gebhart/patrepeval huggingface dataset:
Sequestration of Inflammation in Parkinson’s Disease via Stem Cell Therapy (2022)

Parkinson's disease is the second most common neurodegenerative disease. Insidious and progressive, this disorder is secondary to the gradual loss of dopaminergic signaling and worsening neuroinflammation, affecting patients' motor capabilities. Gold standard treatment includes exogenous dopamine therapy in the form of levodopa-carbidopa, or surgical intervention with a deep brain stimulator to the subcortical basal ganglia. Unfortunately, these therapies may ironically exacerbate the already pro-inflammatory environment. An alternative approach may involve cell-based therapies. Cell-based therapies, whether endogenous or exogenous, often have anti-inflammatory properties. Alternative strategies, such as exercise and diet modifications, also appear to play a significant role in facilitating endogenous and exogenous stem cells to induce an anti-inflammatory response, and thus are of unique interest to neuroinflammatory conditions including Parkinson's disease. Treating patients with current gold standard therapeutics and adding adjuvant stem cell therapy, alongside the aforementioned lifestyle modifications, may ideally sequester inflammation and thus halt neurodegeneration.
Thermally induced interface degradation in (111) Si/Si<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>traced by electron spin resonance (1996)

Thermal post-oxidation interface degradation in (111) Si/Si${\mathrm{O}}_{2}$ has been isolated by electron-spin resonance (ESR) as a permanent ${P}_{b}$ (Si \ensuremath{\equiv} ${\mathrm{Si}}_{3}$) interface defect creation. This process, initiating from \ensuremath{\sim}640 \ifmmode^\circ\else\textdegree\fi{}C onward, reveals interface breakdown on an atomic scale as interfacial SiO bond rupture. The crucial creation step has been isolated as thermal cycling in an O-free ambient. Once created, the new ${P}_{b}$ system exhibits similar fully reversible H passivation-depassivation kinetics as the preexisting one, naturally introduced during oxidation. ESR is herewith raised to a powerful probe for Si/Si${\mathrm{O}}_{2}$ degradation.
A 90-nm Low-Power 32-kB Embedded SRAM With Gate Leakage Suppression Circuit for Mobile Applications (2004)

In sub-100-nm generation, gate-tunneling leakage current increases and dominates the total standby leakage current of LSIs based on decreasing gate-oxide thickness. Showing that the gate leakage current is effectively reduced by lowering the gate voltage, we propose a local dc level control (LDLC) for SRAM cell arrays and an automatic gate leakage suppression driver (AGLSD) for peripheral circuits. We designed and fabricated a 32-kB 1-port SRAM using 90-nm CMOS technology. The six-transistor SRAM cell size is 1.25 /spl mu/m/sup 2/. Evaluation shows that the standby current of 32-kB SRAM is 1.2 /spl mu/A at 1.2 V and room temperature. It is reduced to 7.5% of conventional SRAM.
Safety of Vaccinating Beef Replacement Heifers at Weaning Against 18 Antigens (1994)

Humoral immune responses to vaccination, mean daily gains, morbidity, and mortality were compared in groups of beef replacement heifers from weaning to 4 months after weaning. The only difference in management among groups of heifers was the number and type of vaccines they received. Heifers were vaccinated at weaning (mean age, 205 days) and again 28 days later against 0, 1, 9, 10, 17, or 18 antigens, using commercially available monovalent and multivalent vaccines. Mean daily gain, morbidity, mortality, and serum neutralization antibody titers to bovine respiratory syncytial virus, infectious bovine rhinotracheitis virus, and bovine viral diarrhea virus did not differ among treatment groups. Although the study revealed the safety of vaccinating beef heifers against 18 antigens at weaning, our data emphasized the need for serial vaccination to induce a measurable serum antibody response in animals not exposed previously to the vaccine antigens.
Erratum: Corrigendum: Analysis of self-antigen specificity of islet-infiltrating T cells from human donors with type 1 diabetes (2017)

Nat. Med.; 10.1038/nm.4203; corrected online 15 November 2016 In the version of this article initially published online, the authors forgot to acknowledge the islet-isolation team at the Diabetes Research Institute, University of Miami. This oversight has been corrected for the print, PDF and HTML versions of this article.
Development of a novel large damage site mitigation technique (2022)

