gebhart/patrepeval huggingface dataset:
Berberine elevates cardiolipin in heart of offspring from mouse dams with high fat diet-induced gestational diabetes mellitus (2021)

Berberine (BBR) is an isoquinoline alkaloid from plants known to improve cardiac mitochondrial function in gestational diabetes mellitus (GDM) offspring but the mechanism is poorly understood. We examined the role of the mitochondrial phospholipid cardiolipin (CL) in mediating this cardiac improvement. C57BL/6 female mice were fed either a Lean-inducing low-fat diet or a GDM-inducing high-fat diet for 6 weeks prior to breeding. Lean and GDM-exposed male offspring were randomly assigned a low-fat, high-fat, or high-fat diet containing BBR at weaning for 12 weeks. The content of CL was elevated in the heart of GDM offspring fed a high fat diet containing BBR. The increase in total cardiac CL was due to significant increases in the most abundant and functionally important CL species, tetralinoleoyl-CL and this correlated with an increase in the expression of the CL remodeling enzyme tafazzin. Additionally, BBR treatment increased expression of cardiac enzymes involved in fatty acid uptake and oxidation and electron transport chain subunits in high fat diet fed GDM offspring. Thus, dietary BBR protection from cardiac dysfunction in GDM exposed offspring involves improvement in mitochondrial function mediated through increased synthesis of CL.
Design of an Electric Motor Transmission System Without Friction Synchronization (2019)

Abstract This paper investigates the design of a new transmission system without a friction synchronizer for high-performance hybrid vehicles. Manual and automated manual transmission systems traditionally use friction synchronizers to facilitate smooth transitions during a gearshift, ensuring speed matching and proper engagement of the gears. Active position sensing technology for dogteeth is being developed, along with the potential of speed matching using electric motors, eliminating the need for the friction synchronizer. However, in removing these friction synchronizer components, significant shock could be introduced to the transmission system with speed or position errors during a shift. This paper proposes a solution through a gear system that utilizes a face mesh design, torsional springs, and alternating teeth height. A prototype of this design was created and successfully tested as a proof of concept for a transmission system, which has the potential to improve hybrid, automated manual transmission design.
ChemInform Abstract: Enantioselective Ring Opening of Epoxides with Trimethylsilyl Azide (TMSN3) in the Presence of β‐Cyclodextrin: An Efficient Route to 1,2‐Azido Alcohols. (2000)

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.
REGAL: Transfer Learning For Fast Optimization of Computation Graphs. (2019)

We present a deep reinforcement learning approach to minimizing the execution cost of neural network computation graphs in an optimizing compiler. Unlike earlier learning-based works that require training the optimizer on the same graph to be optimized, we propose a learning approach that trains an optimizer offline and then generalizes to previously unseen graphs without further training. This allows our approach to produce high-quality execution decisions on real-world TensorFlow graphs in seconds instead of hours. We consider two optimization tasks for computation graphs: minimizing running time and peak memory usage. In comparison to an extensive set of baselines, our approach achieves significant improvements over classical and other learning-based methods on these two tasks.
Deep brain stimulation of the ventralis intermedius nucleus for the treatment of essential tremor (2017)

A 59-year-old woman with a 30-year history of essential tremor refractory to medical therapy underwent staged deep brain stimulation of the ventralis intermedius nucleus of the thalamus (VIM). Left-sided lead placement was performed first. Once in the operating room, microelectrode recording (MER) was performed to confirm the appropriate trajectory and identify the VIM border with the ventralis caudalis nucleus. MER was repeated after repositioning 2 mm anteriorly to reduce the likelihood of stimulation-induced paresthesias. Physical examination prior to permanent lead placement demonstrated micro-lesion effect, suggesting optimal trajectory. After implantation of the permanent lead, physical examination showed excellent results. The video can be found here: https://youtu.be/nn3KRdmRCZ4 .
An integrated inductor for parallel interleaved VSCs connected in a whiffletree configuration (2015)

The quality of voltage waveform of the parallel connected inverters can be improved by interleaving the carrier signals. However, an additional coupled inductors (CIs) are required to suppress the circulating current between the interleaved VSCs and often connected in a whiffletree configuration. The integration of the line filter inductor and the coupled inductors in a single magnetic component for such systems is proposed. The fundamental frequency component of the flux is confined to the limbs around which the coils are placed, whereas other parts only experiences high frequency flux excitation. As a result, the inductor can be made smaller. The inductor is analyzed and performance is verified by simulation and experimental studies.
Experimental performance evaluation of inter-domain path provisioning with multiple PCEs (2008)

