gebhart/patrepeval huggingface dataset:
Humanizing the Problem of Transplant Vasculopathy (2012)

A frequent problem in transplantation is allograft survival, which can be exacerbated by nonimmune mechanisms in response to perioperative injury of the blood vessels. Similar pathology is also observed in other solid organ graft types, such as renal allografts. It is unclear whether this type of GA is a direct response of the vasculature to injury, including rejection and perioperative injury, or whether it is an indirect response to injury that changes the way the immune system interacts with the graft.
Supplementary Figure 2 from A Hypusine–eIF5A–PEAK1 Switch Regulates the Pathogenesis of Pancreatic Cancer (2023)

&lt;p&gt;Contains additional data on the growth of PDAC cells with eIF5A knockdown or overexpression.&lt;/p&gt;
High quality GaN microplatelets grown by metal-organic vapor phase epitaxy on patterned silicon-on-insulator substrates: Toward micro light-emitting diodes (2023)

In this paper, we report the use of three pendeo-epitaxy growth approaches as a way of reducing the threading dislocation density (TDD) of 20 × 20 μm2 GaN platelets to be used for the development of micro light-emitting diodes (μLEDs). The method relies on the coalescence of GaN crystallites grown on top of a network of deformable pillars etched into a silicon-on-insulator substrate. Our approach takes advantage of the creeping properties of SiO2 at the usual GaN epitaxial growth temperature, allowing the GaN crystallites to align and reduce the grain boundary dislocations. Furthermore, this bottom-up approach allows to get rid of the dry plasma etching step for μLEDs fabrication, which highly deteriorates sidewalls, reducing the efficiency of future displays. By optimizing the growth conditions and inducing asymmetric nucleation, a TDD of 2.5 × 108 cm−2 has been achieved on the GaN platelets, while keeping a smooth surface.
Modelling of a linear PM machine including magnetic saturation and end effects: Maximum force to current ratio (2003)

The use of linear permanent-magnet (PM) actuators increases in a wide variety of applications because of their high force density, robustness and accuracy. These linear PM motors are often heavily loaded during short intervals of high acceleration, so that magnetic saturation occurs. This paper models saturation and end effects in linear PM motors using magnetic circuit models. The saturating parts of the magnetic circuit are modelled as nonlinear reluctances. Magnetomotive forces represent the currents and the magnets. This paper shows that when saturated, a negative d-axis current increases the force developed by the motor. Although the increase is not large, it is nevertheless useful, because a negative d-axis current also results in a decrease in the amplifier rating. Further, the trajectory for the maximum force to current ratio is derived. The correlation between the calculated and the measured force justifies the model.
On multiple‐domain cooperative diversity for communications with distributed content in G.hn networks (2015)

Summary Broadband data applications can be delivered to homes over the available home network infrastructure (i.e., mediums). Further enhancement of the network performance is possible by exploiting spatial, time, or frequency diversity. Recently, MIMO systems have been proposed for power line communication (PLC) networks. Because of the extremely diverse physical characteristics of the mediums, an implementation of MIMO systems in G.hn across different domains represents a non‐trivial task. In this paper, we present and theoretically evaluate the performance of multiple‐domain diversity mechanism in G.hn using a cross‐layer classification algorithm. In the proposed network architecture, the signal is transmitted over different mediums selected by the classification algorithm in order to meet the quality‐of‐service demands. At the receiver, joint signal combining and equalization are done to take advantage of the multiple‐domain cooperative diversity and increase the signal‐to‐noise ratio. The merit of the proposed multiple‐domain PLC network has been confirmed by analytical performance analysis and computer simulation. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Translational dynamics revealed by genome-wide profiling of ribosome footprints in <i>Arabidopsis</i> (2013)

