gebhart/patrepeval huggingface dataset:
The minor gentamicin complex component, X2, is a potent premature stop codon readthrough molecule with therapeutic potential (2018)

Nonsense mutations, resulting in a premature stop codon in the open reading frame of mRNAs are responsible for thousands of inherited diseases. Readthrough of premature stop codons by small molecule drugs has emerged as a promising therapeutic approach to treat disorders resulting from premature termination of translation. The aminoglycoside antibiotics are a class of molecule known to promote readthrough at premature termination codons. Gentamicin consists of a mixture of major and minor aminoglycoside components. Here, we investigated the readthrough activities of the individual components and show that each of the four major gentamicin complex components representing 92-99% of the complex each had similar potency and activity to that of the complex itself. In contrast, a minor component (gentamicin X2) was found to be the most potent and active readthrough component in the gentamicin complex. The known oto- and nephrotoxicity associated with aminoglycosides preclude long-term use as readthrough agents. Thus, we evaluated the components of the gentamicin complex as well as the so-called "designer" aminoglycoside, NB124, for in vitro and in vivo safety. In cells, we observed that gentamicin X2 had a safety/readthrough ratio (cytotoxicity/readthrough potency) superior to that of gentamicin, G418 or NB124. In rodents, we observed that gentamicin X2 showed a safety profile that was superior to G418 overall including reduced nephrotoxicity. These results support further investigation of gentamicin X2 as a therapeutic readthrough agent.
Inhibition of Prolyl Hydroxylase Domain-Containing Protein Downregulates Vascular Angiotensin II Type 1 Receptor (2011)

Inhibition of prolyl hydroxylase domain-containing protein (PHD) by hypoxia stabilizes hypoxia-inducible factor 1 and increases the expression of target genes, such as vascular endothelial growth factor. Although the systemic renin-angiotensin system is activated by hypoxia, the role of PHD in the regulation of the renin-angiotensin system remains unknown. We examined the effect of PHD inhibition on the expression of angiotensin II type 1 receptor (AT(1)R). Hypoxia, cobalt chloride, and dimethyloxalylglycine, all known to inhibit PHD, reduced AT(1)R expression in vascular smooth muscle cells. Knockdown of PHD2, a major isoform of PHDs, by RNA interference also reduced AT(1)R expression. Cobalt chloride diminished angiotensin II-induced extracellular signal-regulated kinase phosphorylation. Cobalt chloride decreased AT(1)R mRNA through transcriptional and posttranscriptional mechanisms. Oral administration of cobalt chloride (14 mg/kg per day) to C57BL/6J mice receiving angiotensin II infusion (490 ng/kg per minute) for 4 weeks significantly attenuated perivascular fibrosis of the coronary arteries without affecting blood pressure level. These data suggest that PHD inhibition may be beneficial for the treatment of cardiovascular diseases by inhibiting renin-angiotensin system via AT(1)R downregulation.
Förfärande få förstaårsstudenter förstår fysiklaborationerna (2013)

Fysiklaborationer i grundkurserna pa LTH fungerar inte tillfredsstallande eftersom de inte ger studenterna en vasentligt okad forstaelse for den fysik som laborationen behandlar och for att studenterna inte upplever laborationerna som meningsfulla. Utgaende fran litteraturstudier och ett exempel pa en nyutvecklad fysikkurs dar laborationerna fungerar battre foreslar rapporten ett antal losningar pa situationen. Tyngdpunkten i losningarna ligger pa att studenterna skall ges battre mojligheter till att bearbeta och ackommodera sin nyvunna kunskap. Detta skall uppnas bland annat genom att minska antalet laborationer och mangden material som ingar i varje laboration.
Application and realization of gateways between conventional automotive and IP/ethernet-based networks (2011)

