gebhart/patrepeval huggingface dataset:
Optimization of the CRISPR/Cas9 System to Manipulate Gene Function in Rhizopus delemar (2017)

The genus Rhizopus is the main cause of mucormycosis, a life-threatening infection that affects predominantly hosts with an impaired immune system. However, patients with severe trauma and burns, without prior immune deficiency, are also at increased risk of developing mucormycosis. Despite aggressive treatment that involves disfiguring surgery and antifungal therapy, mortality rates range from ~50 to 100%. Genetic manipulation of Rhizopus is critical for identifying fungal targets to develop more effective therapies. However, Rhizopus genetics are challenging because of lack of dominant selection markers, low efficiency of transformation, and rarity of chromosomal integration. Here we attempted to adapt the CRISPR/Cas9 technology to disrupt genes in R. delemar. We used the Gibson cloning strategy to assemble all necessary elements of the CRISPR/Cas9 system in one plasmid using the pyrF as a selection marker. The targeted gene for disruption was a toxin-encoding gene with similarity to ricin. This disruption cassette was transformed using biolistic delivery system into R. delemar pyrF - strain (M16). Recombination events were studied by Southern blot analysis and ricin gene expression was analyzed by qRT-PCR. Furthermore, damage to alveolar epithelial cells (A549) and nasal epithelial cells (CCL30) was studied with 51Cr-release assay. Five stable transformants were obtained with the CRISPR/Cas9 construct. Southern blot analysis and nucleotide sequencing confirmed a partial deletion of the ricin gene, in the region where the guide RNA was designed. Moreover, gene disruption was confirmed by abrogation of ricin expression in comparison to reference strains (wild type or mutant with the CRISPR/Cas9 plasmid void of ricin gene sequence). Finally, ricin-mutants showed significant reduction in damage to A549 cells and CCL30 cells when compared with the reference strains (20–30% reduction, P < 0.01 by t-test). We have successfully adapted the CRISPR/Cas9 system to disrupt the ricin-like gene in R. delemar. This tool will enable us to better understand the pathogenesis of mucormycosis and ultimately aid in designing novel and more successful strategies to manage this lethal fungal infection. All authors: No reported disclosures.
CHORUS: Foundation Models for Unified Data Discovery and Exploration (2023)

We apply foundation models to data discovery and exploration tasks. Foundation models include large language models (LLMs) that show promising performance on a range of diverse tasks unrelated to their training. We show that these models are highly applicable to the data discovery and data exploration domain. When carefully used, they have superior capability on three representative tasks: table-class detection, column-type annotation and join-column prediction. On all three tasks, we show that a foundation-model-based approach outperforms the task-specific models and so the state of the art. Further, our approach often surpasses human-expert task performance. We investigate the fundamental characteristics of this approach including generalizability to several foundation models and the impact of non-determinism on the outputs. All in all, this suggests a future direction in which disparate data management tasks can be unified under foundation models.
Sustained Cytoplasmic Delivery of Drugs with Intracellular Receptors Using Biodegradable Nanoparticles (2003)

Efficient cytoplasmic delivery of therapeutic agents is especially important for drugs with an intracellular site of action for elicitation of a maximal therapeutic effect. In this study, we demonstrate the efficacy of biodegradable nanoparticles for cytoplasmic delivery of dexamethasone, a glucocorticoid, whose site of action is intracellular. Equal doses of two formulations of drug-loaded nanoparticles releasing different doses of the encapsulated drug were tested for antiproliferative activity in vascular smooth muscle cells. The antiproliferative activity of the drug was significantly greater and sustained with nanoparticles that released a higher dose of the drug than with nanoparticles which released a lower dose of the drug. The greater antiproliferative activity of the nanoparticles that released a higher dose of the drug correlated with sustained and higher intracellular drug levels. The antiproliferative activity of the drug in solution was lower and relatively transient compared to that with drug-loaded nanoparticles. The mechanism of inhibition of cell proliferation was mediated through inhibition of cell-cycle progression with a relatively higher percentage of cells in the G0/G1 arrest phase in the group that was treated with drug-loaded nanoparticles compared to that treated with the drug in solution. Results of the study thus suggest that the dose and duration of a drug's availability at the intracellular site of action determine its therapeutic efficacy. In conclusion, biodegradable nanoparticles could be used as an effective delivery mechanism for sustained intracellular delivery of different therapeutic agents.
A review of the lumped element kinetic inductance detector (2010)