We present the development of carefully tailored shape - increased size (0.9 mm diameter) input surface mitigation sites that shadow and thus supress damage growth on the exit surface of optics. Results from downstream intensification measurements and laser induced damage experiments are presented. The results show a 6X reduction in expanding wave intensification on the exit surface of an optic, being the dominant damage onset mechanism. The tailored rounded cone design can withstand over 30 J/cm<sup>2</sup> sub aperture input surface fluence. A significant decrease in laser induced damage initiation and growth was observed compared to shadow cones with linear profiles at input fluences higher than 10 J/cm<sup>2</sup>.
The mechanical creep compliance of tissue cells is gamma distributed (2010)

Investigations of natural variation among cells within a population are essential for understanding the stochastic nature of tissue cell deformation under applied load. In the existing literature, the population variation of single-cell creep compliance has so far been modeled universally by using a log-normal distribution. Here we use optical stretching, a non-contact and relatively high-throughput technique for probing cell mechanics, to accumulate a sufficient data set that demonstrates robustly that cell compliance varies according to the similar but distinct gamma distribution. Additionally, we re-examine existing simulations that were originally proposed to justify a log-normal fit, and show that in fact these simulation data also correspond to the gamma distribution. Finally, we propose a general stochastic differential equation that analytically predicts a gamma distribution of creep compliance during cell stretching, as well as the Gaussian distribution of cell recovery that we observe experimentally upon removal of applied load. The population variation is well characterized by just a single parameter in each of the creep and recovery regimes. We expect our correction of a phenomenological distribution fit, enabled by an expansive data set for mesenchymal stem cells, to enable the development of more accurate constitutive laws to describe cytoskeletal deformation. These findings thus serve to replace an empirical distribution with a better-fitting model that rests on a more solid experimental and theoretical foundation, and also provides a basis to predict and understand the stochastic nature of the mechanical response of individual cells within populations.
Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying essential circRNAs (2020)

Abstract Circular RNAs (circRNAs) are widely expressed, but their functions remain largely unknown. To study circRNAs in a high-throughput manner, short hairpin RNA (shRNA) screens 1 have recently been used to deplete circRNAs by targeting their unique back-splicing junction (BSJ) sites. Here, we report frequent discrepancies between shRNA-mediated circRNA knockdown efficiency and the corresponding biological effect, raising pressing concerns about the robustness of shRNA screening for functional circRNAs. To address this issue, we leveraged the CRISPR/Cas13d system 2 for circRNAs functional screenings. We optimized a strategy for designing single guide RNAs to deplete circRNAs. We then performed shRNA and CRISPR/Cas13d parallel screenings and demonstrated that shRNA-mediated circRNAs screening yielded a high rate of false positives phenotypes, while optimized CRISPR/Cas13d led to the identification of bona-fide functional circRNAs. Collectively, we developed a specific and reliable approach to functionalize circRNAs in a high-throughput manner.
New atomic force microscope method for critical dimension metrology (2003)

We have developed a new atomic force microscope method that we call Step-in mode. The Step-in mode can realize a high aspect ratio structure observation without tip damage becasue of its unique probing method. Three types of high aspect ratio probe, a silicon probe sharpened by focused ion beam, a high density carbon probe and a carbon nanotube probe, are analyzed to make clear which probe is appropriate for high aspect ratio structure metrology. It is demonstrated that fine measurement can be carried out with all types of probes and we conclude that the high density carbon probe is the best at the present time. Experimental results show that the pitch repeatability for a standard grating sample is 1.2 nm at 3&sigma;, height repeatability is 1.2nm at 3&sigma; and width repeatability of a poly-silicon gate with side-wall is less than 3 nm at 3&sigma;. It is also demonstrated that there is no tip damage after taking 1000 profiles of 512 data points in the Step-in mode. The experimental results show that the Step-in mode. The experimental results show that the Step-in mode has a potential for application to critical dimension metrology for a LSI process monitor.
Analysis of a PM Machine with Concentrated Fractional Pitch Windings (2004)

