gebhart/patrepeval huggingface dataset:
ras gene mutations in non-small cell lung cancers are associated with shortened survival irrespective of treatment intent. (1991)

We analyzed 66 non-small cell lung cancer cell lines for mutations at codons 12, 13, and 61 of all three ras genes and correlated the findings with patient survival. We used designed restriction fragment-length polymorphisms to detect mutations after amplification of ras-specific sequences by the polymerase chain reaction. We found 19 mutations of ras genes (29%), and 11 of these 19 (58%) were at codon 12 of the K-ras gene. By univariate analysis, the presence of any ras mutation in cell lines from patients who received curative intent treatment was associated with a shorter survival (P2 = 0.002). For patients who received only palliative treatment, detection of K-ras mutations at codon 12 was associated with a shortened survival (P2 = 0.0103), but this analysis was not statistically significant for the group with any ras mutation (P2 = 0.093). The Cox proportional hazards model also predicted a higher risk for patients with any type of ras mutations. We conclude that ras mutations, present in a subset of non-small cell lung cancers, are independently associated with the shortened survival of patients, irrespective of treatment intent.
Group-aware stream filtering. (2008)

In this paper we are concerned with disseminating high-volume data streams to many simultaneous context-aware applications over a low-bandwidth wireless mesh network. For bandwidth efficiency, we propose a group-aware stream filtering approach, used in conjunction with multicasting, that exploits two overlooked, yet important, properties of these applications: 1) many applications can tolerate some degree of slack in their data quality requirements, and 2) there may exist multiple subsets of the source data satisfying the quality needs of an application. We can thus choose the alternative subset for each application to maximize the data overlap within the group to best benefit from multicasting. An evaluation of our prototype implementation shows that group-aware data filtering can save bandwidth with low CPU overhead.
Polyols made from vegetable oil and their applications (2005)

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.
Clinical Utility of LDL-apheresis in the Treatment of Sudden Hearing Loss: a Prospective, Randomized Study (1999)

Although the pathogenesis of sudden hearing loss (SHL) is not as yet known, the clinical picture and the frequent association with vascular risk factors make an ischaemic event likely. This study aimed to assess the effect of an extracorporeal procedure (H.E.L.P.) in removing LDL-cholesterol, fibrinogen and lipoprotein (a) from the plasma, on the recovery of hearing SHL. This procedure using the HELP-system was compared with the usual standard treatment with prednisolone, dextranes and pentoxifyllin. We undertook a single centre, prospective, randomized study in which 18 patients were assigned to H.E.L.P.-apheresis and 9 patients were assigned to standard treatment (2:1 randomization). Audiometric and laboratory testing was performed at baseline, 24 h and 6 weeks after start of treatment. Primary endpoint was the improvement of the average pure-tone threshold between 0.125 and 8 kHz after 24 h. Twenty-four hours after H.E.L.P. treatment average pure-tone threshold recovered by 10.4 dB and by 26.4 dB after 6 weeks. The recovery of hearing of the standard treated patients was 5.8 dB and 16.8 dB after 24 h and 6 weeks respectively. LDL-cholesterol, fibrinogen and lipoprotein (a) were significantly reduced in the HELP treated patients compared with standard therapy, resulting in a significant improve in plasma viscosity, erythrocyte aggregation and resistance to oxidative stress of LDL particles. Our results suggest that the clinical outcome of SHL after a single extracorporeal LDL-apheresis is superior or at least equal to the more expensive standard treatment with prednisolone, dextranes and pentoxifyllin. Re-establishment of vascular endothelial function and improved blood rheology may be the underlying cause. These results must be confirmed in larger-scale trials.
Transient visual effects and laser safety standards (1997)

Laser/Optical Radiation Program, US Army Center for Health Promotion and Preventive Medicine, Aberdeen Proving Ground, MD 21010-5422, USA
A Germylene/Borane Lewis Pair and the Remarkable C=O Bond Cleavage Reaction toward Isocyanate and Ketone Molecules (2016)