The Lumped Element Kinetic Inductance Detector (LEKID) was first proposed in 2007 as a solution for using kinetic inductance type detectors for sub-mm astronomy (450 - 200μm). Since then the LEKID has been demonstrated to have applications over a much wider range of wavelength. Examples of this have been 200μm detection of a cold blackbody and successful testing of a demonstration array operating at 2mm on the IRAM telescope in October 2009. Due to the combination of absorber and detector in a single element, the LEKID is an extremely simple detector to fabricate requiring only one deposition and etch step to produce an array of up to 1000 pixels multiplexed onto a single feedline. The LEKID is also a very compact detector making it ideal for producing arrays with high filling factors. The suitability of the LEKID for use in large arrays has prompted a return visit to the IRAM telescope with a dual band instrument in 2010. This presentation will review the progress to date of the LEKIDs development and outline design considerations for producing LEKIDs for future FIR astronomical instruments such as SPICA. Also reviewed will be possible applications for the LEKID outside sub-mm and mm astronomy.
Photodarkening and photobleaching of an ytterbium-doped silica double-clad LMA fiber (2007)

We studied the temporal evolution of the photodarkening effect in an Yb-doped silica LMA fiber. The absorption spectra exhibit an increase in absorption in the visible and in the near infrared spectral range when the fiber is exposed to pump light around 980 nm. We show the influence of the photodarkening on the cw lasing properties of the fiber, and demonstrate photobleaching of the same fiber by exposure to UV light at 355 nm. The corresponding absorption spectra and lasing performances are shown and are entirely comparable to those of a new fiber
Surface Characterization of Octadecylamine Films Prepared by Langmuir−Blodgett and Vacuum Deposition Methods by Dynamic Contact Angle Measurements (1999)

The behavior of octadecylamine (ODA) monolayers on various subphases is investigated. The monolayer is then transferred to a hydrophilic glass surface to prepare a LB film of one monolayer. The uniformity, stability, and molecular orientation of the LB films were studied by the measurement of dynamic contact angle and compared with characteristics of vacuum-deposited films. The results show that the ODA monolayer is especially stable on alkaline solution. The LB film transferred from the alkaline solution is stable and uniform in wettability. The advancing and receding contact angles of water on one layer of ODA film are about 113° and 62°, respectively. These values are the same as those on a vacuum-deposited ODA film of equivalent thickness. The growth of ODA on a glass surface in a vacuum deposition is thus found to follow a mode of layer growth. The orientation and arrangement of molecules on the LB films are affected by the surface pressure and transferring rate during the transferring procedure. When the transfer is proceeded at low surface pressure and high transferring rate, the ODA molecules are irregularly packed without uniform orientation. However, during the analysis of dynamic contact angle (DCA), the movement of the three-phase contact line has an effect to rearrange the irregularly packed molecules of ODA on the LB films and the surface becomes more and more uniform with the analytic cycles of the DCA. By comparing between the LB films of ODA and stearic acid, the advancing contact angles are identical for both, but the very small value of receding contact angle on stearic acid reflects the exposure of the hydrophilic glass on the stearic acid film. The existence of holes in the stearic acid monolayer is thus proved by the measurement of wettability.
Results of a Randomized, Double-Blind Trial of Fluconazole (FLU) vs. Voriconazole (VORI) for the Prevention of Invasive Fungal Infections (IFI) in 600 Allogeneic Blood and Marrow Transplant (BMT) Patients. (2007)