Translational regulation contributes to plasticity in metabolism and growth that enables plants to survive in a dynamic environment. Here, we used the precise mapping of ribosome footprints (RFs) on mRNAs to investigate translational regulation under control and sublethal hypoxia stress conditions in seedlings of Arabidopsis thaliana. Ribosomes were obtained by differential centrifugation or immunopurification and were digested with RNase I to generate footprint fragments that were deep-sequenced. Comparison of RF number and position on genic regions with fragmented total and polysomal mRNA illuminated numerous aspects of posttranscriptional and translational control under both growth conditions. When seedlings were oxygen-deprived, the frequency of ribosomes at the start codon was reduced, consistent with a global decline in initiation of translation. Hypoxia-up-regulated gene transcripts increased in polysome complexes during the stress, but the number of ribosomes per transcript relative to normoxic conditions was not enhanced. On the other hand, many mRNAs with limited change in steady-state abundance had significantly fewer ribosomes but with an overall similar distribution under hypoxia, consistent with restriction of initiation rather than elongation of translation. RF profiling also exposed the inhibitory effect of upstream ORFs on the translation of downstream protein-coding regions under normoxia, which was further modulated by hypoxia. The data document translation of alternatively spliced mRNAs and expose ribosome association with some noncoding RNAs. Altogether, we present an experimental approach that illuminates prevalent and nuanced regulation of protein synthesis under optimal and energy-limiting conditions.
Radical Allylation, Vinylation, Alkynylation, and Phenylation Reactions of α-Halo Carbonyl Compounds with Organoboron, Organogallium, and Organoindium Reagents (2005)

Allylic gallium and indium reagents are found to mediate radical allylation reactions of α-iodo or α-bromo carbonyl compounds. Treatment of benzyl bromoacetate with allylgallium, prepared from allylmagnesium chloride and gallium trichloride, in the presence of triethylborane provided benzyl 4-pentenoate in excellent yield. Addition of water as a co-solvent improved the yields of allylated products. Allylic indium reagents are also useful and can replace the gallium reagents. A diallylborane reagent can allylate an α-iodo ester in good yield. Alkenylation reactions of α-halo carbonyl compounds with alkenylindium proceeded via a radical process in the presence of triethylborane. Unactivated alkene moieties and styryl groups were introduced by this method. The carbon-carbon double bond geometry of the alkenylindiums was retained during the alkenylation. Preparation of an alkenylindium via a hydroindation of 1-alkyne and subsequent radical alkenylation established an efficient one-pot strategy. Radical alkynylations and phenylations with organoindium reagents are disclosed herein.
An Empirical Study of Throughput Prediction in Mobile Data Networks (2014)

Bandwidth-sensitive applications such as adaptive video streaming rely on accurate prediction of future network throughput to enable them to react to and compensate for the rapidly fluctuating bandwidth often found in mobile networks. Researchers have developed various prediction algorithms in the literature of which many have been employed in real-world applications. However, there is a lack of systematic study on the comparative performance of the existing prediction algorithms in the context of mobile networks. This work addresses this void by conducting a systematic performance comparison of 7 prediction algorithms, and analyzes their characteristics when applied to the prediction of TCP throughput in mobile networks. The performance results are obtained from extensive trace-driven simulations where the throughput trace data were captured in production 3G/HSPA mobile networks in 3 locations over a period of 9 months and hence offer a good representation of the prediction algorithms' real- world performance. Furthermore, we applied the theory of differential entropy in information theory to obtain an estimated lower bound on throughput prediction errors which, for the first time, enables one to evaluate the absolute performance of these prediction algorithms. The results revealed that more complex algorithms are not necessarily better, and there exists a specific range of operating parameters where predictions are generally more accurate.
Effect of Dosing and Dosing Frequency on the Efficacy of Ceftizoxime and the Emergence of Ceftizoxime Resistance during the Early Development of Murine Abscesses Caused by <i>Bacteroides fragilis</i> and <i>Enterobacter cloacae</i> Mixed Infection (2007)

