gebhart/patrepeval huggingface dataset:
Prkdc participates in mitochondrial genome maintenance and prevents Adriamycin-induced nephropathy in mice (2010)

Adriamycin (ADR) is a commonly used chemotherapeutic agent that also produces significant tissue damage. Mutations to mitochondrial DNA (mtDNA) and reductions in mtDNA copy number have been identified as contributors to ADR-induced injury. ADR nephropathy only occurs among specific mouse inbred strains, and this selective susceptibility to kidney injury maps as a recessive trait to chromosome 16A1-B1. Here, we found that sensitivity to ADR nephropathy in mice was produced by a mutation in the Prkdc gene, which encodes a critical nuclear DNA double-stranded break repair protein. This finding was confirmed in mice with independent Prkdc mutations. Overexpression of Prkdc in cultured mouse podocytes significantly improved cell survival after ADR treatment. While Prkdc protein was not detected in mitochondria, mice with Prkdc mutations showed marked mtDNA depletion in renal tissue upon ADR treatment. To determine whether Prkdc participates in mtDNA regulation, we tested its genetic interaction with Mpv17, which encodes a mitochondrial protein mutated in human mtDNA depletion syndromes (MDDSs). While single mutant mice were asymptomatic, Prkdc/Mpv17 double-mutant mice developed mtDNA depletion and recapitulated many MDDS and ADR injury phenotypes. These findings implicate mtDNA damage in the development of ADR toxicity and identify Prkdc as a MDDS modifier gene and a component of the mitochondrial genome maintenance pathway.
Ultrasonic coronal scanning of left upper quadrant. (1981)

The left upper quadrant of the abdomen is frequently a "blind" area for ultrasonographic scanning due to the preponderance of gas in the stomach and splenic flexure of the colon, which obscures the deeper structures. Longitudinal scans, particularly when done vertically, are generally of no use in this region. A portion of the transverse scan, aiming the beam horizontally from the left midaxillary line can be somewhat helpful. Coronal planes of section using real-time equipment, aimed medially from the midaxillary line with the patient supine, allow improved visualization of the left upper quadrant. Conventional scanning with the patient rotated into a right posterior oblique or right-side-down decubitus position can also be useful. cases are presented to illustrate this technique.
Code related to "Implications of non-linearities between cumulative CO2 emissions and CO2-induced warming for assessing the remaining carbon budget" (2020)

Code and data to create our publication about remaining carbon budget assessment frameworks (https://doi.org/10.1088/1748-9326/ab83af).
Near‐infrared Raman spectroscopy for optical diagnosis of lung cancer (2003)

Raman spectroscopy is a vibrational spectroscopic technique that can be used to optically probe the molecular changes associated with diseased tissues. The objective of our study was to explore near-infrared (NIR) Raman spectroscopy for distinguishing tumor from normal bronchial tissue. Bronchial tissue specimens (12 normal, 10 squamous cell carcinoma (SCC) and 6 adenocarcinoma) were obtained from 10 patients with known or suspected malignancies of the lung. A rapid-acquisition dispersive-type NIR Raman spectroscopy system was used for tissue Raman studies at 785 nm excitation. High-quality Raman spectra in the 700-1,800 cm(-1) range from human bronchial tissues in vitro could be obtained within 5 sec. Raman spectra differed significantly between normal and malignant tumor tissue, with tumors showing higher percentage signals for nucleic acid, tryptophan and phenylalanine and lower percentage signals for phospholipids, proline and valine, compared to normal tissue. Raman spectral shape differences between normal and tumor tissue were also observed particularly in the spectral ranges of 1,000-1,100, 1,200-1,400 and 1,500-1,700 cm(-1), which contain signals related to protein and lipid conformations and nucleic acid's CH stretching modes. The ratio of Raman intensities at 1,445 to 1,655 cm(-1) provided good differentiation between normal and malignant bronchial tissue (p < 0.0001). The results of this exploratory study indicate that NIR Raman spectroscopy provides significant potential for the noninvasive diagnosis of lung cancers in vivo based on the optic evaluation of biomolecules.
Name anomaly detection for ICN (2016)