A germylene/borane Lewis pair (2) was prepared from a 1,1-carboboration of amidinato phenylethynylgermylene (1) by B(C6 F5 )3 . Compound 2 reacted with iPrNCO and (4-MeOC6 H4 )C(O)Me, respectively, with cleavage of the C=O double bond. In the first instance, O and iPrNC insert separately into the Ge-B bond to yield a GeBC2 O-heterocycle (3) and a GeBC3 -heterocycle (4). In the second case (4-MeOC6 H4 )(Me)C inserts into the Ge-N bond of 2 while O is incorporated in the Ge-B bond to form a Ge-centered spiroheterocycle (5). The reaction of 2 with tBuNC to give 6, which has almost the same structure as 4, proved the formation of the isonitrile during transformation from 2 and iPrNCO to 3 and 4. The kinetic study of the reaction of 2 and iPrNCO gave evidence of proceeding through a GeBC3 O-heterocycle intermediate. In addition, a DFT study was performed to elucidate the reaction mechanism.
Gardenamide A fromRothmannia urcelliformis (Rubiaceae) − Isolation, Absolute Stereostructure, and Biomimetic Synthesis from Genipine (2001)

The iridoid alkaloid gardenamide A (3) was isolated from the phytochemically uninvestigated East African Rubiaceae species Rothmannia urcelliformis (Hiern) Bullock. Its absolute stereostructure was determined by quantum chemical CD calculations, which constitutes the first application of this useful chiroptical tool within the class of iridoids. An additional stereochemical proof succeeded by its biomimetic partial synthesis starting from the well-known nitrogen-free iridoid genipine (1).
Network‐ and attribute‐based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability (2012)

Autism spectrum disorders (ASD) are a group of related neurodevelopmental disorders with significant combined prevalence (∼1%) and high heritability. Dozens of individually rare genes and loci associated with high-risk for ASD have been identified, which overlap extensively with genes for intellectual disability (ID). However, studies indicate that there may be hundreds of genes that remain to be identified. The advent of inexpensive massively parallel nucleotide sequencing can reveal the genetic underpinnings of heritable complex diseases, including ASD and ID. However, whole exome sequencing (WES) and whole genome sequencing (WGS) provides an embarrassment of riches, where many candidate variants emerge. It has been argued that genetic variation for ASD and ID will cluster in genes involved in distinct pathways and protein complexes. For this reason, computational methods that prioritize candidate genes based on additional functional information such as protein-protein interactions or association with specific canonical or empirical pathways, or other attributes, can be useful. In this study we applied several supervised learning approaches to prioritize ASD or ID disease gene candidates based on curated lists of known ASD and ID disease genes. We implemented two network-based classifiers and one attribute-based classifier to show that we can rank and classify known, and predict new, genes for these neurodevelopmental disorders. We also show that ID and ASD share common pathways that perturb an overlapping synaptic regulatory subnetwork. We also show that features relating to neuronal phenotypes in mouse knockouts can help in classifying neurodevelopmental genes. Our methods can be applied broadly to other diseases helping in prioritizing newly identified genetic variation that emerge from disease gene discovery based on WES and WGS.
[Biomechanics and bio-energetics of smooth muscle contraction. Relation to bronchial hyperreactivity]. (2000)

Mechanical studies of isolated muscle and analysis of molecular actomyosin interactions have improved our understanding of the pathophysiology of airway smooth muscle. Mechanical properties of airway smooth muscle are similar to those of other smooth muscles. Airway smooth muscle exhibits spontaneous intrinsic tone and its maximum shortening velocity (Vmax) is 10-30 fold lower than in striated muscle. Smooth muscle myosin generates step size and elementary force per crossbridge interaction approximately similar to those of skeletal muscle myosin. Special slow cycling crossbridges, termed latch-bridges, have been attributed to myosin light chain dephosphorylation. From a mechanical point of view, it has been shown that airway hyperresponsiveness is characterized by an increased Vmax and an increased shortening capacity, with no significant change in the force-generating capacity.
Hydroxychavicol: A phytochemical targeting cutaneous fungal infections (2016)

