gebhart/patrepeval huggingface dataset:
Mouse Paternal RNAs Initiate a Pattern of Metabolic Disorders in a Line-Dependent Manner (2022)

A wide range of diseases result from environmental effects, and the levels of many native transcripts are altered. The alteration of non-coding RNAs (ncRNAs) and transmission of the variation to the next generation is increasingly recognized as a marker of disease. However, the determining signals and mechanisms of RNA-induced heritability remain unclear. We performed functional tests with four different genotypes of mice maintained on a high-fat diet to trace the transfer of the obesity/diabetes phenotype to the next generation in order to detect common signals. Two founders of four mouse lines (<i>B6/D2</i> hybrid and <i>Dnmt2</i> <sup><i>-/-C57BL/6</i></sup> ) resist and do not change their phenotype while their sperm RNAs after microinjection into fertilized mouse eggs transfer the newly acquired phenotypes in a susceptible inbred line (<i>C57BL/6</i> or <i>Balb/c</i>). Unexpectedly, in the same line of experiments, sperm RNA from animals raised on a normal diet when mixed with the sperm RNA from animals raised on a diet high in fat or synthetic miR-19b (inducer of obesity) affects or prevents the development of obesity and diabetes. However, it remains unclear what happens to ncRNA signaling under diet. With a comprehensive new analysis of the transcripts maintained as an RNA/DNA hybrid in sperm, we suggest that a fraction of the RNAs are stably attached to the genome. Thus, we propose that changes in the dynamics of ncRNA retention on DNA by factors such as transcriptional variations or lack of adequate methylation could serve as molecular markers to trace these epigenetics events.
Co-production of lactic acid and chitin using a pelletized filamentous fungusRhizopus oryzaecultured on cull potatoes and glucose (2008)

The three-step process using pelletized R. oryzae fermentation innovatively integrates utilization of agricultural residues into the process of co-producing lactic acid and chitin, so as to improve the efficiency, revenues and cost of fungal lactic acid production.
Absence of Cytomegalovirus‐Resistance Mutations after Valganciclovir Prophylaxis, in a Prospective Multicenter Study of Solid‐Organ Transplant Recipients (2004)

We investigated the emergence of cytomegalovirus (CMV) ganciclovir-resistance mutations in 301 high-risk solid-organ transplant (SOT) recipients after oral prophylaxis, for 100 days, with either valganciclovir or ganciclovir. For patients treated with ganciclovir, the incidence of CMV UL97 mutations was 1.9% (2/103) at the end of prophylaxis and 6.1% (2/33) for patients with suspected CMV disease up to 1 year after transplantation. No resistance mutations were detected in samples from valganciclovir-treated patients. Dual polymerase (UL54) and UL97 resistance mutations were not seen. Valganciclovir was associated with negligible risk of resistance and thus constitutes a useful alternative to ganciclovir prophylaxis for CMV in high-risk SOT recipients.
Water Splitting: Periodic Porous 3D Electrodes Mitigate Gas Bubble Traffic during Alkaline Water Electrolysis at High Current Densities (Adv. Energy Mater. 46/2020) (2020)

In article number 2002955 Rui Wu, Cheng Zhu, Yat Li and co-workers demonstrate a new approach for the deterministic design of 3D electrodes to minimize the deleterious effects of gas bubbles by carefully engineering porous highways and transport networks that facilitate rapid bubble transport and release to enhance the total electrode catalytic activity at commercially relevant current densities.
Anderson localization of light in a random configuration of semiconductor nanocolumns (2011)

In the two-dimensional random system composed of a disordered array of a dielectric cylindrical column ensemble, Anderson localization of light is possible. We show localization parameter maps for the light localization adopting parameters of gallium nitride nanocolumn samples, which consist of random arrays of parallel nanosized columnar semiconductor crystals. The maps indicate parametric dependence of the localization characteristics on the light frequency, the radius of the columns, and the filling fraction of the columns. To obtain the maps, we have simulated temporal light diffusion in random media using the two-dimensional finite-difference time-domain method and analyzed the simulation results by Fourier transformation. We conclude that the main mechanism for localization varies continuously with the column filling fraction from Mie resonance of single column to Bragg-like diffraction of the column ensemble.
Technology impacts on sub-90nm CMOS circuit design &amp; design methodologies (2006)