Information leakages are one of the main security threats in today's Internet. As ICN is expected to become the core architecture for Future Internet, it is therefore mandatory to prevent this threat. This paper proves that some ICN configuration prevents information leakages via Data packets and shows that it is an open problem to prevent interest packets from carrying encoded crucial information in their names. Assuming that names in ICN will follow the current URL format commonly used in the Internet, we get the statistics of web URL based on extensive crawling experiments of main internet organizations. Then we propose a simple filtering technique based on these statistics for firewall to detect anomalous names in ICN. The experiment shows that our filtering technique recognizes 15% of names in our dataset as malicious. As the false positive rate is still high for this filter to be used in a real world operation, this work is an important step for detecting anomalous names and preventing information-leakage in ICN.
Acute inflammation alters the response to stretch in mouse extensor digitorum longus muscle afferents (2012)

Inflammatory pain alters muscle spindle responses to stretch (Wenngren, et al, 1998; Ro &amp; Capra, 2001), but the exact mechanism of sensitization is unknown. We used an in vitro mouse hindlimb muscle‐nerve preparation to study plasticity in afferent responses to ramp and hold stretches following acute inflammation (0.5 mg/kg lipopolysaccharide (LPS) 18 hrs before experiment). Following LPS, units had lower baseline firing and more units were only active during stretch (6/16 LPS vs. 3/26 control). The LPS units also displayed a significantly greater decrease in firing frequency over the 4 s stretch. Some LPS units (3/16) are likely group III/IV instead of muscle spindle afferents; they had very small responses to stretch and did not show the characteristic frequency adaptation. Overall, the acute systemic inflammatory state induced by LPS clearly alters the response profile of muscle afferents to stretch, and therefore proprioceptive signaling. Further study on these changes are planned to provide insight into underlying mechanisms, their behavioral relevance, and to identify strategies that normalize function. Supported by K12 GM000680 NIH/NIGMS More Division (KAW) and Pfizer (SH) .
Hydroxamate Siderophores of Histoplasma capsulatum (2000)

The zoopathogenic fungus Histoplasma capsulatum, like other eukaryotic aerobic microorganisms, requires iron for growth. Under conditions of low iron availability, the fungus secretes hydroxamates that function as siderophores (iron chelators). The experiments to be reported were designed to gather further information on the hydroxamate siderophores of H. capsulatum. The fungus was grown in a synthetic medium deferrated with the cationic exchange resin Chelex 100. Siderophores were detected after 4 days of incubation at 37 degrees C in media containing 0.3 to 1.0 microM iron. The secretion was suppressed by 10 microM iron. The hydroxamates were purified by reverse-phase and size-exclusion chromatography. On the basis of ions observed during electrospray mass spectroscopy, five hydroxamate siderophores were tentatively identified: dimerum acid, acetyl dimerum acid, coprogen B, methyl coprogen B, and fusarinine (monomeric). A polyclonal antibody to dimerum acid was generated. This reagent cross-reacted with coprogen B and fusarinine. Thus, the antibody detects hydroxamates in all three families of siderophores excreted by H. capsulatum.
Synergism between Different Germinant Receptors in the Germination of Bacillus subtilis Spores (2011)

Rates of commitment to germinate and germination of Bacillus subtilis spores with mixtures of low concentrations of germinants acting on different germinant receptors (GRs) were much higher than the sums of the rates of commitment and germination with individual germinants alone. This synergism with mixtures of nutrient germinants was not seen with spores lacking GRs responsible for recognizing one or several components of the germinant mixtures and was not eliminated by either a gerD mutation or overexpression of one of the GRs involved in this synergism. This synergism was also not seen between the germinant L-valine, which acts via a GR, and the germinant dodecylamine, which does not act via any GR. These results indicate that spores not only integrate but can also amplify signals from multiple germinants and multiple GRs in determining rates of commitment and overall spore germination. This amplification can be explained by a simple mechanism in which a single signal integrator triggers germination above an accumulation threshold. Direct cooperative action between GRs may further add to the synergism seen in germination triggered by multiple GRs. Further experiments and modeling are required to determine the relative contributions of these different mechanisms.
Novel therapies in the treatment of spondyloarthritis (2002)

