gebhart/patrepeval huggingface dataset:
Explaining Dioscorides' "Double Difference": Why Are Some Mushrooms Poisonous, and Do They Signal Their Unprofitability? (2005)

The adaptive significance of toxins in mushrooms has received very little consideration, although it is clear that poisons have appeared (and/or disappeared) many times in mushrooms' evolutionary history. One possibility is that poisons have evolved in some mushroom species to deter their consumption by would‐be fungivores before spore dispersal. If this is so, then one might expect poisonous mushrooms to signal their unprofitability in some way. In this study, we have conducted the first formal analysis of the ecological and morphological traits associated with edible and poisonous mushrooms in North America and Europe. Poisonous mushrooms do not tend to be more colorful or aggregated than edible mushrooms, but they are more likely to exhibit distinctive odors even when phylogenetic relationships are accounted for. This raises the intriguing possibility that some poisonous species of mushrooms have evolved warning odors (and perhaps tastes) to enhance avoidance learning by fungivores.
A Highly Integrated 1.8 GHz Frequency Synthesizer Based on a MEMS Resonator (2009)

A highly integrated 1.7-2.0 GHz digitally programmable frequency synthesizer using a MEMS resonator as its reference is presented. Due to the dimensions of the MEMS device (e.g., 25 mum by 114 mum), the entire system with a total area of 6.25 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> can be housed in a small standard chip package. This considerably reduces the form factor and cost of the system, compared to using an external crystal as a reference. The MEMS resonators are clamped-clamped beams fabricated using a CMOS-compatible process. The main structural layer is made of silicon carbide, which provides the resonators with higher power handling capabilities and higher operating frequencies, compared to silicon. The resonators are electrostatically and thermally tunable - an 8.4% frequency tuning is demonstrated for a 9 MHz resonator. The 100 nm vertical transducer gaps of the resonators allow the use of electrostatic actuation voltages as low as 2 V. An integrated high gain-bandwidth trans-impedance amplifier (TIA) is combined with a resonator to generate the synthesizer's input reference signal. The TIA employs automatic gain control to mitigate the inherent low power handling capabilities and the non-linearities of the MEMS device, thus minimizing their effect on phase noise. The fractional- N synthesizer employs a 3rd-order 20-bit delta-sigma modulator to deliver a theoretical output resolution of ~ 11 Hz, in order to allow for high output frequency stability when used with an appropriate feedback loop. A fully integrated on-chip dual path loop filter is used to maintain a high level of system integration. With a supply voltage of 2 V, the phase noise for a 1.8 GHz output frequency and a ~12 MHz reference signal is -122 dBc/Hz at a 600 kHz offset, and -137 dBc/Hz at a 3 MHz offset.
Emerging genomic landscape and therapeutic targets in young patients with colorectal cancer (CRC). (2016)

3589 Background: Patients younger than 50 years comprise roughly 10% of the total incidence of CRC, but the incidence in young patients is increasing. This study investigated genomic differences between younger and older CRC tumors to identify potential therapeutic targets for this patient population. Methods: DNA was extracted from formalin-fixed, paraffin-embedded sections from 4699 cases of colorectal cancer (4001 colon and 698 rectal). Comprehensive genomic profiling was performed on hybridization-captured, adaptor ligation-based libraries to a mean specimen median sequencing depth of 688X for all coding exons and selected introns of up to 403 cancer-related genes. Younger patients with CRC were defined as < 40 years and older patients with CRC were defined as ≥ 55 years. P values were calculated using Fisher’s exact test; false discovery rate (FDR) and 95% confidence intervals (95%CI) were also calculated. Results: Gene alteration rates in the younger and older cohorts were similar in a majority of the genes analyzed. In the colon cancer analysis, alterations in CTNNB1 (p < 0.001, FDR = 0.08) and MLH1 (p < 0.001, FDR = 0.03) were found to be more common in younger patients compared to older patients. Older patients were more likely to have alterations in APC (p < 0.01, FDR < 0.01) and FAM123B (p < 0.01, FDR = 0.03). In the combined colon and rectal analysis, CTNNB1 (p < 0.001, FDR = 0.07) and MLH1 (p < 0.001, FDR = 0.02) alterations were found to be more common in younger patients with CRC, and APC (p < 0.01, FDR < 0.01) was more commonly altered in older patients with CRC. When focusing on truncating mutations and deletions only, young rectal cancer patients were found to have a log ratio of 3.7 for lesions in FAM123B (p = 0.02, 95%CI: 0.08-0.96) compared to colon cancer. CTNNB1 was found to have a 1.5X rate of mutation in colon compared to rectal cancer, not reaching statistical significance. Conclusions: In this analysis, younger patients and older patients demonstrated similar overall rates of genomic alterations. However, younger patients with CRC exhibited an increased rate of alteration in CTNNB1 and MLH1. These data may provide support to explore the WNT signaling pathway as a potential therapeutic target for younger patients with CRC.
sCD163 levels as a biomarker of disease severity in leprosy and visceral leishmaniasis (2017)