In order to fulfill the continuously rising communication demands within vehicles the usage of Ethernet as vehicle network is planned, since it is offering high bandwidth, robustness and has a high market penetration. The automotive industry has strong requirements with respect to safety and reliability; hence the introduction of new technologies is usually done in an evolutionary approach. This implies that for the introduction of Ethernet a gateway to currently existing automotive networking technologies is required for achieving a smooth migration. Within this paper a concept for such a gateway maintaining the Quality of Service (QoS) offered by the existing automotive networks is proposed. In order to support the same level of QoS the usage of Ethernet Audio Video Bridging (AVB) is suggested. The implementation of such a QoS gateway is investigated specifically for the automotive networks MOST and FlexRay. For evaluation of the proposed concepts a validation system was built up, and promising results showing the feasibility of such a QoS gateway have been achieved. Furthermore this implies that AVB has the capability to replace other automotive network technologies in the midterm.
Assembly and task planning: a taxonomy (1994)

After over two decades of research in the field of assembly and task planning, an IEEE Technical Committee on Assembly and Task Planning has been created. One of the first activities of this committee has been to develop a taxonomy of the field. We will now present this taxonomy, which should be viewed as a dynamic description of the field that will change shape as the field progresses. The reasons for developing such a taxonomy are many: to aid in building a coherent picture of the field which is particularly useful to newcomers to assembly and task planning, to help active researchers better understand how their work relates to the rest of the field. Finally such a taxonomy is useful for administrative purposes such as aiding program committee members and editors in selecting reviewers and as an aid in selecting keywords to be associated with various articles. To further aid the reader of this taxonomy, we have incorporated into it an extensive, but by no means complete, bibliography.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The head-injured outpatient: presentations and rehabilitation. (1989)

Head injury, which annually affects 154 per 100,000 persons in Maryland, is a serious problem requiring attention from the medical community. The role of the general practitioner is viewed as central to the process of rehabilitation since this medical professional has a pre-existent relationship with the patient and the family.
Improved fat suppression in diffusion MRI using eddy current compensation gradient (2023)

In this work, we propose to compensate the residual eddy current field caused by diffusion gradients at the time when chemically selective fat suppression gets applied with an additional gradient applied after the EPI readout. Using an analytic solution, the amplitude of the eddy currents can be cancelled under certain assumptions. The experimental results based on a volunteer scan demonstrate improved fat suppression in diffusion MRI with the proposed method.
Single Crossover-Mediated Markerless Genome Engineering in Clostridium acetobutylicum (2016)

A novel genome-engineering tool in Clostridium acetobutylicum was developed based on singlecrossover homologous recombination. A small-sized non-replicable plasmid, pHKO1, was designed for efficient integration into the C. acetobutylicum genome. The integrated pHKO1 plasmid backbone, which included an antibiotic resistance gene, can be excised in vivo by Flp recombinase, leaving a single flippase recognition target sequence in the middle of the targeted gene. Since the pSHL-FLP plasmid, the carrier of the Flp recombinase gene, employed the segregationally unstable pAMβ1 replicon, the plasmid was rapidly cured from the mutant C. acetobutylicum. Consequently, our method makes it easier to engineer C. acetobutylicum.
Engineering Immunity against HIV - a Stem Cell Vaccine (132.12) (2009)

Abstract An effective vaccine against HIV is urgently needed. We are pursuing a novel gene therapy approach to combat HIV by engineering HSCs to produce human B cells programmed to make anti-HIV broadly neutralizing antibodies (bNAbs). We accomplish this by using lentiviral vectors to modify the long-lived HSCs with engineered bNAb genes. We hypothesize the transplantation of the engineered HSCs will confer life-long HIV-specific immunity; in effect, a "Stem Cell Vaccine" for HIV. In nature the soluble Ab and membrane BCR are produced by complex alternative splicing events difficult to implement in the context of a lentiviral vector. We have overcome this obstacle by developing a novel "Synthetic-Switch" antibody gene that mimics the function of the membrane-bound BCR and secretory antibody. Furthermore, the Synthetic-Switch approach enables us to produce "isotype-switched" anti-HIV B cells without the need for complex DNA rearrangement. The Synthetic-Switch approach thus successfully captures the essential functions of the roughly 2-Mbp immunoglobulin loci in a compact 10kb lentiviral vector. Herein we present this successful first step toward an anti-HIV stem cell vaccine.
Cloning DNA sequences from influenza viral RNA segments. (1980)