Abstract—Permanent magnet machines with concentrated fractional pitch windings for servo and traction applications are growing in popularity. This paper deals with analysis of a novel synchronous permanent magnet machine using concentrated windings and grain-oriented and non-oriented silicon iron sheets for the teeth and yoke, respectively. Parasitic effects like unbalanced radial forces and alternating magnetic fields in the rotor, due to a non-symmetrical magnetic design of the presented machine, are described. Measurements on a laboratory prototype are performed and the results are compared to finite element method computation results to identify the heat transfer coefficients of the electrical machine. Index Terms—Permanent magnet machines, concentrated windings, thermal calculations, parasitic effects, measurements. I.
Disorder in P3HT Nanoparticles Probed by Optical Spectroscopy on P3HT-<i>b</i>-PEG Micelles (2021)

We employ photoluminescence (PL) spectroscopy on individual nanoscale aggregates of the conjugated polymer poly(3-hexylthiophene), P3HT, at room temperature (RT) and at low temperature (LT) (1.5 K), to unravel different levels of structural and electronic disorder within P3HT nanoparticles. The aggregates are prepared by self-assembly of the block copolymer P3HT-<i>block</i>-poly(ethylene glycol) (P3HT-<i>b</i>-PEG) into micelles, with the P3HT aggregates constituting the micelles' core. Irrespective of temperature, we find from the intensity ratio between the 0-1 and 0-0 peaks in the PL spectra that the P3HT aggregates are of H-type nature, as expected from π-stacked conjugated thiophene backbones. Moreover, the distributions of the PL peak ratios demonstrate a large variation of disorder between micelles (inter-aggregate disorder) and within individual aggregates (intra-aggregate disorder). Upon cooling from RT to LT, the PL spectra red-shift by 550 cm<sup>-1</sup>, and the energy of the (effective) carbon-bond stretch mode is reduced by 100 cm<sup>-1</sup>. These spectral changes indicate that the P3HT backbone in the P3HT-<i>b</i>-PEG copolymer does not fully planarize before aggregation at RT and that upon cooling, partial planarization occurs. This intra-chain torsional disorder is ultimately responsible for the intra- and inter-aggregate disorder. These findings are supported by temperature-dependent absorption spectra on thin P3HT films. The interplay between intra-chain, intra-aggregate, and inter-aggregate disorder is key for the bulk photophysical properties of nanoparticles based on conjugated polymers, for example, in hierarchical (super-) structures. Ultimately, these properties determine the usefulness of such structures in hybrid organic-inorganic materials, for example, in (bio-)sensing and optoelectronics applications.
Author response: The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria (2013)

Microbes are ubiquitous in the world and exist in complex communities called microbiomes that have colonized many environments, including the human gut. Until modern techniques for sequencing nucleic acids became available, many of the organisms found in these microbiomes could not be studied because they could not be cultured in the laboratory. However, advances in sequencing technology have made it possible to study the evolution and properties of these microbes, including their impact on human health. Bacteria belonging to the phylum Cyanobacteria had a significant effect on the prehistoric Earth because they were the first organisms to produce gaseous oxygen as a byproduct of photosynthesis, and thus shaped the Earth’s oxygen-rich atmosphere. Early plants took up these bacteria in a symbiotic relationship, and plastids—the organelles in plant cells that perform photosynthesis and produce oxygen–are the descendants of Cyanobacteria. Organisms evolutionarily related to Cyanobacteria have been found in the human gut and in various aquatic sources, but these bacteria have not been studied because it has not been possible to isolate or culture them. Now, Di Rienzi, Sharon et al. have used modern sequencing techniques to obtain complete genomes for some of these bacteria, which they assign to a new phylum called Melainabacteria. By analyzing these genomes, Di Rienzi, Sharon et al. were able to make predictions about the cell structure and metabolic abilities of Melainabacteria. Like Cyanobacteria, they have two membranes surrounding the bacterial cell; unlike Cyanobacteria, however, they have flagella that propel them through liquid or across surfaces. Most interestingly, Melainabacteria are not able to perform photosynthesis, but instead produce energy through fermentation and release hydrogen gas that can be consumed by other microorganisms. The genome of the bacteria isolated from water reveals that it has the capacity to fix nitrogen. Cyanobacteria can also fix atmospheric nitrogen, but the protein complexes used by the two phyla are not related, which suggests that nitrogen fixation evolved after the evolutionary divergence of Cyanobacteria and Melainabacteria. By exploring previously published datasets of bacterial communities, Di Rienzi, Sharon et al. found that Melainabacteria are common in aquatic habitats. They are also prevalent in the guts of herbivorous mammals and humans with a predominantly vegetarian diet. Melainabacteria from the human gut also synthesize several B and K vitamins, which suggests that these bacteria are beneficial to their host because in addition to aiding with the digestion of plant fibers, they are also a source of vitamins.
High resolution electron microscopy of molecular crystals. IV. Paraffins and their solid solutions (1997)