The present study was designed to investigate the potency of hydroxychavicol on selected cutaneous human pathogenic fungi by the use of in vitro and in vivo assays and mechanistic characterization along with toxicological effects. Hydroxychavicol consistently displayed a fungicidal effect against all fungal species tested. Inoculum concentrations over the range of 10<sup>4</sup> to 10<sup>7</sup> CFU/ml did not significantly alter its antifungal potential and time-kill curve results revealed concentration-dependent killing. It also inhibited the growth of biofilm generated by Trichophyton mentagrophytes and Candida parapsilosis and reduced the preformed biofilms. Hydroxychavicol was highly effective in the treatment, and mycological eradication of an experimentally induced topical infection model of dermatophytosis (tinea corporis) and cutaneous candidiasis in guinea pigs, respectively. The mode of action of hydroxychavicol appears to originate from the disruption of cell membrane integrity. Administration of hydroxychavicol in mice at 500 mg per kg of body weight by orally produced no overt toxicity. The retention capacity of hydroxychavicol in vitro, in the presence of keratin has attributed to its in vivo effectiveness in the guinea pig model of topical infections. Furthermore, it is suggestive of its potential use as phytochemical for topical use in cutaneous fungal infections.
Status of the Neonatal Rat Brain after NMDA-Induced Excitotoxic Injury as Measured by MRI, MRS and Metabolic Imaging (1996)

Intrastriatal injection of the excitotoxin N-methyl-dsc-aspartate (NMDA) in neonatal rat brain resulted in an acute ipsilateral decrease of the apparent diffusion coefficient (ADC) of brain tissue water, as measured with diffusion-weighted MRI. The early diffusion changes were accompanied by only mild changes in the overall metabolic status as measured by in vivo 1H MRS and 31P MRS and metabolic imaging of brain sections. Minimal decreases in the high-energy phosphate levels and a small hemispheric acidosis were observed in the first 6 h after NMDA administration. In addition, there was very modest lactate accumulation. Twenty-four hours after the induction of the excitotoxic injury the tissue energy status was still only moderately affected, whereas an overall decrease of 1H MRS-detected brain metabolites was found. Treatment with the non-competitive NMDA-antagonist MK-801 given within 90 min after NMDA injection rapidly reversed the NMDA-induced changes in the entire ipsilateral hemisphere. The effect of the competitive NMDA-antagonist D-CPPene was restricted to the cortical areas and was accomplished on a slower time scale. Our results indicate that; (i) early excitotoxicity in the neonatal rat brain does not lead to profound changes in the metabolic status; and (ii) brain tissue water ADC changes are not necessarily associated with a metabolic energy failure.
Fitting the Coulomb potential variationally in Xα molecular calculations (1983)

The method of Mintmire and Dunlap which variationally fits the Coulomb potential rather than the charge density is extended to linear combination of Gaussian-type orbitals Xα calculations on molecules. This approach is more efficient than fitting the charge density since the same integrals are used to treat the Coulomb and exchange potentials. Furthermore, the required Fock matrix elements are simple overlap rather than Coulomb integrals. However, the method is somewhat less accurate than fitting the charge density in a test on H2.
Subsurface-AFM: sensitivity to the heterodyne signal (2013)

Applying heterodyne force microscopy (HFM), it has been impressively demonstrated that it is possible to obtain subsurface information: 20 nm large gold nanoparticles that were buried 500 nm deep have been imaged. It is the heterodyne signal that contains the subsurface information. We elucidate, both theoretically and experimentally, the sensitivity to the heterodyne signal as a function of the tip-sample distance. This is crucial information for experiments as the distance, and therefore the sensitivity, is tunable. We show that the amplitude of the heterodyne signal has a local maximum in the attractive part of the tip-sample interaction, before it surprisingly reaches an even higher plateau, when the tip-sample interaction is repulsive. This can only be explained by a non-decreasing amplitude of the ultrasonic motion of the tip, although it is in full contact with the surface. We confirm this counterintuitive tip behavior experimentally even on a hard surface like silicon.
Automatic parallelization, performance predictability and power control for mobile-applications (2013)

Currently few mobile applications exploit the power- and performance capabilities of multi-core architectures. As the number of cores increases, the challenges become more pressing. We picked three challenges: application parallelization, performance-predictability/portability and power control for mobile devices. We tackled the challenges with our auto-parallelizing compiler and operating system enhancements.
Schwann Cell Surface Proteins and Glycoproteins (1982)

