Creation and Implementation of a Backpack Course to Teach Cross-Cultural and Virtual Communications Skills to Students in an International Capstone Experience (2020)

As international engineering teams become more prevalent, universities need to adapt educational opportunities to prepare students to work in a global environment. As part of an NSF grant to study global, virtual, engineering teams, a backpack course designed to teach crosscultural competencies and virtual communication skills to engineering students was created. The course is taught concurrently to students participating in a global, virtual, engineering capstone team experience. This educational experience mixes practical hands-on experience of working on a global virtual team with instruction designed to help facilitate global virtual team interactions. This paper discusses the creation, implementation and revisions of this course's first year of implementation. It will highlight course content as well as practical considerations in teaching such a course.
Identifying audio clips with RARE (2003)

In this paper, we describe RARE (Robust Audio Recognition Engine): a system for identifying audio streams and files. RARE can be used in a variety of applications: from enhancing the consumer listening experience to cleaning large audio databases. RARE was designed with two key qualities in mind: robustness to distortion of the audio, and lookup speed. RARE identifies audio clips in a stream against a database of 1/4 million songs in real time using approximately 10% CPU on an 850 MHz P3, and with a measured false positive rate of 1.5x10-8 per clip, per database entry, at a false negative rate of 0.2% per clip. We demo RARE in real-time on a stream and on distorted files.
High Performance White OLED for Lighting Applications (2010)

The development of white-light-emitting OLEDs for general lighting will be introduced. High external quantum efficiency of 25[[Unsupported Character - ?]]30% achieved by phosphorescent emitters and long device lifetime achieved by using the multiphoton structure will be discussed. Article not available.
Members of Prevotella Genus Distinctively Modulate Innate Immune and Barrier Functions in a Human Three-Dimensional Endometrial Epithelial Cell Model (2020)

Collectively, findings indicate that Prevotella species are metabolically diverse and overall not cytotoxic or overtly inflammatory in EEC; however, these bacteria can form biofilms, alter barrier properties of the endometrial epithelium, and ultimately impact colonization of secondary colonizers.
Suppression of the critical current of a balanced superconducting quantum interference device (2008)

We present an experimental study of the magnetic flux dependence of the critical current of a balanced superconducting quantum interference device (SQUID) with three Josephson junctions in parallel. Unlike for ordinary direct current (dc) SQUIDs, the suppression of the critical current does not depend on the exact parameters of the Josephson junctions. The suppression is essentially limited only by the inductances of the SQUID loops. We demonstrate a critical current suppression ratio of higher than 300 in a balanced SQUID with a maximum critical current 30nA.