Lattice images of dislocations, growth boundaries and surface structure, of the n-paraffin series have been obtained by high resolution electron microscopy. The crystals were grown so that the chain axes of the paraffin molecules were normal to the incident beam enabling distortion created by chain end interactions to be resolved. Solid solutions of paraffins within four carbon units in length, crystallized without eutectic segregation, irrespective of the even or odd numbers of carbon in the chains. However, for paraffins separated by only one or two carbon units there was lattice exfoliation at the crystal boundaries, which we have interpreted as evidence for an interblock structure with segregation of the minor component to the crystal boundaries.
The measurement of lysosomal phospholipase A2 activity in plasma (2010)

A deficiency of lysosomal phospholipase A2 (LPLA2) causes macrophage-associated phospholipidosis, suggesting that the enzyme is important in the lipid catabolism. Because LPLA2 is secreted by macrophages, extracellular LPLA2 activity may potentially reflect a change in macrophage activation. In this report, the detection of LPLA2 activity in plasma was established by the measurement of the transacylase activity of LPLA2 under acidic conditions. No transacylase activity of LPLA2 was detected in normal human plasma when the plasma was incubated with liposomes consisting of 1,2-dioleoylphosphatidylcholine/sulfatide/N-acetylsphingosine (NAS) at pH 4.5. However, the transacylase activity in the plasma was detected when liposomes consisting of 1,2-dioleoylphosphatidylglycerol/NAS were used as a substrate. To establish the specificity of the assay, ceramide transacylase activity was detected in the plasma of wild-type mice. By contrast, the plasma obtained from LPLA2-knockout mice had no measurable transacylase activity under the same conditions. The enzymatic activity of recombinant LPLA2 was inhibited by treatment with methylarachidonylfluorophosphonate. The inhibitor also suppressed the transacylase activity observed in both normal human and wild-type mouse plasma, establishing that the transacylase activity observed in plasma is due to LPLA2. Plasma LPLA2 activity may be a useful bioassay marker for the identification of LPLA2-related disorders.
Compact Microwave Rectifier with Wide Input Power Dynamic Range Based on Integrated Impedance Compression Network (2019)

A compact rectifier with high efficiency at wide input power dynamic range is proposed in this paper. The circuit consists of a matching network, two shunt connected diodes with an integrated impedance compression network (IICN) and a dc-pass filter. The IICN significantly reduces the diode impedance variation when input power changes, hence improves matching as well as efficiency of the rectifier at wide input power dynamic range. Different from the conventional resistance/impedance compression networks, which can only work under certain impedance condition with dual-branch topology, the IICN can directly operate two diodes in parallel in a single-branch with no impedance limitation. Thus, less components and branch are needed, resulting in size reduction and lower circuit complexity. The design flexibility is also enhanced. Mechanism of the IICN is analyzed. A prototype operating at 2.45 GHz is optimized, fabricated and measured. The total size of the prototype is 0.18λ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The efficiency higher than 70% of the peak value is realized at input power ranging from 0.8 dBm to 18.0 dBm.
Frontline: An in‐depth evaluation of the production of IL‐2 by antigen‐specific CD8 T cells <i>in vivo</i> (2004)