Taken together, our results reveal sCD163 as a potential biomarker of severity of diseases caused by intracellular pathogens M. leprae and Leishmania spp. and have a modulatory role, with a mix of an inflammatory property induced by TNF-α release, but that potentially induces an anti-inflammatory T cell response, related to IL-4 release.
Therapeutic targeting of prenatal pontine ID1 signaling in diffuse midline glioma (2022)

H3K27M-mediated re-activation of ID1 in DMG results in a SPARCL1+ migratory transcriptional program that is therapeutically targetable with CBD.
The Phosphine Oxide Route toward Lead Halide Perovskite Nanocrystals (2018)

We report an amine-free synthesis of lead halide perovskite (LHP) nanocrystals, using trioctylphosphine oxide (TOPO) instead of aliphatic amines, in combination with a protic acid (e.g., oleic acid). The overall synthesis scheme bears many similarities to the chemistry behind the preparation of LHP thin films and single crystals, in terms of ligand coordination to the chemical precursors. The acidity of the environment and hence the extent of protonation of the TOPO molecules tune the reactivity of the PbX<sub>2</sub> precursor, regulating the size of the nanocrystals. On the other hand, TOPO molecules are virtually absent from the surface of our nanocrystals, which are simply passivated by one type of ligand (e.g., Cs-oleate). Furthermore, our studies reveal that Cs-oleate is dynamically bound to the surface of the nanocrystals and that an optimal surface coverage is critical for achieving high photoluminescence quantum yield. Our scheme delivers NCs with a controlled size and shape: only cubes are formed, with no contamination with platelets, regardless of the reaction conditions that were tested. We attribute such a shape homogeneity to the absence of primary aliphatic amines in our reaction environment, since these are known to promote the formation of nanocrystals with sheet/platelet morphologies or layered phases under certain reaction conditions. The TOPO route is particularly appealing with regard to synthesizing LHP nanocrystals for large-scale manufacturing, as the yield in terms of material produced is close to the theoretical limit: i.e., almost all precursors employed in the synthesis are converted into nanocrystals.
Abstract 650: Animal Study Results Support that Biometal Artificial Muscle Restores Atrial Kick and Could Replace Oral Anticoagulation in Permanent Atrial Fibrillation (2008)