Summary form only for tutorial. This tutorial discusses design challenges of scaled CMOS circuits in sub-90nm technologies and the design methodologies required to design them in order to produce robust designs with desired power performance trade-off. It is increasingly difficult to sustain supply and threshold voltage scaling to provide the required performance increase, limit energy consumption, control power dissipation, and maintain reliability. These requirements pose several difficulties across a range of disciplines. On the technology front, the question arises whether we can continue along the traditional CMOS scaling path - reduce effective oxide thickness, improve channel mobility, and minimize parasitics. On the design front, researchers are exploring various circuit design techniques to deal with process variation, leakage and soft errors.
Uncertainty Propagation in the Discrete-Time (2005)

Signal analysis based on the wavelet transform is applied in many fields. Whenever the application is oriented to measurement purposes, the uncertainty evaluation has to be per- formed. In this paper, an analytical model for the evaluation of the uncertainty affecting the detail and the approximation coefficients determined by means of the discrete-time wavelet transform is proposed. The results of some simulation-based work showing the performance of the model are also presented and discussed. Index Terms—Digital signal processing, power quality, signal analysis, transients, uncertainty, wavelet transform.
A comparison of troglitazone and metformin on insulin requirements in euglycemic intensively insulin-treated type 2 diabetic patients. (1999)

Troglitazone and metformin lower glucose levels in diabetic patients without increasing plasma insulin levels. We compared the insulin sparing actions of these two agents and their effects on insulin sensitivity and insulin secretion in 20 type 2 diabetic patients. To avoid the confounding effect of improved glycemic control on insulin action and secretion, patients were first rendered euglycemic with 4 weeks of continuous subcutaneous insulin infusion (CSII) before randomization to CSII plus troglitazone (n = 10) or CSII plus metformin (n = 10); euglycemia was maintained for another 6-7 weeks. Insulin sensitivity was assessed by a hyperinsulinemic-euglycemic clamp 1) at baseline, 2) after 4 weeks of CSII, and 3) after CSII plus either troglitazone or metformin. The 24-h glucose, insulin, and C-peptide profiles were performed on the day before the second and third glucose clamps. Good glycemic control was achieved with CSII alone and was maintained with CSII plus an oral agent (mean 24-h glucose: troglitazone, 6.2+/-0.6 mmol/l; metformin, 6.2 +/-0.3 mmol/l). Insulin requirements decreased 53% with troglitazone compared with CSII alone (48+/-4 vs. 102+/-13 U/day, P < 0.001), but only 31% with metformin (76+/-13 vs. 110+/-18 U/day, P < 0.005). The 24-h C-peptide profiles were similar. Normal fasting hepatic glucose output was maintained with both agents despite lower insulin levels than on CSII alone. Insulin sensitivity did not change significantly with CSII alone or with CSII plus metformin, but improved 29% with CSII plus troglitazone (P < 0.005 vs. CSII alone) and was then 45% higher than in the CSII plus metformin patients (P < 0.005). In conclusion, metformin has no effect on insulin-stimulated glucose disposal independent of glycemic control in type 2 diabetes. Troglitazone (600 mg/day) has greater insulin-sparing effects than metformin (1,700 mg/day) in CSII-treated euglycemic patients. This is probably explained by the peripheral tissue insulin-sensitizing effects of troglitazone.
Oncostatin M promotes epithelial barrier dysfunction and is elevated in eosinophilic mucosal disease (HYP7P.255) (2015)

Abstract Epithelial barrier dysfunction is thought to play a role in many mucosal diseases including asthma, chronic rhinosinusitis (CRS), and eosinophilic esophagitis (EoE). Oncostatin M (OSM), was elevated in both mRNA (28.3 fold, p&amp;lt;.01, n=12) and protein (4.4 fold, p&amp;lt;.05, n=12-19) in the nasal polyps of CRS patients compared to control tissue. OSM protein was also elevated in bronchoalveolar lavage (BAL) of allergic asthma (AA) patients following segmental allergen challenge (SAC) vs. saline challenge (14 fold, p&amp;lt;.0001). Additionally, OSM mRNA was elevated in esophageal biopsies of EoE patients vs. controls, (3 fold, p&amp;lt;.01). OSM stimulation of differentiated airway epithelium induced barrier dysfunction, as measured by decreased transepithelial electrical resistance (63% reduction, p&amp;lt;.0001, n=11) and increased permeability to 10kD dextran (2.45 fold, p&amp;lt;.05, n=5). Staining for the tight junction protein, occludin showed that OSM stimulation of differentiated airway epithelium impaired the organization of the tight junctions compared to unstimulated controls (n=5). Levels of OSM protein in tissue lysates from CRS and controls correlated with levels of α2-macroglobulin, a marker of epithelial leak, in matched nasal secretions (r=.5055, p&amp;lt;.01). Additionally, OSM in the BAL following SAC in AA patients correlated with serum albumin, another marker of epithelial leak (r=.8062, p&amp;lt;.001). These results suggest that OSM may play a role in epithelial barrier dysfunction in mucosal disease.
The Hermeticity of Compression Seals in Microchannel Hemodialyzers (2014)