Abstract: To identify surface sialoglycoproteins of rat Schwann cells and to compare molecular weights of these sialoglycoproteins with those present in rat peripheral nervous system myelin, we prepared Schwann cells from sciatic nerves of 1–3‐day‐old rats and cultured them in monolayer. Surface sialoglycoproteins of the cultured cells were tritium‐labeled by the periodateborohydride procedure and compared with sialoglycoproteins of adult rat peripheral nervous system myelin by fluorography following polyacrylamide slab gel electrophoresis in sodium dodecyl sulfate. Three radioactive bands with apparent molecular weights of 114,000–132,000, 105,000–115,000, and 44,000–56,000 were observed in both the Schwann cell and myelin preparations. Bands of similar apparent molecular weights were noted in Schwann cells metabolically radiolabeled with d ‐[1,6‐ 3 H]glucosamine. A band co‐migrating with myelin P 0 glycoprotein was the most intensely radiolabeled of all peptides in periodate‐B 3 H 4 − treated myelin, but was present in only trace amounts in periodate‐B 3 H 4 − or d ‐[1,6‐ 3 H]glucosamine radiolabeled Schwann cells. Many presumably non‐myelin glycoproteins were identified in the cultured Schwann cells by the periodate‐borohydride procedure and by incubation of the cells with d ‐[1,6‐ 3 H]glucosamine. An immunoprecipitation technique was used to detect radiolabeled peptides in a nonionic detergent extract of freshly prepared, surface‐radioiodinated Schwann cells that were bound by a rabbit anti‐Schwann cell serum preabsorbed with rat fibroblasts. Many radioactive peptides were detected in the immunoprecipitate, but the two most intensely radiolabeled had apparent molecular weights of 105,000–115,000 and 95,000–106,000. This study has identified a number of glycoproteins synthesized by cultured rat Schwann cells which resemble in apparent molecular weight the glycoproteins expressed in rat peripheral nervous system myelin and has defined Schwann cell surface proteins recognized by a specific anti‐rat Schwann cell antiserum.
Mechanism of bilirubin elimination in urine: insights and prospects for neonatal jaundice (2021)

Despite a century of research, bilirubin metabolism and the transport mechanisms responsible for homeostasis of bilirubin in serum remain controversial. Emerging evidence on the hepatic membrane transporters and inherited disorders of bilirubin metabolism have contributed to a greater understanding of the various steps involved in bilirubin homeostasis and its associated excretory pathways. We discuss these recent research findings on hepatic membrane transporters and evaluate their significance on the newborn bilirubin metabolism and excretion. New insights gained speculate that a proportion of conjugated bilirubin is excreted via the renal system, as an alternative to the intestinal excretion, even in normal physiological jaundice with no associated pathological concerns. Finally, this paper discusses the clinical relevance of targeting the altered renal excretory pathway, as bilirubin in urine may hold diagnostic importance in screening for neonatal jaundice.
Understanding and Preventing Recurring Bacterial Vaginosis: Important Considerations for Clinicians (2023)

Bacterial vaginosis (BV) is the most common vaginal infection worldwide. It is associated with an increased risk of acquisition of HIV and other sexually transmitted infections (STIs) as well as pelvic inflammatory disease and adverse birth outcomes. During BV, a polymicrobial biofilm forms on the surface of the vaginal mucosa. However, the exact etiology of BV remains controversial which has impeded significant advances in diagnosis, treatment, and prevention. Despite 30-day cure rates approaching 80% in BV-infected women treated with 7 days of oral metronidazole, recurrence within 12 months is common. This article provides a current review of the epidemiology, pathogenesis, diagnosis, and treatment of recurrent BV for practicing clinicians who commonly see women with this recurrent vaginal infection. Regarding management, we focus primarily on antimicrobial measures that may be effective. Future areas of research in this field are also discussed.
Integrated system of white LED visible-light communication and power-line communication (2003)