Abstract A multi-center, randomized, double blind trial was performed to determine the impact of FLU (400 mg daily in adults) vs. VORI (200 mg twice daily in adults) on the prevention of IFIs in standard risk allogeneic BMT patients receiving full-intensity conditioning regimens. 600 patients with AML (n=230), ALL (n=122), CML (n=103), MDS (n=98), lymphoma (n=43) and other diseases (n=4) were randomized; 295 to FLU, 305 to VORI between 2003 and 2006 (1 not transplanted). Study drugs were given for 100 days; in those receiving prednisone at a dose of ≥1 mg/kg/day at day 100 or for recipients of T cell depleted grafts with CD4+ counts &amp;lt;200 at day 100, drugs were administered for 180 days. All patients had serum galactomannan (GM) assayed twice weekly for 60 days, then once to twice weekly until day 100, depending on severity of graft versus host disease (GVHD). Positive GM, radiology or the presence of suspicious symptoms or signs triggered intensive evaluation for IFI. Empirical antifungal therapy was permitted for suspected IFI during diagnostic assessment but was limited to ≤14 days. The primary endpoint was freedom from IFI or death at 6 months (fungal-free survival) in the intent to treat cohort. Median recipient age was 43 years (range, 3-66) with 92% &amp;gt;18 years; 55% male; 95% with HLA A, B, and DRB1 matched donor; stem cell graft was related donor marrow or PBSC in 56%. There were no significant differences between the two arms in patient, disease type or risk, or transplant characteristics. Rates of engraftment, acute or chronic GVHD, non-fungal infections, expected or unexpected severe adverse events, and rates of premature study drug withdrawal were similar in both arms (p=NS). At a median follow-up of 12 months, overall survival was 80% at 6 months and 67% at 12 months. A blinded data review committee reviewed source documents of all reported fungal infections, deaths, patients with a positive GM and those given empirical antifungal therapy. There were 25 proven, 30 probable, 15 presumptive, and 74 possible IFIs. The cumulative rates of proven, probable and presumptive IFI were similar in the two arms: 10.6% for FLU and 6.6% for VORI at 6 months (p=0.11) and 13.1% and 11.6% at 12 months (p=0.50), respectively. Microbiologically documented IFIs at 6 months in each arm (FLU and VORI) were caused by Aspergillus (16 and 7, p=0.05), Candida (3 and 3), Zygomycetes (3 and 2), and other (1 and 1). Fungal-free survival rates were similar: 76% for FLU and 78% for VORI at 6 months (p=NS) and 65% and 63% at 12 months (p=NS), respectively. Event-free and overall survival rates also were similar in both arms at 6 and 12 months (p=NS). There were no differences in fungal-free survival rates in patients who received prophylactic fluconazole or voriconazole when intensive monitoring and early empirical therapy were employed in standard risk allogeneic BMT recipients.
Role of Advanced Glycation End Products on Aortic Calcification in Patients with Type 2 Diabetes Mellitus (2020)

The aim of this study was to evaluate the relationship between serum levels of advanced glycation end products (AGEs) and abdominal aortic calcification (AAC) in patients with type 2 diabetes mellitus (DM2). This was a prospective cross-sectional study conducted from January 2017 to June 2018. One-hundred and four consecutive patients with DM2 were given lateral lumbar X-rays in order to quantify aortic abdominal calcification AAC. Circulating levels of AGEs and classical cardiovascular risk factors were determined. Clinical history was also registered. Patients with higher AGEs values had higher grades of aortic calcification and higher number of diabetic related complications. Multivariate logistic regression analysis showed that being older, male and having high levels of AGEs and triglycerides were the independent risk factors associated to moderate-severe AAC when compared to no-mild AAC. Our results suggest that AGEs plays a role in the pathogenesis of aortic calcifications. In addition, the measurement of AGEs levels may be useful for assessing the severity of AAC in the setting of diabetic complications.
Mixed plastics waste valorization through tandem chemical oxidation and biological funneling (2022)

Mixed plastics waste represents an abundant and largely untapped feedstock for the production of valuable products. The chemical diversity and complexity of these materials, however, present major barriers to realizing this opportunity. In this work, we show that metal-catalyzed autoxidation depolymerizes comingled polymers into a mixture of oxygenated small molecules that are advantaged substrates for biological conversion. We engineer a robust soil bacterium, <i>Pseudomonas putida</i>, to funnel these oxygenated compounds into a single exemplary chemical product, either β-ketoadipate or polyhydroxyalkanoates. This hybrid process establishes a strategy for the selective conversion of mixed plastics waste into useful chemical products.
CELL 92-Modified galactoglucomannan from forestry wastewater utilized for oxygen barrier films and hydrogels (2007)