Most end stage renal disease patients receive kidney hemodialysis three to four times per week at central medical facilities. At-home kidney dialysis increases the convenience and frequency of hemodialysis treatments which has been shown to produce better patient outcomes. One limiting factor in realizing home hemodialysis treatments is the cost of the hemodialyzer. Microchannel hemodialyzers produced using compression sealing techniques show promise for reducing the size and cost of hemodialyzers. Challenges include the use of a 25 μm thick elastoviscoplastic (EVP) mass transfer membrane for gasketing. This paper provides a framework for understanding the hermeticity of these compression seals. The mechanical properties of a Gambro AN69ST membrane are determined and used to establish limits on the dimensional tolerances of the polycarbonate (PC) laminae containing sealing bosses used to seal the hemodialyzer. The resulting methods are applied to the fabrication of a hemodialysis device showing constraints on the scaling of this method to larger device sizes. The resulting hemodialysis device is used to perform urea mass transfer experiments without leakage.
A high-speed, low input current CMOS integrated front end for multi-spectral photodiode arrays (2011)

A low current front end trans-impedance amplifier (TIA) switching bank for multi-spectral photodiode (PD) arrays is presented. The design mitigates PD capacitance effects by using a g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> -boosted input common-gate stage. Simulation results show that a bandwidth of 97 MHz can be reached with a maximal gain of 7.53 MΩ with a tuning range of 24 dB. The system is suited to low PD currents as its total input referred rms current noise over a 100 MHz bandwidth is of 41 nA.
Strengthening of steel beams using iron-based shape memory alloy (Fe-SMA) strips (2019)

&lt;p&gt;The current study presents a retrofit system, which can be used for strengthening of steel bridge beams using (un-bonded) mechanically-anchored iron-based shape memory alloy (Fe-SMA, ‘memory-steel’) strips. After anchoring, the Fe-SMA strips are activated by a heating and a subsequent cooling process. The anchorage system can simultaneously hold two strips (each with 50-mm width and 1.5-mm thickness) and transfer their prestressing force to the steel beam at the strip ends. The system is based on friction and does not introduce any damage to the parent metallic substrate. Owing to the so-called ‘shape memory effect’ (SME) of the alloy, the strips are prestressed after activation by heating up to a defined maximum temperature. After strengthening, the beam was statically loaded up to 60% of its yield capacity. Finally, in order to examine efficiency of the proposed SMA-strengthening solution, the steel beam was subjected to cyclic loading. The results of the static tests demonstrated the positive effects of the prestressed Fe-SMA strips on reducing tensile stresses in the beam bottom flange. Furthermore, the evolution of the prestress level in the strips during the fatigue loading was studied. The presented experimental study on the strengthened steel beam shows the effectiveness of un-bonded Fe- SMA strips as a retrofitting technique to enhance the static and fatigue performance of metallic bridge girders.&lt;/p&gt;
Inverse-designed multi-wavelength, multi-mode optical interconnects using soliton microcombs (2022)

We demonstrate 130 Gbps transmission in each of 4 spatial modes using Si 3 N 4 soliton microcombs and inverse-designed silicon mode multiplexers. Out of 52 carriers, 42 data channels show natively error-free data transmission.
Efficient frontier formulation for additive and restrictive metrics in hierarchical routing (2002)