The efficacy of beta-lactams is thought to be dependent on the time that the unbound concentrations exceed the MIC (fT>MIC). However, the pharmacokinetic/pharmacodynamic index (PDI) that correlates best to the selection of resistance is not yet clear. The selection of ceftizoxime (CZX)-resistant Enterobacter cloacae mutant strains during the development of murine mixed-infection abscesses was studied to determine the PDI that is important for the emergence of resistance and the PDI value needed for the prevention of resistance. Studies were carried out 24 h after inoculation with Bacteroides fragilis ATCC 23745 and E. cloacae 22491. Six to 1,536 mg of CZX/kg of body weight/day given every 2 h (q2h), q4h, q6h, or q8h was started 30 min before inoculation and continued for 24 h. Resistant mutants were isolated to determine mutant frequencies (MF). The fT>MIC varied from 9 to 98% for E. cloacae, the peak concentration (unbound fraction) was 0.6 to 578 mg/liter, and the area under the concentration-time curve (unbound fraction) (fAUC) was 1.9 to 553 mg.h/liter. The fAUC-to-MIC ratio best explained the in vivo efficacy. CZX-resistant B. fragilis and E. cloacae mutants were isolated from untreated controls at an MF of 10(-5) to 10(-7). The MF of resistant B. fragilis did not increase during therapy. The selection of resistant E. cloacae strains at an MF of 10(-1) to 10(-2) was related to the fT>MIC and the ratio of fAUC to MIC following an inverse U shape. However, the ratio of fAUC to MIC was the stronger driver of resistance. The highest MFs were 0.7 to 0.9 at an fAUC-to-MIC ratio of approximately 250. We conclude that the ratio of fAUC to MIC is the PDI that correlated best to the in vivo efficacy of CZX and probably also to the emergence of resistant E. cloacae mutants. An fAUC-to-MIC ratio of 1,000 was needed to prevent the emergence of this resistance.
Improved RF power extraction from 1.55µm Ge/Si n-i-p photodiodes with load impedance optimization (2010)

The RF output power of Ge/Si n-i-p waveguide photodetectors is improved by increasing the load impedance. The maximum extracted RF power at 3GHz is 17.13dBm with a compression current of 42mA using a 100Ω load.
Osteochondritis dissecans of the talus treated by the transplantation of tissue‐engineered cartilage (2004)

Management of osteochondral lesions of the joint has been difficult, because articular cartilage has a poor healing capacity as a result of its lack of vessels, nerve supply, and its isolation of systemic regulation. Although a lot of basic research and surgical treatments for cartilage repair have focused on osteochondral lesions in the knee joint, orthopedic surgeons have recently diverted their attention to osteochondral lesions in the ankle joint, partly because of the widespread introduction of arthroscopy in ankle surgery. There have been many attempts to treat articular cartilage defects in the ankle joint as well as in the knee joint. However, no treatment has achieved efficient healing with hyaline cartilage. Recently, tissue engineering technique for cartilage repair has been gaining much attention in the orthopedic field. In this study, we reported on a patient with osteochondritis dissecans of the talar dome, successfully treated by transplantation of tissue-engineered cartilage made ex vivo using atelocollagen gel and low tibial osteotomy.
Regulation of leg size and shape by the Dachsous/Fat signalling pathway during regeneration (2009)

An amputated cricket leg regenerates all missing parts with normal size and shape, indicating that regenerating blastemal cells are aware of both their position and the normal size of the leg. However, the molecular mechanisms regulating this process remain elusive. Here, we use a cricket model to show that the Dachsous/Fat (Ds/Ft) signalling pathway is essential for leg regeneration. We found that knockdown of ft or ds transcripts by regeneration-dependent RNA interference (rdRNAi) suppressed proliferation of the regenerating cells along the proximodistal (PD) axis concomitantly with remodelling of the pre-existing stump, making the regenerated legs shorter than normal. By contrast, knockdown of the expanded (ex) or Merlin (Mer) transcripts induced over-proliferation of the regenerating cells, making the regenerated legs longer. These results are consistent with those obtained using rdRNAi during intercalary regeneration induced by leg transplantation. We present a model to explain our results in which the steepness of the Ds/Ft gradient controls growth along the PD axis of the regenerating leg.
Cell surface glycoproteins of corneal epithelium. (1995)

This study has demonstrated that during corneal epithelial cell migration, the level of one membrane glycoprotein is markedly reduced, and the levels of four membrane glycoproteins are elevated. Further characterization of these glycoproteins should contribute to a better understanding of the mechanisms that modulate corneal epithelial sheet migration and wound healing.
Supplementary Table 4: H4 from A Mutation in Histone H2B Represents a New Class of Oncogenic Driver (2023)