Spondyloarthritis represents one of the commonest groups of inflammatory arthritides with onset in the third and fourth decades and primarily affecting the axial skeleton. Current treatment is primarily symptomatic, non-steroidal anti-inflammatory drugs being used most commonly. No therapeutics have been shown to prevent structural damage. The development of validated and standardised outcome instruments and a composite criterion of response should encourage evaluation of new therapeutics. Anti-TNF- alpha -directed therapeutics have been shown to be dramatically effective in short-term (12 week) placebo-controlled trials in both ankylosing spondylitis and psoriatic arthritis whilst observational cohorts describe efficacy that is maintained for over one year. Treatment has been well-tolerated, with mycobacterial infections being the primary concern. Significant costs and the requirement for continuous therapy are likely to spur the development of orally bioavailable agents targeting TNF- alpha expression.
Microscopic evidence of a metallic state in the one-pot organic conductor ammonium tetrathiapentalene carboxylate (2015)

1H NMR (nuclear magnetic resonance) and high-field ESR (electron spin resonance) measurements were carried out for self-doped organic conductors in the ammonium tetrathiapentalene carboxylate (TTPCOO)2[(NH41+)1–x(NH30)x ] system. While the pristine TTPCOOH molecule is closed-shell, self-doped carriers are generated by substitution of the carboxyl proton by (NH30) and (NH41+), which can be regarded as a charge reservoir. The π-extended system TTPCOO has a uniaxial g -tensor, indicating a 2D isotropic structure such as a herring-bone-like or parallel cross donor arrangement. The NMR-relaxation rate indicated the Korringa relation in the temperature dependence, and the ESR linewidth followed the Elliot mechanism. Both of these observations provide supporting evidence for a stable metallic state. In this paper, we introduce self-doped organic conductors as a branch of materials design, and emphasize that advanced magnetic resonance measurements are powerful tools for developing functional materials. (© 2015 WILEY-VCH Verlag GmbH &Co. KGaA, Weinheim)
Semiautonomous Wheelchair Based on Quarry of Environmental Information (2006)

In this paper, an intelligent wheelchair robot for adaptation to an unknown environment is developed. Environmental information is a key factor to comply to an unknown and/or unstructured environment. Since the environment has an infinite number of modes, the environmental information should be classified into some modes. This paper develops a novel viewpoint of robot motion control based on quarry of environmental information. The robot adapts to the environment based on the remote and contact information. In order to adapt to the remote environment, the obstacle avoidance problem is treated. This kind of robot motion control is based on position control. On the contrary, in order to adapt to the contact information, compliance control is applied to a robot. If the robot collides with the obstacles, the impact force is relaxed by the method, and safety is improved. This controller, on the other hand, is based on force control. In this paper, position control and force control are integrated in the acceleration dimension based on acceleration control. The robust acceleration control is attained by the disturbance observer. Finally, a semiautonomous function is installed for the improvement of human operationality. The numerical and experimental results show viability of the proposed method
Multiple sclerosis and ECT: possible value of gadolinium-enhanced magnetic resonance scans for identifying high-risk patients (1992)

Electroconvulsive therapy (ECT) has been used effectively in treating depressed patients with multiple sclerosis (MS). However, several reports have observed that some patients with MS may suffer neurological deterioration during ECT. The authors describe the outcomes of 3 depressed patients with MS who were treated with ECT. Consistent with previous works, ECT effectively treated the psychiatric symptoms; however, 1 patient deteriorated neurologically during ECT. The brain MRI findings and clinical courses of all 3 patients are discussed, along with the possible value of gadolinium-contrast MRI scans for identifying high-risk patients.
Facile Functionalization of Poly(Dimethylsiloxane) Elastomer by Varying Content of Hydridosilyl Groups in a Crosslinker (2019)