Treatment of persistent atrial fibrillation (AF) consists of ventricular rhythm control and the use of anticoagulant agents to decrease the high risk of stroke. However, patients under lifetime anticoagulation therapy are exposed to hemorrhagic stroke (1–3% patients/year). The best treatment to prevent stroke may induce stroke itself. Because decreased flow within the fibrillating atrium is associated with spontaneous echo contrast, thrombus formation and embolic events, any device able to restore the atrial kick (AK) should significantly reduce the risk of stroke and eventually improve cardiac output (CO). A motorless, volume displacement pump based on artificial muscle technology could reproduce the AK when placed onto a fibrillating atrium. This study has been designed to assess mechanical effects of this pump on the right cavities in an animal model of AF. Atripump (Nanopowers SA, Switzerland) is a dome shape silicone coated biometal actuator 5 × 45mm. The biometal is electrically actuated by a pacemaker like control unit. In 10 sheep the right atrium (RA) was surgically exposed and the dome sutured onto it. AF was induced with rapid epicardial pacing (600 beats/min). RA ejection fraction (EF) and spontaneous echo contrast was assessed with intracardiac ultrasound in baseline, AF and assisted AF status. A flow meter placed on pulmonary artery measured CO. Results The dome’s contraction rate was 60/min. Mean temperature on the RA was 39±1.5 °C. RA EF was 30% in baseline, 5% in AF and 22% in assisted AF conditions. During the AF state, spontaneous echo contrast was present in all animals and in 2 a thrombus appeared in the right appendix. Neither spontaneous echo contrast nor thrombi were present in baseline and AF assisted status. Thrombi were washed out when the pump was turned on. CO was 5.3±0.3 l/min in baseline, 4.4±0.6 l/min in AF and 5.1±0.3 l/min in assisted AF status (p&lt;0.01). Placed on the right side, the artificial muscle restores the AK, improves CO and shows a mechanical anti coagulant effect. In patients with permanent AF, if implanted on both sides, it would improve CO and prevent embolism of cardiac origin. The implantation technique could be comparable to that of a pacemaker.
Expression, Receptor Binding, and Biophysical Characterization of Guinea Pig Insulin desB30: A Monomeric Insulin Variant (2015)

Here we report, for the first time, the heterologous expression of desB30 guinea pig insulin (GI desB30) in the yeast Saccharomyces cerevisiae. The affinities of GI desB30 for the insulin receptor A and the IGF-I receptor were also quantified for the first time. Small-angle X-ray scattering and analytical ultracentrifugation studies confirmed that GI desB30 did not form dimers or hexamers, in contrast to human insulin. Size-exclusion chromatography connected to inductively coupled plasma mass spectrometry revealed that GI desB30 has affinity towards several divalent metal ions. These studies did not indicate the formation of any larger structures of GI desB30 in the presence of various divalent metal ions, but did indicate that GI desB30 has an affinity towards Mn, Co, and Cu ions. Finally, the low affinity for the insulin receptor and the very low affinity for the IGF-I receptor by GI desB30 were quantified.
Chemoprotection by Transfer of Resistance Genes (2009)

Dose-limiting toxicity of chemotherapeutic agents, i.e., myelosuppression, can limit their effectiveness. The transfer and expression of drug-resistance genes might decrease the risks associated with acute hematopoietic toxicity. Protection of hematopoietic stem/progenitor cells by transfer of drug-resistance genes provides the possibility of intensification or escalation of antitumor drug doses and consequently an improved therapeutic index. This chapter reviews drug-resistance gene transfer strategies for either myeloprotection or therapeutic gene selection. Selecting candidate drug-resistance gene(s), gene transfer methodology, evaluating the safety and the efficiency of the treatment strategy, relevant in vivo models, and oncoretroviral transduction of human hematopoietic stem/progenitor cells under clinically applicable conditions are described.
Class A Orphans in GtoPdb v.2022.3 (2022)

Table 1 lists a number of putative GPCRs identified by NC-IUPHAR [161], for which preliminary evidence for an endogenous ligand has been published, or for which there exists a potential link to a disease, or disorder. These GPCRs have recently been reviewed in detail [121]. The GPCRs in Table 1 are all Class A, rhodopsin-like GPCRs. Class A orphan GPCRs not listed in Table 1 are putative GPCRs with as-yet unidentified endogenous ligands.Table 1: Class A orphan GPCRs with putative endogenous ligands GPR3GPR4GPR6GPR12GPR15GPR17GPR20 GPR22GPR26GPR31GPR34GPR35GPR37GPR39 GPR50GPR63GPR65GPR68GPR75GPR84GPR87 GPR88GPR132GPR149GPR161GPR183LGR4LGR5 LGR6MAS1MRGPRDMRGPRX1MRGPRX2P2RY10TAAR2 In addition the orphan receptors GPR18, GPR55 and GPR119 which are reported to respond to endogenous agents analogous to the endogenous cannabinoid ligands have been grouped together (GPR18, GPR55 and GPR119).
A Sensitive Formaldehyde Sensor Based on Cataluminescence Coupled with Thermal Desorption (2014)