&lt;p&gt;List of all H4 missense mutations in cBioPortal nad dbSNP analysis&lt;/p&gt;
Unlocking the diagnostic and therapeutic potential of metagenomics (2019)

During the past decade, rapid advancements in sequencing technologies have enabled the study of human-associated microbiomes at an unprecedented scale. Metagenomics, specifically, is emerging as a clinical tool to identify the agents of infection, track the spread of diseases, and surveil potential pathogens. Yet, despite advances in high-throughput sequencing technologies and bioinformatics algorithms, metagenomics still has limitations barring mass clinical acceptance and broad implementation. Algorithms currently struggle to balance sensitivity and specificity of discovered biomarkers, genomic reference databases are incomplete, and studies are frequently not reproducible beyond the original environmental settings. Once these hurdles are overcome, clinical metagenomics will be able to inform doctors of the best, targeted treatment for their patients and provide early detection of disease. Here we present an overview of metagenomics methods with a discussion of computational challenges and limitations. Our review covers clinical applications and presents applications for strain identification of Mycobacterium tuberculosis (TB), identification of infectious agents in cases of encephalitis, biomarkers for Inflammatory Bowel Disease, and explores the challenges of sampling the microbiome in various tissues. Our review also summarizes 11 of the most recent clinical metagenomics studies and discusses their commonalities and unique features.
Fiber lasers for CARS microscopy (2009)

We report a fiber-based high-power picosecond laser system for coherent Raman microscopy (CRM). This source generates 3-ps pulses with 6 W average power at 1030 nm. Frequency-doubling yields more than 2 W of green light, which can be used to pump a commercial optical parametric oscillator to produce the pump and Stokes beams for CRM. The design and performance of the laser are described, along with an application to CARS imaging.
Tunable reactivity of silver nanoclusters: a facile route to synthesize a range of bimetallic nanostructures (2023)

Quantized energy levels and unique optoelectronic properties of atomically precise noble metal nanoclusters (NCs) have made them important in materials science, catalysis, sensors, and biomedicine. Recent studies on the profound chemical interactions of such NCs within themselves and with ultrasmall plasmonic nanoparticles (NPs) indicate that depending on the size, shape, and composition of the second reactant, NCs can either take part in colloidal assembly without any chemical modifications or lead to products with atoms exchanged. Anisotropic NPs are a unique class of plasmonic nanomaterials as their sharp edges and protrusions show higher chemical reactivity compared to flat surfaces, often leading to site-specific growth of foreign metals and metal oxide shells. Here, using chemical interactions between gold nanotriangles (AuNTs) and Ag NCs of different compositions, we show for the first time that metal atom etching, alloying/atom exchange, and colloidal assembly can all happen at a particular length scale. Specifically, Ag<sub>25</sub>(DMBT)<sub>18</sub> NCs (denoted as 1), upon reacting with AuNTs of ∼57 nm edge length, etch gold atoms from their sharp tips and edges. Simultaneously, the two nanosystems exchange metal atoms, resulting in Ag-doped AuNTs and Au<sub><i>x</i></sub>Ag<sub>24-<i>x</i></sub>(DMBT)<sub>18</sub> (<i>x</i> = 1, 2). However, another Ag NC with the same metallic core, but a different ligand shell, namely, Ag<sub>25</sub>H<sub>22</sub>(DPPE)<sub>8</sub> (denoted as 2), creates dendritic shells made of Ag, surrounding these AuNTs under the same reaction conditions. Furthermore, we show that in the case of a more reactive thiol-protected Ag NC, namely, Ag<sub>44</sub>(pMBA)<sub>30</sub> (denoted as 3), gold etching is faster from the edges and tips, which drastically alters the identities of both the reactants. Interestingly, when the AuNTs are protected by <i>p</i>MBA, 3 systematically assembles on AuNTs through H-bonding, resulting in an AuNT core-Ag NC shell nanocomposite. Thus, while shedding light on various factors affecting the reactivity of Ag NCs towards AuNTs, the present study proposes a single strategy to obtain a number of bimetallic nanosystems of targeted morphology and functionality.
Multicolor Organometallic Mechanophores for Polymer Imaging Driven by Exciplex Level Interactions (2019)