Crosslinked poly(dimethylsiloxane) (PDMS) has been widely used as a dielectric elastomer for electrically driven actuators because it exhibits high elasticity, low initial modulus, and excellent moldability in spite of low dielectric constant. However, further improvement in the characteristics of the PDMS elastomer is not easy due to its chemical non-reactivity. Here, we report a simple method for functionalizing the elastomer by varying content of hydridosilyl groups in PDMS acted as a crosslinker. We synthesized poly(dimethylsiloxane-<i>co</i>-methylvinylsiloxane) (VPDMS) and poly(dimethylsiloxane-<i>co</i>-methylsiloxane) (HPDMS). Tri(ethylene glycol) divinyl ether (TEGDE) as a polar molecule was added to the mixture of VPDMS and HPDMS. TEGDE was reacted to the hydridosilyl group in HPDMS during crosslinking between VPDMS and HPDMS in the presence of platinum as a catalyst. Permittivity of the crosslinked film increased from ca. 25 to 36 pF/m at 10 kHz without a decline in other physical properties such as transparency and elasticity (<i>T</i> > 85%, <i>E</i> ~150 kPa, ɛ ~270%). It depends on the hydridosilyl group content of HPDMS. The chemical introduction of a new molecule into the hydridosilyl group in HPDMS during crosslinking would provide a facile, effective method of modifying the PDMS elastomers.
Photobiomodulation inside the brain: a novel method of applying near-infrared light intracranially and its impact on dopaminergic cell survival in MPTP-treated mice (2013)

In summary, the authors showed that NIr can be applied intracranially, does not have toxic side effects, and is neuroprotective.
Osmium Tetroxide (2002)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTOsmium TetroxideJay A. Young View Author Information Chemical Consultant, Silver Spring, MD 20904-3105Cite this: J. Chem. Educ. 2002, 79, 9, 1064Publication Date (Web):September 1, 2002Publication History Received3 August 2009Published online1 September 2002Published inissue 1 September 2002https://doi.org/10.1021/ed079p1064RIGHTS & PERMISSIONSArticle Views407Altmetric-Citations3LEARN 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 InReddit PDF (62 KB) Get e-AlertsSUBJECTS:Osmium Get e-Alerts
Synthetic Biology in the Engineering of CAR-T and CAR-NK Cell Therapies: Facts and Hopes (2022)

The advent of modern synthetic-biology tools has enabled the development of cellular treatments with engineered specificity, leading to a new paradigm in anticancer immunotherapy. T cells have been at the forefront of such development, with six chimeric antigen receptor-modified T-cell products approved by the FDA for the treatment of hematologic malignancies in the last 5 years. Natural killer (NK) cells are innate lymphocytes with potent cytotoxic activities, and they have become an increasingly attractive alternative to T-cell therapies due to their potential for allogeneic, "off-the-shelf" applications. However, both T cells and NK cells face numerous challenges, including antigen escape, the immunosuppressive tumor microenvironment, and potential for severe toxicity. Many synthetic-biology strategies have been developed to address these obstacles, most commonly in the T-cell context. In this review, we discuss the array of strategies developed to date, their application in the NK-cell context, as well as opportunities and challenges for clinical translation.
Naked Sugars as Synthetic Intermediates - Stereospecific Synthesis of L-Daunosamine (1985)

LGSA
Initial Tests of Nonlinear Quasi-Integrable Optics at the University of Maryland Electron Ring (2018)

An octupole channel has been inserted into the University of Maryland Electron Ring (UMER), in order to investigate the mitigation of destructive resonances as a novel approach in high-intensity beam transport. The individual octupole magnets have been characterized using our in-house 3-dimensional magnet mapping stage, with a measured gradient of 51.6 ± 1.5 T/m3/A. A single section (20°) of an 18-cell FODO lattice has been replaced by a longitudinally-varying octupole channel constructed from seven flexible printed circuits (PCBs). We present the design of the channel and preliminary beam based measurements on the ring.
Circulating tumor cells (CTC) as a biomarker of response in patients with extensive-stage small cell lung cancer (EX-SCLC). (2013)