DNA sequences corresponding to gene segments that code for the nonstructural protein, the matrix protein, and the hemagglutinin of influenza A virus [strain A/Udorn/72 (H3N2)] were cloned in Escherichia coli pBR 322. Initially, positive and negative cDNA strands were prepared separately by reverse transcription. The positive strands of cDNA were transcribed from genomic RNA segments by using a specific dodecamer DNA sequence as a primer; the negative strands of cDNA were transcribed from cytoplasmic viral mRNA segments by using an oligo(dT) primer. DNA duplexes corresponding in size to the virus RNA segments were then purified, inserted into the plasmid DNA, and used for transformation of E. coli. The influenza virus-specific DNA sequences isolated from recombinant plasmid molecules were characterized by mapping restriction enzyme cleavage sites. In addition, the orientation of cloned DNA was determined with reference to the 3' terminus of viral RNA.
New Insights into the Pathophysiology of Sickle Cell Disease-Associated Priapism (2011)

As the science underlying priapism further emerges, increasingly effective therapeutics for sickle cell disease-associated priapism is certain to follow.
Specific influence of striatal target neurons on the in vitro outgrowth of mesencephalic dopaminergic neurites: a morphological quantitative study (1983)

In previous studies, we have shown that dissociated dopaminergic neurons from embryonic mouse in co-culture with striatal target neurons take up and synthesize dopamine to a greater extent. We now report that striatal target cells influence the morphology of dopaminergic neurons as well. In co-culture, the total length of neuritic arborization visualized by autoradiography is reduced when compared to cultures of mesencephalic neurons alone or to co-cultures with cerebellar cells. Experiments performed in the presence of striatal glial cells at the same density as striatal neurons or with media conditioned with striatal glia or neurons suggest that striatal neurons regulate dopaminergic afferent growth in vitro through specific neuro-neuronal interactions.
Enhanced transparent conducting networks on plastic substrates modified with highly oxidized graphene oxide nanosheets (2016)

Atomically thin and two-dimensional graphene oxide (GO) is a very fascinating material because of its functional groups, high transparency, and solution processability. Here we show that highly oxidized GO (HOGO) nanosheets serve as an effective interfacial modifier of transparent conducting films with one-dimensional (1D) silver nanowires (AgNWs) and single-walled carbon nanotubes (SWCNTs). Optically transparent and small-sized GO nanosheets, with minimal sp(2) domains, were successfully fabricated by step-wise oxidation and exfoliation of graphite. We demonstrated that under-coated HOGO further decreases the sheet resistance of the SWCNT film top-coated with HOGO by increasing the contact area between the SWCNTs and HOGO nanosheets by generating hole carriers in the SWCNT as a result of charge transfer. Moreover, HOGO nanosheets with AgNWs contribute to the efficient thermal joining of AgNW networks on plastic substrates by limiting the thermal embedding of AgNWs into the plastic surface, resulting in efficient decrease of the sheet resistance. Furthermore, flexible organic photovoltaic cells with GO-modified AgNW anodes on a flexible substrate were successfully demonstrated.
Data from Intratumoral Comparison of Nanoparticle Entrapped Docetaxel (CPC634) with Conventional Docetaxel in Patients with Solid Tumors (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;CPC634 is a novel nanoparticle entrapping docetaxel, developed to enhance the intratumoral chemotherapy exposure. This randomized cross-over study compared the intratumoral and plasma pharmacokinetics of CPC634 with conventional docetaxel.&lt;/p&gt;Patients and Methods:&lt;p&gt;Adult patients with solid tumors were randomized to receive CPC634 (75 mg/m&lt;sup&gt;2&lt;/sup&gt;) in cycle 1, and conventional docetaxel (75 mg/m&lt;sup&gt;2&lt;/sup&gt;) in cycle 2 or &lt;i&gt;vice versa&lt;/i&gt;. The study was powered to identify a 25% increase of intratumoral total docetaxel exposure after CPC634 infusion compared with conventional docetaxel. Four patients were allocated per tumor sampling time point, that is, 24, 48, 72, and 96 hours, 7 and 14 days after infusion during both cycles. Total docetaxel and released docetaxel from the nanoparticle were determined in tumor tissue derived from a metastatic lesion and in plasma. Pharmacokinetic data were analyzed using linear mixed modeling.&lt;/p&gt;Results:&lt;p&gt;In total, 24 evaluable patients were included. In the tumor, CPC634 exhibited a 461% higher total docetaxel (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) and a comparable released docetaxel concentration (&lt;i&gt;P&lt;/i&gt; = 0.43). Plasma AUC&lt;sub&gt;inf&lt;/sub&gt; was 27% higher (&lt;i&gt;P&lt;/i&gt; = 0.001) and &lt;i&gt;C&lt;/i&gt;&lt;sub&gt;max&lt;/sub&gt; was 91% lower (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) for CPC634 released docetaxel. The median observed neutrophil count nadir after conventional docetaxel treatment was lower (0.50 × 10&lt;sup&gt;9&lt;/sup&gt;/L) compared with CPC634 (4.30 × 10&lt;sup&gt;9&lt;/sup&gt;/L; &lt;i&gt;P&lt;/i&gt; &lt; 0.001).&lt;/p&gt;Conclusions:&lt;p&gt;Here, we demonstrated that CPC634 enhanced the intratumoral total docetaxel exposure compared with conventional docetaxel. The lower incidence of neutropenia during CPC634 treatment is presumably related to lower plasma &lt;i&gt;C&lt;/i&gt;&lt;sub&gt;max&lt;/sub&gt; of released docetaxel. The unique pharmacokinetic profile of CPC634 nanoparticles has the potential to improve docetaxel treatment. A phase II efficacy trial of CPC634 is currently ongoing.&lt;/p&gt;&lt;/div&gt;
Folding of Oligoglutamines: A Theoretical Approach Based Upon Thermodynamics and Molecular Mechanics (1999)