In this paper, PCE-based inter-domain path computation has been discussed. Interworking of multiple PCEs with the BRPC procedure enables not only end-to-end shortest path computation but also end-to-end diverse path computation over multiple networks. We have analyzed various PCE-based inter-domain path computation strategies using BRPC, in terms of the path computation complexity. To reduce path computation time, a simplified path computation strategy was proposed and evaluated experimentally with our prototyped PCE system. Our experimental results show good correspondence with analytical ones. The proposed strategy drastically reduced path computation time down to one-seventh in comparison with the conventional strategy.
ChemInform Abstract: Structure of 2‐Chloro‐7,12‐dihydropyrido(3,2‐b:5,4‐b′)diindole (1992)

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.
Universal Semi-Supervised Semantic Segmentation (2018)

In recent years, the need for semantic segmentation has arisen across several different applications and environments. However, the expense and redundancy of annotation often limits the quantity of labels available for training in any domain, while deployment is easier if a single model works well across domains. In this paper, we pose the novel problem of universal semi-supervised semantic segmentation and propose a solution framework, to meet the dual needs of lower annotation and deployment costs. In contrast to counterpoints such as fine tuning, joint training or unsupervised domain adaptation, universal semi-supervised segmentation ensures that across all domains: (i) a single model is deployed, (ii) unlabeled data is used, (iii) performance is improved, (iv) only a few labels are needed and (v) label spaces may differ. To address this, we minimize supervised as well as within and cross-domain unsupervised losses, introducing a novel feature alignment objective based on pixel-aware entropy regularization for the latter. We demonstrate quantitative advantages over other approaches on several combinations of segmentation datasets across different geographies (Germany, England, India) and environments (outdoors, indoors), as well as qualitative insights on the aligned representations.
iProgram (2015)

Heating, ventilation, and air conditioning (HVAC) accounts for over 50% of a typical home's energy usage. A thermostat generally controls HVAC usage in a home to ensure user comfort. In this paper, we focus on making existing "dumb" programmable thermostats smart by applying energy analytics on smart meter data to infer home occupancy patterns and compute an optimized thermostat schedule. Utilities with smart meter deployments are capable of immediately applying our approach, called iProgram, to homes across their customer base. iProgram addresses new challenges in inferring home occupancy from smart meter data where i) training data is not available and ii) the thermostat schedule may be misaligned with occupancy, frequently resulting in high power usage during unoccupied periods. iProgram translates occupancy patterns inferred from opaque smart meter data into a custom schedule for existing types of programmable thermostats, e.g., 1-day, 7-day, etc. We implement iProgram as a web service and show that it reduces the mismatch time between the occupancy pattern and the thermostat schedule by a median value of 44.28 minutes (out of 100 homes) when compared to a default 8am-6pm weekday schedule, with a median deviation of 30.76 minutes off the optimal schedule. Further, iProgram yields a daily energy saving of 0.42kWh on average across the 100 homes. Utilities may use iProgram to recommend thermostat schedules to customers and provide them estimates of potential energy savings in their energy bills.
Influence of age, irradiation and humanization on NSG mouse phenotypes (2015)

Humanized mice are frequently utilized in bench to bedside therapeutic tests to combat human infectious, cancerous and degenerative diseases. For the fields of hematology-oncology, regenerative medicine, and infectious diseases, the immune deficient mice have been used commonly in basic research efforts. Obstacles in true translational efforts abound, as the relationship between mouse and human cells in disease pathogenesis and therapeutic studies requires lengthy investigations. The interplay between human immunity and mouse biology proves ever more complicated when aging, irradiation, and human immune reconstitution are considered. All can affect a range of biochemical and behavioral functions. To such ends, we show age- and irradiation-dependent influences for the development of macrocytic hyper chromic anemia, myelodysplasia, blood protein reductions and body composition changes. Humanization contributes to hematologic abnormalities. Home cage behavior revealed day and dark cycle locomotion also influenced by human cell reconstitutions. Significant age-related day-to-day variability in movement, feeding and drinking behaviors were observed. We posit that this data serves to enable researchers to better design translational studies in this rapidly emerging field of mouse humanization.
Plasma conditions for as-grown low temperature poly-Si formation on SiO2 substrate by sputtering and plasma enhanced chemical vapor deposition processes (1998)

We investigated the deposition condition of the plasma processing for the formation of as-grown poly-Si thin film on the SiO2 substrate with low temperature (300 °C) processing. We intended to compensate the thermal energy loss due to the low temperature processing with the low kinetic energy ion bombardment assist. We adopted both plasma enhanced chemical vapor deposition (PECVD) (SiH4/Ar/H2) and sputtering (Si-target/Ar/H2) processes. Plasma parameters were measured by the advanced Langmuir probe method tuned for 182.5 MHz rf plasma. Crystallinity of the film was estimated mainly by x-ray diffraction. Crystallization occurred by in situ hydrogenation during the deposition. In our experiment, ion bombardment energy was approximately 23 eV. We define the normalized ion (ni) flux number and investigated the correlation between the ni and the film crystallinity. The result is as follows, the crystal size enlarges with the increasing ni up to ∼20 but it diminishes as the ni increases over ∼20. Under the same plasma condition, the PECVD processed Si films have better crystallinity than the sputtering processed ones. The film thickness and crystal size are 1000 and 219 Å, respectively, at the optimum value of the ni in the PECVD process. Atomic hydrogen is thought to be very effective for the crystallization of the film and, as for the ion assist effect, there exists an optimum value of ni for a certain ion bombardment energy.
GSTP1 Promoter Methylation is Associated with Recurrence in Early Stage Prostate Cancer (2014)