Photoluminescent compounds can undergo various structural changes upon interaction with light. When these changes manifest themselves in the excited state, the resulting emitters can obtain a sensory function. In this work, we designed coordination compounds that can vary their emission color in response to thermal and mechanical stimuli. When embedded in a polymer matrix, Cu-NHC sensors act as mechanophores, and their color-based response can readily describe mechanical stress and phase transition phenomena. A strong practical advantage of new mechanophores over previous generations of organometallic stress sensors stems from their reliance on emission color variations that are easy to detect. In a broad context, our work implies that emission color variations that we often view as thermally governed can also be triggered mechanically and used to generate sensory information.
Development of an automatic opening system for sliding and casement windows to control the natural ventilation rate (2023)

Under the influence of COVID-19, ventilation is recommended to reduce the risk of infection in the room. Window openings can increase the ventilation rate caused by indoor and outdoor temperature differences. However, there is a concern that opening the window in the air-conditioned room will increase the heating and cooling loads due to air leakage. In addition, it is difficult to maintain an adequate ventilation rate because the outdoor temperature changes from time to time. To solve this problem, we have developed an automatic opening system to control the natural ventilation rate. This system can control the adequate ventilation rate for the room by adjusting the opening area of the window automatically. In this study, the control equations for the system for sliding windows were derived, and actual measurements were taken with the system. Additionally, the flow coefficients of the casement windows were numerically analyzed. Then, the control equation for the system for casement windows was derived from the relationship between the opening angle and the flow coefficient. As a result, the ventilation rate could be controlled using an automatic opening system for the sliding windows. Also, the flow coefficient of the casement window could be approximated by a sinusoidal function of the opening angle.
pySBOL3: SBOL3 for Python Programmers (2022)

The Synthetic Biology Open Language version 3 (SBOL3) provides a data model for representation of synthetic biology information across multiple scales and throughout the design-build-test-learn workflow. To support practical use of this data model, we have developed pySBOL3, a Python library that allows programmers to create and edit SBOL3 documents. Here we describe this library and key engineering decisions in its design. The resulting implementation is a compact and maintainable core that provides both a familiar, pythonic interface for manipulating SBOL3 objects as well as mechanisms for building additional extensions and representations on this base.
Modeling and Mitigation of Rotor Eddy-Current Losses in High-Speed Solid-Rotor Induction Machines by a Virtual Permanent Magnet Harmonic Machine (2018)

Being much more rugged than a rotor made of traditional steel sheets, a solid rotor is frequently used in high-power high-speed induction machines (IMs). Furthermore, by a solid-rotor machine, a higher rotating speed can be achieved. However, the solid rotor also has certain disadvantages, the relatively high solid-rotor eddy-current losses being the most serious one. Basically, solid-rotor eddy-current losses are mainly induced by time-spatial air-gap flux density high-order harmonics. The suppression of the high-order harmonics is the key means to mitigate the rotor eddy-current losses. In this paper, a novel computational model is proposed for evaluating the rotor harmonic eddy-current losses of a 2 MW, 12 000 r/min IM. The model was built on a special machine referred to as a virtual permanent magnet harmonic machine (VPMHM). The model was constructed by applying the finite-element method (FEM), and it is based on the time-spatial harmonics produced by a rotating magnet with sinusoidal magnetization. The VPMHM model links the air-gap flux density harmonics directly to the specific rotor eddy-current losses. Furthermore, according to the proposed model, three options, namely, the use of air-gap permeance modifying notches on the stator teeth, semimagnetic wedges, and their combination, were investigated in detail for mitigating the rotor eddy-current losses in the motor nominal operating point. The results and conclusions in this paper are based on the FEM analysis.
The statistical analysis plan for the unification of treatments and interventions for tinnitus patients randomized clinical trial (UNITI-RCT) (2023)

ClinicalTrials.gov NCT04663828 . The trial is ongoing. Date of registration: December 11, 2020. All patients that finished their treatment before 19 December 2022 are included in the main RCT analysis.