Folding of oligoglutamine chains of different lengths is of crucial interest for exploring the molecular mechanisms of Huntington's disease. A simple oligoglutamine model based upon the Flory-Huggins theory of polymer solutions demonstrates a random coil instability in chains containing more than 40 glutamine residues with respect to beta-sheet formation. This is in striking quantitative agreement with biochemical results on the chain length dependence of polyglutamine aggregation in vivo and in vitro, as well as with clinical data on the polyglutamine chain length dependence of the onset of Huntington's disease. Furthermore, a detailed molecular-mechanical investigation of a polypeptide chain carrying 40 glutamine residues was performed. Two possible folding modes of such an oligoglutamine chain were revealed: a) a beta-hairpin and b) a highly compact random coil entity stabilized by a wealth of H-bonds among the glutamine side chains. A possible role of these folding modes in polyglutamine aggregation, as well as in the onset of Huntington's disease, is discussed.
Review on the thermo-oxidative degradation of polymers during processing and in service (2008)

Abstract During processing as well as in service life, polymers degrade. For the majority of polymers this is due to oxidative processes. In this review the mechanism of the thermo-oxidative degradation of the most important (unstabilized) polymers as well as the factors determining the degradation rates are discussed.
PCR-amplification of mixed 16S rRNA genes from an anaerobic, cyanide-degrading consortium (1994)

The microorganisms participating in the anaerobic biodegradation of cyanide were characterized using 16S rRNA genes as genetic markers of diversity. Segments of mixed population 16S rRNA genes were amplified using the polymerase chain reaction (PCR) and prokaryote-specific amplification primers. Restriction fragment length polymorphism (RFLPs) and screening with the 926f universal sequencing primer were used to categorized the cloned PCR products. Six unique prokaryote sequences were obtained, including four similar to methanogens and two similar to Gram-positive eubacteria.
Culture Conditions and Pathogenicity (1992)