Greater GSTP1 promoter methylation in cancer tissue was independently associated with the risk of recurrence in patients with early prostate cancer. This suggests that GSTP1 promoter methylation may be a potential tissue based recurrence marker.
Arthroplasty Registries, Patient Safety and Outlier Surgeons: the case for change. (2015)

Joint registries were created to follow-up on the failure rate of different types of joint replacements. Since the only end-point is revision to another implant the registries are missing out today on essential data informing us about patients' outcome. Ideally, a modern and complete registry should capture 3 strata of data: 1) patient reported outcomes including both function and activity levels from before and after surgery, 2) morbidity including infection rates and mortality related to surgery, and 3) the cost of consecutive revision surgery. A modern knee specialist offering conservative solutions for defined problems enabling return to higher level activities may be reported as an outlier surgeon by registries today.
Crystallization of the complex between cyclophilin A and cyclosporin derivatives: the use of cross-seeding (1994)

With ammonium sulfate as the precipitant, different crystal forms of the complex between cyclosporin A (CsA) and cyclophilin A (CypA) have been crystal- lized [Zurini, Kallen, Mikol, Pflügl, Jansonius & Walkinshaw (1990). FEBS Lett. 276, 63-66]. All have large unit cells and contain a pentamer or a decamer in the asymmetric unit. Using a more water soluble CsA analog, orthorhombic crystals containing only one molecule per asymmetric unit could be grown. They diffract to significantly higher resolution (2.1 A). In this crystal form, CsA has no packing interactions with neighbouring molecules and these crystals could be used to cross-seed other CypA/CsA analog complexes. Nine different CypA/ CsA analog complexes could be crystallized using this technique, most of them yielding highly diffracting crystals, quickly solvable by Fourier difference methods.
Making latex microspheres in space. (1986)

Equipment yields larger, more uniform particles. Two NASA reports describe first commercial product to be manufactured in space. Product monodisperse latex, suspension of spherical particles of essentially same diameter. Carried aboard Space Shuttle on its orbital missions, monodisperse latex reactor (MLR) produces spheres of much larger size than possible on Earth. Mircospheres 30 micrometers in diameter produced, whereas 5 micrometers is limit for Earthbound reactors. Microspheres as large as 100 micrometers scheduled for production in MLR.
Hybrid silicon on silicon carbide integrated photonics platform (2019)

We demonstrate a hybrid on-chip photonics platform based on crystalline silicon resonators and waveguides patterned on top of silicon carbide. The devices were fabricated with membrane transfer followed by standard electron beam patterning procedures. The platform allows the integration of high quality silicon photonics with color centers in silicon carbide operating in the near infrared for spin-photon interfaces used in quantum information processing applications. We measure waveguide-coupled ring resonators with loaded quality factors up to 23 000 at cryogenic temperatures.
Subunit interactions influence the biochemical and biological properties of Hsp104 (2001)

Point mutations in either of the two nucleotide-binding domains (NBD) of Hsp104 (NBD1 and NBD2) eliminate its thermotolerance function in vivo. In vitro, NBD1 mutations virtually eliminate ATP hydrolysis with little effect on hexamerization; analogous NBD2 mutations reduce ATPase activity and severely impair hexamerization. We report that high protein concentrations overcome the assembly defects of NBD2 mutants and increase ATP hydrolysis severalfold, changing V(max) with little effect on K(m). In a complementary fashion, the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate inhibits hexamerization of wild-type (WT) Hsp104, lowering V(max) with little effect on K(m). ATP hydrolysis exhibits a Hill coefficient between 1.5 and 2, indicating that it is influenced by cooperative subunit interactions. To further analyze the effects of subunit interactions on Hsp104, we assessed the effects of mutant Hsp104 proteins on WT Hsp104 activities. An NBD1 mutant that hexamerizes but does not hydrolyze ATP reduces the ATPase activity of WT Hsp104 in vitro. In vivo, this mutant is not toxic but specifically inhibits the thermotolerance function of WT Hsp104. Thus, interactions between subunits influence the ATPase activity of Hsp104, play a vital role in its biological functions, and provide a mechanism for conditionally inactivating Hsp104 function in vivo.
A non-contact, quantitative dosimetry calibration using CT radiodensity and Cherenkov imaging (2021)