A sensitive cataluminescence-based detecting technology using nanosized Mo 4 V 6 Ti 10 O 47 as a probe was proposed for determination of formaldehyde in air. Trace formaldehyde was firstly absorbed on active carbon at room temperature to concentrate, then desorbed at 75°C to determine. The method showed high selectivity to formaldehyde at wavelength of 575nm, satisfying activity at temperature of 260°C and good stability at carrier flow rate of 145 ml/min. The linear range of CTL intensity versus concentration of formaldehyde was 0.04~78 mg/m 3 , and the detection limit (3σ) was 0.02 mg/m 3 . The recovery of artificial sample was 96.8%-103.4% by this method. There was no response to CO, CO 2 , SO 2 , NH 3 , methanol, ethanol, benzene, toluene and xylenes.
The Solanum americanum pangenome and effectoromics reveal new resistance genes against potato late blight (2022)

Abstract Late blight caused by the oomycete pathogen Phytophthora infestans continues to cause major worldwide losses in potato and tomato. Most accessions of Solanum americanum , a globally distributed, wild Solanaceae plant, are highly resistant to late blight. We generated high-quality reference genomes of four S. americanum accessions, re-sequenced 52 accessions, and we defined variation in the NLR immune receptor genes (the S. americanum NLRome). We further screened for variation in recognition of ∼315 P. infestans RXLR effectors in 52 S. americanum accessions. Using these genotypic and phenotypic data, we cloned three novel NLR-encoding genes Rpi-amr4, Rpi-amr16 and Rpi-amr17 , and determined their corresponding RXLR effector genes Avramr4 ( PITG_22825 ), Avramr16 ( PITG_02860 ) and Avramr17 ( PITG_04373 ) from P. infestans . These genomic resources and methodology will support efforts to convert potato into a “nonhost” of late blight and can be applied to diseases of other crops.
Optimizing CNNs on Multicores for Scalability, Performance and Goodput (2017)

Convolutional Neural Networks (CNN) are a class of Ar- tificial Neural Networks (ANN) that are highly efficient at the pattern recognition tasks that underlie difficult AI prob- lems in a variety of domains, such as speech recognition, object recognition, and natural language processing. CNNs are, however, computationally intensive to train. This paper presents the first characterization of the per- formance optimization opportunities for training CNNs on CPUs. Our characterization includes insights based on the structure of the network itself (i.e., intrinsic arithmetic inten- sity of the convolution and its scalability under parallelism) as well as dynamic properties of its execution (i.e., sparsity of the computation).
Site Selective Formation of Thymine Glycol-Containing Oligodeoxynucleotides by Oxidation with Osmium Tetroxide and Bipyridine-Tethered Oligonucleotide (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSite Selective Formation of Thymine Glycol-Containing Oligodeoxynucleotides by Oxidation with Osmium Tetroxide and Bipyridine-Tethered OligonucleotideKazuhiko Nakatani, Shinya Hagihara, Shinsuke Sando, Hiroshi Miyazaki, Kazuhito Tanabe, and Isao SaitoView Author Information Department of Synthetic Chemistry and Biological Chemistry Faculty of Engineering, Kyoto University CREST, Japan Science and Technology Corporation (JST) Kyoto 606-8501, Japan Cite this: J. Am. Chem. Soc. 2000, 122, 26, 6309–6310Publication Date (Web):June 17, 2000Publication History Received7 February 2000Published online17 June 2000Published inissue 1 July 2000https://pubs.acs.org/doi/10.1021/ja0004478https://doi.org/10.1021/ja0004478rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views712Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Genetics,Osmium,Oxidation,Thymine Get e-Alerts
Rivlin’s Representation Formula is Ill-Conceived for the Determination of Response Functions via Biaxial Testing (2006)