In a hierarchical network, groups of nodes are represented by logical nodes for the purposes of simplifying routing. Each group has a set of ingress-egress nodes, and routing information is conveyed to the outside world in the form of a transition matrix that gives the cost of traversing the network between each ingress-egress node pair. In this paper, we present a minimal logical node representation that has sufficient descriptive power to enable path selection in support of connection admission control for services that have both path (restrictive) and link (additive) constraints. For example, the representation can be used to find a path that maximizes bandwidth subject to a delay constraint or minimizes delay subject to a bandwidth constraint. We present our solution in the form of a matrix whose elements are vectors, each of which specifies the efficient frontier of the solution space, and we specify an efficient procedure for constructing the efficient frontier. We present the least upper bound on the number of elements that must be present in the efficient frontier. We provide numerical examples that illustrate construction of the efficient frontier.
polymake: a Framework for Analyzing Convex Polytopes (2000)

polymake is a software tool designed for the algorithmic treatment of polytopes and polyhedra. We give an overview of the functionality as well as of the structure. This paper can be seen as a first approximation to a polymake handbook. The tutorial starts with the very basics and ends up with a few polymake applications to research problems. Then we present the main features of the system including the interfaces to other software products. polymake is free software; it is available on the Internet at http://www.math.tu-berlin.de/diskregeom/polymaka/.
A method to increase the resolution of sodium images from simultaneous 1H MRF/23Na MRI (2023)

In this work, we present an algorithm to generate a high-resolution 23 Na image from simultaneously-acquired low-resolution 23 Na density-weighted MRI (2.85&amp;times;2.85&amp;times;5 mm 3 ) and high-resolution 1 H density, T 1 , and T 2 maps from MRF (1.5&amp;times;1.5&amp;times;5 mm 3 ) in brain at 7 T. As a result, the mean value of the difference between the generated and ground truth high-resolution 23 Na images is 0.5% with a standard deviation of 6.2% and multi-scale structural similarity index of 0.97.
SPINAL MOTION IN ELITE ROWERS: CHARACTERISING GOOD TECHNIQUE (1999)

1807 Introduction Recent increase in lumbar spine problems in rowers has produced speculation that most spinal injuries are mechanical in origin and related to the training regime and rowing technique1. At present the definition of good rowing technique does not include spinal and pelvic motion2. Objectives To measure and characterise lumbar spinal motion in elite rowers and characterise good technique, and 3 typical bad rowing techniques. Methods An electromagnetic measurement device3 was used to measure lumbar spinal motion by fixing receivers to the subject: femur, lumbo-sacral and thoraco-lumbar junctions. Six male international rowers rowed on an ergometer using 'good technique', and 3 bad technique variants. They were then instructed to row for 10 minutes at maximum output. In all cases spinal and pelvic motion was measured and characterised in terms of three rotations: flexion, rotation, and twist. Flexion only was analysed. Results All four rowing techniques displayed different flexion characteristics. Lumbar sacrum flexion was affected in different ways for all rowers. Lumbar thorasic flexion was more consistent between rowers for the different techniques: for example, overall flexion was increased in all cases for the 'heavy follow through'. Conclusions Good rowing technique is difficult to characterise using spinal and pelvic flexion alone. Some bad rowing techniques can be characterised using this technique, thus providing input to the trainee rower and coach.
Laser spectroscopy of crossed molecular beams: The dissociation energy of BaI from energy-balance measurements (1990)

Through application of energy-balance arguments to the crossed-beam reaction Ba(1S0)+HI(X 1Σ+) →BaI(X 2Σ+) +H(2S1/2), a lower limit for the BaI bond dissociation energy is determined to be D00(BaI) ≳76.8±1.7 kcal/mol (3.33±0.07 eV). Based on the upper bound of D00(BaI) ≲78.5±0.5 kcal/mol, as determined from earlier predissociation studies [M. A. Johnson, J. Allison, and R. N. Zare, J. Chem. Phys. 85, 5723 (1986)], we recommend a BaI bond strength of 77.7±2.0 kcal/mol (3.37±0.09 eV). This dissociation energy is more than 5 kcal/mol higher than the previously accepted value of D00(BaI) as derived from mass spectrometric measurements.
Effect of Chitosan as a Biological Sanitizer for Salmonella Typhimurium and Aerobic Gram Negative Spoilage Bacteria Present on Chicken Skin (2013)