SUMMARY. Difficulties in preparing suitable antigen for the microagglutination (MA) test led to the discovery of a filamentous form of Bordetella avium. Broth media high in nutrients, vigorous shaking, and incubation at 37 C appeared to promote the development of filamentous forms of the organism. Peptone broth did not induce the development of filamentous forms. Eleven different isolates having both smooth and rough colony types were tested and observed to form filaments of various lengths. Filamentous forms of B. avium hemagglutinated guinea pig erythrocytes were motile, had pili and flagella, and were stable up to the fourth or fifth passage in broth media, at which time a predominance of typical coccobacillus organisms were observed. Filamentous forms of B. avium originating from smooth-colony types were pathogenic in turkey poults, whereas the filamentous forms of B. avium originating from rough-colony types were not pathogenic. RESUMEN. Formas filamentosas de Bordetella avium: Condiciones de cultivo y patogenicidad.
Lexical stress and phonetic information: which segments are most informative? (1987)

investigates the relative usefulness of different parts of the speech signal for word recognition, and daims that a front end which is able to provide "fine dass" (phonemic) information about segments in stressed syllables and "mid dass" information about those in unstressed would on average be less helpful for word identification than one which was able to attach a fine dass Iabel to the same proportion of segments, but scattered at random throughout words. Altmann condudes that his results "demonstrate the desirability of a front-end which outputs occasional fine dass information not systematically, but at random" .
Enabling New Multicast Distribution Architectures Through The Introduction Of Igmp/Mld Proxy With Multiple Upstream Interfaces (2018)

The deployment of IGMP/MLD proxy functionality in telecom networks is now common from long, with clear engineering and operational rules. Existing IGMP/MLD proxy implementations are limited to a single upstream interface, then receiving all the multicast traffic through that interface in a well-defined manner. However this mode of operation seems to not be enough for enabling some appealing multicast distribution cases. Such new service scenarios rise the need of extending the proxy functionality by enabling the support of multiple upstream interfaces, at the cost of imposing the support of more functionality in the element acting as a proxy. The paper introduces the use cases of interest and overviews the additional functionality required to evolve next generation of IGMP/MLD proxies in this direction. Future directions on the standardization of this solution are also provided.
A Simple Metric for Predicting Revenue from Electric Peak‐Shaving and Optimal Battery Sizing (2017)

Abstract A major use case for behind‐the‐meter (BTM) electricity storage is peak‐shaving for commercial and industrial customers who must pay peak‐demand charges. Quantifying the value proposition for individual customers currently requires an optimization model, the development of which can be costly in human and computing resources. We disclose here a simple econometric model to predict revenue from retail peak‐shaving. Geared toward electric utilities, third‐party storage providers, and consumers, this model eliminates the need to formulate a model in specialized optimization software. The model is based on a predictive metric that is derived from the building's load profile. During model fitting, we discovered that the revenue estimates generated are independent of the power capacity of the battery if the maximum power‐to‐energy ratio of the storage is held constant. This effect can be used to calculate the profit‐maximizing storage size, which we explore in a case study.
New interpretations for the MLM and DASE spectral estimators (2005)

This paper provides new interpretations for two modern spectral estimators, the Data Adaptive Spectral Estimator (DASE) of Davis and Regier, and the earlier Maximum Likelihood Method (MLM) of Capon, a special case of DASE. These methods provide estimates for spectral power in some region of frequency space, in terms of an estimate for a correlation matrix. They are conventionally interpreted as window-type spectral estimates, where the window is a function of the estimated correlation matrix. Assuming that the estimated correlation matrix is correct, it is shown that the problem of determining the spectral power is ill-posed. Specifically it is shown that DASE and MLM provide upper bounds on spectral power in some region of frequency space where the spectral density is assumed constant. Furthermore, it is shown that the assumptions and constraints that determine these upper bounds yield trivial lower bounds of zero.
Tunable all-optical time-slot-interchange and wavelength conversion using difference-frequency-generation and optical buffers (2002)

In this letter, we demonstrate a module that simultaneously performs optical time-slot interchange and wavelength conversion of the bits in a 2.5-Gb/s data stream to achieve a reconfigurable time/wavelength switch. Our switch uses difference-requency-generation (DFG) for wavelength conversion and fiber Bragg gratings as wavelength-dependent optical time buffers. This tunable technique employs high-extinction-ratio and low-additive-noise DFG.