The experimental determination of a strain energy function W for a rubber specimen must address departures from an elastic ideal in a rational fashion. Herein, such a rational experimental method is developed for biaxial stretching experiments and applied to rubber data in the literature. It is shown that Rivlin’s representation formula is experimentally ill-conceived because experimental error is magnified to the extent that error obscures trends in the response function plots. Upon developing direct tensor expressions for the response function calculations, we show that Rivlin’s representation formula (or any such constitutive law that has high covariance amongst the response terms) magnifies experimental error greatly. By “high covariance”, we mean the inner product amongst the response terms in the constitutive law is nearly equal to the maximum possible value — i.e., the product of their magnitudes. Moreover, we show that the second partials of W with respect to I1 and I2 should approach infinity as the strain decreases. Using an alternate set of invariants with minimal covariance (i.e., a null inner product amongst the response terms), a W for rubber can be determined forthwith.
Initial investigation of the blood-brain barrier in MS lesions at 7 tesla (2012)

Most active lesions are perivenular, and the smallest lesions enhance centrifugally. This supports the idea that lesions grow outward from a central vein.
Fabrication of diffractive optics for dense optical interconnects in optical computing (2009)

We designed and fabricated an optical system containing high efficiency diffractive optical elements (DOEs) with large numerical apertures (NA) for an all-optical gate, based on a Symmetric Self-Electro-Optic Effect Device (S-SEED) technology. The S-SEEDs are the active elements that perform the optical switching in the optical interconnect. Multiple, off-axis DOEs are used to collect and focus light onto the S-SEEDs and the Input/Output optical fibers. Each S-SEED has at least seven input signals, two alignment signals, and two output signals. Each signal uses a DOE. DOE fabrication is relatively mature and utilizes the precise lateral alignment inherent in photolithography to produce arrays compatible with dense optical interconnects. Losses across the system have a negative impact on the S-SEED switching speeds. The primary challenge of DOEs is the diffractive optic efficiency that corresponds to high NAs. Lower efficiencies, due to requirements for large deflection angles, lead to extremely small feature sizes in the outer zones of the DOEs. We optimize DOE efficiency with modifications to the blaze geometry and by selecting the appropriate number of levels for specific deflection angles. The system layout is modified to reduce complexity by working in collimated space between the S-SEEDs instead of imaging onto relay mirrors. This reduces the spatial frequency of the DOEs and increases system tolerance by not imaging mirror defects. Finally, we quantify the effects of lithographic masks misalignment and look at the step geometry deviations and their effects on DOE efficiency.
Minocycline Reduces Cell Death and Improves Functional Recovery after Traumatic Spinal Cord Injury in the Rat (2003)

We examined the effects of minocycline, an anti-inflammatory drug, on functional recovery following spinal cord injury (SCI). Rats received a mild, weight-drop contusion injury to the spinal cord and were treated with the vehicle or minocycline at a dose of 90 mg/kg immediately after SCI and then twice at a dose of 45 mg/kg every 12 h. Injecting minocycline after SCI improved hind limb motor function as determined by the Basso-Beattie-Bresnahan (BBB) locomotor open field behavioral rating test. Twenty four to 38 days after SCI, BBB scores were significantly higher in minocycline-treated rats as compared with those in vehicle-treated rats. Morphological analysis showed that lesion size increased progressively in both vehicle-treated and minocycline-treated spinal cords. However, in response to treatment with minocycline, the lesion size was significantly reduced at 21-38 days after SCI when compared to the vehicle control. Minocycline treatment significantly reduced the number of terminal deoxynucleotidyl transferase (TdT)-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL)-positive cells 24 h after SCI as compared to that of the vehicle control. DNA gel electrophoresis also revealed a marked decrease in DNA laddering in response to treatment with minocycline. In addition, minocycline treatment significantly reduced the specific caspase-3 activity after SCI as compared to that of vehicle control. Furthermore, RT-PCR analyses revealed that minocycline treatment increased expression of interleukin-10 mRNA but decreased tumor necrosis factor-alpha expression. These data suggest that, after SCI, minocycline treatment modulated expression of cytokines, attenuated cell death and the size of lesions, and improved functional recovery in the injured rat. This approach may provide a therapeutic intervention enabling us to reduce cell death and improve functional recovery after SCI.