e22048 Background: SCLC, a variant of lung cancer marked by early metastases, accounts for 13% of all lung cancers diagnosed in US. Despite high response rates to treatment, it is an aggressive disease with a median survival of 9-11 months for patients with EX-SCLC. Detection of CTCs is a novel laboratory technique currently in use to determine response to therapy and to predict prognosis in breast, colorectal and prostate cancer. We initiated a study to study the role of CTC as a biomarker of response and relapse in patients with EX-SCLC. Methods: We collected blood sample from chemotherapy naïve patients with EX-SCLC prior to initiation of therapy, following completion of systemic therapy, follow up every 6-8 weeks and at relapse. The CTC was determined using the Cell Search system in a central laboratory. The study was conducted in 4 different sites and it was reviewed and approved by respective Research Review Committee and IRBs. Results: We enrolled 27 patients with EX-SCLC, 1 was excluded due ineligibility, all patients were treated with platinum and etoposide. We observed partial response in 16 patients (61%), stable disease in 3 patients, 1 with progression of disease and not assessed in 7 patients (5 deceased, 2 not available); the baseline CTC of 2 patient were not measured (one due instrument failure and one due insufficient blood). The overall median number of CTCs in 24 patients measured at baseline and post-tx was 75 (range 0 to 3430) and 2 (range 0 to 526), respectively. A significant reduction in CTCs from baseline to post-tx was identified; for the 14 subjects with pre and post treatment CTC, the median reduction was 51.5% (51.5% decrease, range -2904% to +5%, p&lt; 0.001). Conclusions: We were able to demonstrate feasibility of using CTC as a biomarker of response in patients with EX-SCLC in clinical setting. CTC could be a useful biomarker in the management of SCLC to predict response to therapy.
Evolutionary Theory of Cancer (2009)

As Theodosius Dobzhansky famously noted in 1973, "Nothing in biology makes sense except in the light of evolution," and cancer is no exception to this rule. Our understanding of cancer initiation, progression, treatment, and resistance has advanced considerably by regarding cancer as the product of evolutionary processes. Here we review the literature of mathematical models of cancer evolution and provide a synthesis and discussion of the field.
Application of metal nanoparticles decorated carbon nanotubes in photovoltaics (2008)

Carbon nanotubes decorated with metal nanoparticles are introduced to photovoltaic application. The introduction of metal nanoparticles in the organic/organic-inorganic heterojunction solar cells is expected to improve the exciton dissociation (due to strong electric field at the metal-organics interface) and hence photovoltaic action. An improved photovoltaic action is indeed observed in n-Si/poly(3-octylthiophene) heterojunction solar cells incorporating multiwalled carbon nanotubes (MWCN) decorated with platinum metal nanoparticles (Pt: 20wt%, 10–15nm) as compared to pristine MWCN. The incorporation of metal nanoparticles should provide an alternative strategy to improve the photovoltaic performance of organic/organic-inorganic solar cells.
Utility of the Trypanosoma cruzi Sequence Database for Identification of Potential Vaccine Candidates by In Silico and In Vitro Screening (2004)

Glycosylphosphatidylinositol (GPI)-anchored proteins are abundantly expressed in the infective and intracellular stages of Trypanosoma cruzi and are recognized as antigenic targets by both the humoral and cellular arms of the immune system. Previously, we demonstrated the efficacy of genes encoding GPI-anchored proteins in eliciting partially protective immunity to T. cruzi infection and disease, suggesting their utility as vaccine candidates. For the identification of additional vaccine targets, in this study we screened the T. cruzi expressed sequence tag (EST) and genomic sequence survey (GSS) databases. By applying a variety of web-based genome-mining tools to the analysis of approximately 2,500 sequences, we identified 348 (37.6%) EST and 260 (17.4%) GSS sequences encoding novel parasite-specific proteins. Of these, 19 sequences exhibited the characteristics of secreted and/or membrane-associated GPI proteins. Eight of the selected sequences were amplified to obtain genes TcG1, TcG2, TcG3, TcG4, TcG5, TcG6, TcG7, and TcG8 (TcG1-TcG8) which are expressed in different developmental stages of the parasite and conserved in the genome of a variety of T. cruzi strains. Flow cytometry confirmed the expression of the antigens encoded by the cloned genes as surface proteins in trypomastigote and/or amastigote stages of T. cruzi. When delivered as a DNA vaccine, genes TcG1-TcG6 elicited a parasite-specific antibody response in mice. Except for TcG5, antisera to genes TcG1-TcG6 exhibited trypanolytic activity against the trypomastigote forms of T. cruzi, a property known to correlate with the immune control of T. cruzi. Taken together, our results validate the applicability of bioinformatics in genome mining, resulting in the identification of T. cruzi membrane-associated proteins that are potential vaccine candidates.