Cherenkov light is emitted in response to therapeutic x-ray beam delivery for the treatment of breast cancer, and serves as a passive, non-contact approach for measuring optical signal that is intrinsically linear with dose. However, the intensity of emitted light is attenuated due to absorbers in the tissue (blood, pigment, radiodensity, etc.). If correction for this attenuation were possible, then absolute dose imaging would be feasible. In this study, the planning CT scan was spatially sampled over the area emitting Cherenkov, and the attenuation of the signal was corrected for, using CT radiodensity. There was a linear correlation between presence of fibroglandular (high HU) versus adipose (low HU) and the emitted Cherenkov light. This relationship was used to generate scale factors to normalize out existing tissue variability in images recorded during fractionated radiotherapy, which reduced patient-to-patient variability to under 10%.
Cloud databases (2010)

The panelists will discuss what characterizes data management in the cloud, and how this differs from the broad range of applications that conventional database management systems have supported over the past few decades. They will examine whether we need to develop new technologies to address demonstrably new challenges, or whether we can largely re-position existing systems and approaches. The discussion will cover data analysis in the cloud using Map-Reduce based systems such as Hadoop, and cloud data serving (and so-called "No SQL" systems).
Design Software for Application-Specific Microfluidic Devices (2007)

Microfluidics-based lab-on-a-chip systems, which feature miniaturization of biological separation and assay techniques, are rapidly transforming biochemical analysis and high-throughput screening. Microfluidic system design requires expertise in materials, chemistry, biology, and engineering, and understanding the complex interplay between variables that influence and limit system performance is difficult without computational assistance. Modeling approaches based on 3-dimensional numerical simulations provide detailed information regarding spatiotemporal variations of the field variables but are computationally very expensive for system-level analysis. Design-modeling tools are needed that rapidly simulate the complex underlying phenomena such as electroosmosis, electrophoresis, sample dispersion, mixing, and biochemical reactions without significantly compromising accuracy (1)(2)(3)(4)(5). In addition, these design tools must be easily usable by the microfluidic community, which comprises scientists and engineers from a variety of disciplines. To meet these challenges, we developed integrated design software that allows rapid layout of microfluidic channel networks, fast system performance simulation using a system solver, and the ability to easily reconfigure chip layout to meet specifications. We illustrate the application of the software to improve the design for an electrokinetic immunoassay chip.

The software design follows a modified form of the traditional client-server architecture. The user interacts with a graphical user interface (GUI) front-end (client). Fig. 1⇓ shows a screenshot of the GUI. The microfluidic lab-on-a-chip system is represented as a network of interconnected components that can be assembled from a component library. The sequence of operations required for the creation of the microfluidic network, analysis, and visualization of results using the GUI is as follows:

(1) Creation of the microfluidic network: The components (such as sample reservoirs, straight channels, bends, biosensors, and interconnects such as Y-, T-, and cross junctions) are selected from the component library and assembled into a network using a drag-and-drop method.

(2) Problem …
Synthesis of the novel trimeric benzamides—potential inhibitors of protein–protein interactions (2012)

The synthesis of the family of new non-natural trimeric oligobenzamides (potential inhibitors of protein–protein interactions) bearing the following groups (R = isobutyl, isopropyl, CH2CONH2, (CH2)4NH2, benzyl) that mimic different amino acid residues (leucine, valine, asparagine, lysine, phenylalanine) was accomplished through an iterative (n + 1) elongation approach that includes reduction of the NO2-group (Pd/C, H2) and subsequent amide coupling in the presence of Mukaiyama's reagent.
trans-Translation inhibitors bind to a novel site on the ribosome and clear Neisseria gonorrhoeae in vivo (2021)

Bacterial ribosome rescue pathways that remove ribosomes stalled on mRNAs during translation have been proposed as novel antibiotic targets because they are essential in bacteria and are not conserved in humans. We previously reported the discovery of a family of acylaminooxadiazoles that selectively inhibit trans-translation, the main ribosome rescue pathway in bacteria. Here, we report optimization of the pharmacokinetic and antibiotic properties of the acylaminooxadiazoles, producing MBX-4132, which clears multiple-drug resistant Neisseria gonorrhoeae infection in mice after a single oral dose. Single particle cryogenic-EM studies of non-stop ribosomes show that acylaminooxadiazoles bind to a unique site near the peptidyl-transfer center and significantly alter the conformation of ribosomal protein bL27, suggesting a novel mechanism for specific inhibition of trans-translation by these molecules. These results show that trans-translation is a viable therapeutic target and reveal a new conformation within the bacterial ribosome that may be critical for ribosome rescue pathways.