IL-2 is an important cytokine that is capable of inducing both proliferation and apoptosis of activated T cells. CD4 T cells are thought to be the major producers of IL-2, but CD8 T cells also produce copious amounts of this cytokine. However, our current understanding regarding the kinetics of IL-2 production by antigen-specific CD8 T cells, and the proportion of these cells that produce IL-2 in vivo, is extremely limited. We now demonstrate that virus-specific CD8 T cells initiate IL-2 production by 6 h post-infection and prior to cell division in vivo. Interestingly, peak levels of IL-2 production were achieved very early during the response and prior to the proliferative peak. We also show -- using transgenic mice expressing herpes simplex virus-1 thymidine kinase under the control of the IL-2 promoter -- that, unlike what has been reported for antigen-specific CD4 T cells, the majority of antigen-specific CD8 T cells produce IL-2 during primary as well as secondary immune responses in vivo.
Urea-Based Inhibitors of Trypanosoma brucei Methionyl-tRNA Synthetase: Selectivity and in Vivo Characterization (2012)

Urea-based methionyl-tRNA synthetase inhibitors were designed, synthesized, and evaluated for their potential toward treating human African trypanosomiasis (HAT). With the aid of a homology model and a structure-activity-relationship approach, low nM inhibitors were discovered that show high selectivity toward the parasite enzyme over the closest human homologue. These compounds inhibit parasite growth with EC(50) values as low as 0.15 μM while having low toxicity to mammalian cells. Two compounds (2 and 26) showed excellent membrane permeation in the MDR1-MDCKII model and encouraging oral pharmacokinetic properties in mice. Compound 2 was confirmed to enter the CNS in mice. Compound 26 had modest suppressive activity against Trpanosoma brucei rhodesiense in the mouse model, suggesting that more potent analogues or compounds with higher exposures need to be developed. The urea-based inhibitors are thus a promising starting point for further optimization toward the discovery of orally available and CNS active drugs to treat HAT.
RE: ARGYROPHILIC NUCLEOLAR ORGANIZER REGION IN PROLIFERATING CELL HAS A PREDICTIVE VALUE FOR LOCAL RECURRENCE IN SUPERFICIAL BLADDER TUMOR (2000)

No AccessJournal of UrologyLETTERS TO THE EDITOR1 May 2000RE: ARGYROPHILIC NUCLEOLAR ORGANIZER REGION IN PROLIFERATING CELL HAS A PREDICTIVE VALUE FOR LOCAL RECURRENCE IN SUPERFICIAL BLADDER TUMOR M. Tomobe, T. Shimazui, K. Uchida, S. Hinotsu, and H. Akaza M. TomobeM. Tomobe More articles by this author , T. ShimazuiT. Shimazui More articles by this author , K. UchidaK. Uchida More articles by this author , S. HinotsuS. Hinotsu More articles by this author , and H. AkazaH. Akaza More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)67665-3AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "RE: ARGYROPHILIC NUCLEOLAR ORGANIZER REGION IN PROLIFERATING CELL HAS A PREDICTIVE VALUE FOR LOCAL RECURRENCE IN SUPERFICIAL BLADDER TUMOR." The Journal of Urology, 163(5), p. 1525 References 1 : Role of the argyrophilic nucleolar organizer regions in tumor detection and prognosis. Cancer Detect Prev1995; 19: 282. Google Scholar 2 : Evaluation of the argyrophilic nucleolar organizer region, nuclear DNA content and mean nuclear area in transitional cell carcinoma of bladder using a quantitative image analyzer. Eur Urol1996; 29: 99. Google Scholar © 2000 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 163Issue 5May 2000Page: 1525 Advertisement Copyright & Permissions© 2000 by American Urological Association, Inc.Metrics Author Information M. Tomobe More articles by this author T. Shimazui More articles by this author K. Uchida More articles by this author S. Hinotsu More articles by this author H. Akaza More articles by this author Expand All Advertisement PDF downloadLoading ...
Dynamic Analysis of Noncollocated Flexible Arms and Design of Torque Transmission Mechanisms (1991)

A new actuation method for one-link flexible arms is presented. The endpoint control of a flexible arm has been known to be a nonminimum phase system due to the noncollocated sensor and actuator. By relocating the actuator near the endpoint, the system can be changed to a minimum phase system. In order to implement this, transmission mechanisms are developed which transform the actuator torque to appropriate force and torque and transmit them to an appropriate point on the arm link. Exact pole-zero configurations are analyzed with regard to the location of the actuation point and the type of transmissions. We then develop an integrated design method, which allows for relocating zeros for an improved control performance. A prototype flexible arm is designed based on the design guidelines and open loop and closed loop tests are made to verify the effectiveness.