CELL 92-Modified galactoglucomannan from forestry wastewater utilized for oxygen barrier films and hydrogels
1.54 μm electroluminescence from erbium-doped SiGe light emitting diodes (1998)

Er-doped SiGe light emitting diodes were fabricated by implanting Er3+ ions into SiGe epi-layers. The fabricated SiGe: diodes show good current–voltage characteristics with a typical reverse breakdown voltage between 10 and 14 V. In the forward bias region, the ideality factor η is found to be 1.84, which indicates that the forward current is dominated by space charge recombinations. By injecting minority carriers into the diodes, Er3+ related emission was observed in the 1.54 μm region at 77 K. To obtain the maximum electroluminescence intensity, the post-implantation annealing under vacuum condition was found to be 800 °C for 30 min.
Next-generation PONs: A performance investigation of candidate architectures for next-generation access stage 1 (2009)

Driven by bandwidth-demanding video applications, next-generation access stage 1, proposed by FSAN as the first stage of next-generation passive optical networks, increases the subscriber bandwidth by upgrading the current GPON network. To reduce the upgrading cost, NGA1 conforms to the standardized GPON and the deployed optical distribution network. This article presents the investigation of five candidate NGA1 architectures from the perspective of the MAC-layer bandwidth allocation including the analysis of the traffic characteristics of the subscribers' applications and the criteria in mapping them into proper transmission containers. Extensive simulations were conducted to investigate and compare the performances of the five candidate NGA1 architectures.
Metallic Artifact Reduction in Midfacial CT Scans Using Patient-Specific Polymer Implants Enhances Image Quality (2023)

Midfacial reconstruction after tumor resection surgery is commonly conducted by using autologous bone grafts or alloplastic implants. Titanium is the most frequently used osteosynthesis material in these cases but causes disturbing metallic artifacts in CT imaging. The purpose of this experimental study was to evaluate whether the use of midfacial polymer implants reduces metallic artifacts in CT imaging to improve image quality. Zygomatic titanium (n = 1) and polymer (n = 12) implants were successively implanted in a human skull specimen. Implants were analyzed for their effect on Hounsfield Unit values (streak artifacts) and virtual growth in CT images (blooming artifacts) as well as image quality. Multi-factorial ANOVA and Bonferroni's post hoc test were used. Titanium (173.7 HU; SD ± 5.1) and hydroxyapatite containing polymers (155.3 HU; SD ± 5.9) were associated with significantly more streak artifacts compared to all other polymer materials. There was no significant difference in blooming artifacts between materials. The metallic artifact reduction algorithm showed no significant difference. Image quality was slightly better for polymer implants compared to titanium. Personalized polymer implants for midfacial reconstruction significantly reduce metallic artifacts in CT imaging which improves image quality. Hence, postoperative radiation therapy planning and radiological tumor aftercare around the implants are facilitated.
Roles of Oxidative Stress and AT 1 Receptors in Renal Hemodynamics and Oxygenation in the Postclipped 2K,1C Kidney (2003)