White LED offers advantageous properties such as high brightness, reliability, lower power consumption and long lifetime. Indoor optical wireless communication systems employing white LED lighting have been proposed. This system will enable high quality of service by the high radiation power from this lighting equipment. And, this system does not cause or suffer from radio or electromagnetic interference. But, it is difficult for existing offices and households to install the communication cable to the ceiling. In this paper, an easy wiring system for optical communication using the existing power-line is proposed. This system is emitted as visible-light from LED lighting according to the transmitted signal waveform without demodulating the signal from the power-line. This system is expected to be applicable from the existing illuminant easily like exchanging electric bulbs. This integrated system will surely have a big impact as a new signal transmission system and its economical effect will be great. The basic performance of this system is analyzed. The actual system is built and its feasibility is shown through experiments.
Immunoglobulin constant heavy G chain genes as risk factors in childhood allergies (2006)

The IGHG*bfn haplotype (=B1 cells) and IGHG2*n allele dominated (51% vs. 24%, P=0.002) and the IGHG*bf-n haplotype (=B2 cells) was infrequent (16% vs. 52%, P < 0.001) in allergic children with a family history of allergy, clinical manifest allergy and positive skin prick test (SPT). The frequency of IGHG genes was similar in children with maternal and paternal heredity and in children with wheezing, eczema or rhinitis, as well as in children with different positive SPT. The IGHG*bfn haplotype with the IGHG2*n allele was strongly associated with heredity for allergy. The IGHG*bf-n haplotype was inversely related to allergy. Conclusions IgG allotypes, immunochemical and functional variants of IgG molecules from IGHG genes are associated with atopy. The IGHG*bfn haplotype (=B1 cells) with the IGHG2*n allele dominates, associated with an increased risk for atopy. In contrast, the IGHG*bf-n haplotype (=B2 cells) with the IGHG2*-n allele is associated with low risk.
Symmetrical and Nonsymmetrical Liquid Crystalline Oligothiophenes: Convenient Synthesis and Transition‐Temperature Engineering (2007)

Abstract Two approaches to transition‐temperature engineering in liquid crystalline oligothiophenes are described: (i) substitution at the aromatic core with two identical branched alkyl chains and (ii) desymmetrization of the molecule with two alkyl substituents of different length or structure. Key steps in the synthesis of symmetrical and nonsymmetrical terthiophenes and quaterthiophenes involve Suzuki coupling and carbanion alkylation. A well‐adjusted balance between the π–π stacking of the aromatic core and the disorder caused by the peripheral alkyl chains is demonstrated to be important for the control of the thermotropic behavior of oligothiophene mesogens. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm (2019)

The transcriptional mechanisms driving lineage specification during development are still largely unknown, as the interplay of multiple transcription factors makes it difficult to dissect these molecular events. Using a cell-based differentiation platform to probe transcription function, we investigated the role of the key paraxial mesoderm and skeletal myogenic commitment factors-mesogenin 1 (Msgn1), T-box 6 (Tbx6), forkhead box C1 (Foxc1), paired box 3 (Pax3), Paraxis, mesenchyme homeobox 1 (Meox1), sine oculis-related homeobox 1 (Six1), and myogenic factor 5 (Myf5)-in paraxial mesoderm and skeletal myogenesis. From this study, we define a genetic hierarchy, with Pax3 emerging as the gatekeeper between the presomitic mesoderm and the myogenic lineage. By assaying chromatin accessibility, genomic binding and transcription profiling in mesodermal cells from mouse and human Pax3-induced embryonic stem cells and Pax3-null embryonic day (E)9.5 mouse embryos, we identified conserved Pax3 functions in the activation of the skeletal myogenic lineage through modulation of Hedgehog, Notch, and bone morphogenetic protein (BMP) signaling pathways. In addition, we demonstrate that Pax3 molecular function involves chromatin remodeling of its bound elements through an increase in chromatin accessibility and cooperation with sine oculis-related homeobox 4 (Six4) and TEA domain family member 2 (Tead2) factors. To our knowledge, these data provide the first integrated analysis of Pax3 function, demonstrating its ability to remodel chromatin in mesodermal cells from developing embryos and proving a mechanistic footing for the transcriptional hierarchy driving myogenesis.