Two experiments were conducted to evaluate the effect of chitosan as a biological sanitizer on chicken skin during storage. For experiment 1 (two trials) five skin samples of equal size were dipped into a solution containing 10 cfu/mL of Salmonella Typhimurium (ST) for 30s. Skin samples were then removed 6 and dipped into a solution containing PBS or 0.5% chitosan for 30s. In experiment 2, aerobic Gram negative spoilage bacteria were used as indicators instead of ST. In both experiments, all samples were placed in individual bags and kept at 4°C. In experiment 1, dipping ST contaminated skin samples in a solution of 0.5% chitosan reduced (p<0.05) the recovery of ST by 24 h. In experiment 2, 0.5% chitosan treatment solution reduced (p<0.05) the presence of spoilage-causing psychrotrophic bacteria below detectable levels. These results suggest that 0.5% chitosan has a potential for use in an intervention technology for the control of foodborne pathogens on the surface of chicken skin contaminated with bacteria during storage.
Dopamine in transplantation: Written off or comeback with novel indication? (2018)

Renal-dose dopamine has fallen out of favor in the intensive care unit (ICU) during past years due to its ineffectiveness to prevent impending or to ameliorate overt renal failure in the critically ill. By contrast, growing evidence indicates that low-dose dopamine administered to the stable organ donor after brain death confirmation improves the clinical course of transplanted organs after kidney and heart transplantation. Ensuring a thorough monitoring for potential circulatory side effects, employment of dopamine at a dose of 4 μg/kg/min is safe in the deceased donor. Among recipients, the advantageous effect is easy to achieve, inexpensive, and devoid of adverse side effects. The mode of action relies on dopamine's propensity to mitigate injury in various cell systems from isolated transplantable organs under cold storage conditions. The present review article summarizes the clinical evidence of dopamine donor pretreatment in solid organ transplantation and focuses on the underlying molecular mechanisms of cellular protection. Introducing the routine use of low-dose dopamine for the management of the brain-dead donor in the ICU before procurement provides an evidence-based strategy to improve graft outcome after kidney transplantation without conferring harm to non-renal grafts, namely to livers and hearts, in cases of multi-organ donation.
Rateless Coding for Arbitrary Channel Mixtures With Decoder Channel State Information (2009)

Rateless coding has recently been the focus of much practical as well as theoretical research. In this paper, rateless codes are shown to find a natural application in channels where the channel law varies unpredictably. Such unpredictability means that to ensure reliable communication block codes are limited by worst case channel variations. However, the dynamic decoding nature of rateless codes allows them to adapt opportunistically to channel variations. If the channel state selector is not malicious, but also not predictable, decoding can occur earlier, producing a rate of communication that can be much higher than the worst case. The application of rateless or ldquofountainrdquo codes to the binary erasure channel (BEC) can be understood as an application of these ideas. Further, this sort of decoding can be usefully understood as an incremental form of erasure decoding. The use of ideas of erasure decoding result in a significant increase in reliability.
Defining the molecular mode of binding for α‐linolenic acid and the synthetic ligand TUG891 at GPR120 (2013)

GPR120 is a receptor for long chain polyunsaturated fatty acids that has received growing interest in recent years for the treatment of type 2 diabetes and obesity. However, its development and validation as a therapeutic target has been hindered by a lack of selective ligands for GPR120 over another long chain fatty acid receptor, FFA1. While the recent description of 3‐(4‐((4‐fluoro‐4’‐methyl‐[1,1’‐biphenyl]‐2‐yl)methoxy)phenyl) propanoic acid (TUG891) as a potent and selective GPR120 agonist improved this situation, the need remains for novel GPR120 ligands. To facilitate ligand development at GPR120 we employed homology models and extensive mutagenesis to define the mode of binding at this receptor for an endogenous ligand, α‐linolenic acid (aLA), and TUG891. These studies confirmed that an ionic interaction between the carboxylate of the ligand with R99 of GPR120 is critical to both aLA and TUG891. Several additional residues, including W104, F115, F211, and W277, were found to define the hydrophobic binding pocket and their mutation reduced function to both aLA and TUG891. Finally, mutation of a group of residues including T119, I280 and I281 predicted to form a narrow binding pocket for the planar biphenyl moiety of TUG891 altered potency of TUG891 but not aLA. Together, our findings define key aspects of ligand interaction for both aLA and TUG891 and will be valuable in future drug development at GPR120.