The spontaneously hypertensive rat (SHR) exhibits angiotensin II (Ang II)-dependent oxidative stress and reduced efficiency of renal oxygen usage (QO2) for tubular sodium transport (TNa). We tested the hypothesis that oxidative stress determines the reduced TNa:QO2 ratio in the clipped kidney of the early 2-kidney, 1-clip (2K,1C) Ang II-dependent model. One week after sham operation (Sham) or clip placement, 2K,1C rats received for 2 weeks either a vehicle, the superoxide dismutase mimetic tempol (Temp), or candesartan (Cand). Oxidative stress was assessed from excretion of 8-isoprostaglandin F2alpha (PGF2alpha) and malondialdehyde (MDA) and renal oxygenation from pO2 in the renal cortex and from the ratio of calculated TNa and QO2 values. The mean arterial pressure (MAP) of Sham (113+/-6 mm Hg) was increased in 2K,1C vehicle-treated rats (148+/-4 mm Hg), but both Temp and Cand restored MAP to Sham levels. The excretions of 8-iso-PGF2alpha and MDA were higher in 2K,1C vehicle-treated rats compared with Sham and were normalized by Temp. The pO2 of Sham (42+/-2 mm Hg) was lower in 2K,1C vehicle-treated animals (28+/-2 mm Hg). This was restored to Sham values by Temp (36+/-3 mm Hg) but not by Cand (28+/-2 mm Hg). The TNa:QO2 of Sham (12.9+/-1.6) was reduced in 2K,1C vehicle-treated rats (9.7+/-2.8) and was restored to Sham values by Temp (13.7+/-2.5) but not by Cand (7.5+/-1.6). We conclude that the correction of oxidative stress in the 2K,1C model partially corrects renal cortical hypoxia and inefficient utilization of O2 for Na+ transport, independent of the fall in blood pressure.
Practical considerations for increasing radiated power from an electrically small antenna by application of a double negative metamaterial (2005)

We have seen that the approach to improving the amount of radiated power from an electrically short antenna can be implemented with a physically realizable antenna geometry, in this case a short monopole over an infinite groundplane. It has also been demonstrated by simulation that the increase in radiated power is not a narrowband phenomenon, though in practice it will likely end up being limited by an overall matching network.
A Distributed User-Cell Association for Spectral and Energy Efficiency Tradeoff in Massive MIMO UDHNs (2019)

Massive MIMO enabled ultra-dense heterogeneous networks (UDHNs) have been considered as the indispensable and emerging approach to meet the demand on growing data traffic for next generation networks. Although deployment of large number of antennas causes high circuit power consumption in massive MIMO UDHNs, there is always a tradeoff between energy efficiency (EE) and spectral efficiency (SE). Therefore, an energy efficient and spectral efficient user-cell association will become crucial and challenging in massive MIMO UDHNs. In this paper, we address a user-cell association problem for EE and SE tradeoff. To this end, we formulate a convex multi-objective optimization problem (MOP) and convert it into a single-objective optimization problem (SOP) where a priority is assigned for EE and SE with a weighting factor which means the problem can be adjusted whether priority is on EE or SE. The problem aims to maximize the weighted sum of the EE and SE. As a solution, Lagrange duality analysis is performed and a distributed game theoretical user-cell association (GTUCA) algorithm considering the fairness among users is developed. The results confirm that the proposed algorithm outperforms the baseline algorithm, namely maximum rate-based cell selection in terms of EE and SE, when the weighting factor is set properly.
Efficient cross-domain mechanisms for building kernel-less operating systems (1996)

We describe a set of efficient cross-domain mechanisms that allow operating systems to be implemented as cooperating applications, eliminating the need for a monolithic kernel. Our implementation, called SPACE[1, 2], can achieve higher-performance than kernel-based systems by allowing applications to build customized system services and tailor system interfaces for performance. On the SPARC architecture we have measured minimal application-to-application system service calls that are 5 times faster than Solaris getpid(), and customized thread creation that is 50 times faster than minimal Solaris threads. SPACE unifies exception handling and cross-domain calls into a single mechanism that allows applications to efficiently interface to the underlying hardware. Conventional memory-management hardware is used to provide multiple protection domains within each address space. Cross-domain calls are implemented by portals, which map an exception in one domain to a handler in another. Portals...
Distributed Open Architecture Controller for Machine Tools (1999)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Conventional computer numerical controllers used for machine tools are not amenable to the adaptation to dynamic changes in operations and environments due to the proprietary closed architecture. This paper presents the design and development of a distributed open architecture controller for machine tools, which exhibits openness, modularity, and other desirable characteristics. With application of the object-oriented methodology, fundamental agents related to machine tool systems are identified and distributed system architecture is achieved. In addition to the overall system design, a main environment of the open architecture controller is developed to integrate existing function modules and to provide an application developing platform. Process monitoring and control schemes developed within this system, as a case study, are presented.&lt;/div&gt;&lt;/div&gt;