gebhart/patrepeval huggingface dataset:
Immune Response and Mitochondrial Metabolism Are Commonly Deregulated in DMD and Aging Skeletal Muscle (2011)

Duchenne Muscular Dystrophy (DMD) is a complex process involving multiple pathways downstream of the primary genetic insult leading to fatal muscle degeneration. Aging muscle is a multifactorial neuromuscular process characterized by impaired muscle regeneration leading to progressive atrophy. We hypothesized that these chronic atrophying situations may share specific myogenic adaptative responses at transcriptional level according to tissue remodeling. Muscle biopsies from four young DMD and four AGED subjects were referred to a group of seven muscle biopsies from young subjects without any neuromuscular disorder and explored through a dedicated expression microarray. We identified 528 differentially expressed genes (out of 2,745 analyzed), of which 328 could be validated by an exhaustive meta-analysis of public microarray datasets referring to DMD and Aging in skeletal muscle. Among the 328 validated co-expressed genes, 50% had the same expression profile in both groups and corresponded to immune/fibrosis responses and mitochondrial metabolism. Generalizing these observed meta-signatures with large compendia of public datasets reinforced our results as they could be also identified in other pathological processes and in diverse physiological conditions. Focusing on the common gene signatures in these two atrophying conditions, we observed enrichment in motifs for candidate transcription factors that may coordinate either the immune/fibrosis responses (ETS1, IRF1, NF1) or the mitochondrial metabolism (ESRRA). Deregulation in their expression could be responsible, at least in part, for the same transcriptome changes initiating the chronic muscle atrophy. This study suggests that distinct pathophysiological processes may share common gene responses and pathways related to specific transcription factors.
Self organized terminode routing simulation (2001)

In this paper we simulated terminode routing. This routing scheme is designed for wide area networks, where a large part or all the nodes are mobile. Terminode routing is a combination of two protocols called Terminode Local Routing (TLR) and Terminode Remote Routing (TRR). TLR is used to route packets to close destinations. TRR is used to route to remote destinations and is composed of the following elements: Anchored Geodesic Packet Forwarding (AGPF), Anchored Path Discovery (APD), multipath routing and path maintenance. We performed simulations of the TLR and TRR protocols using the GloMoSim simulator. In order to do that, we have implemented a new mobility model that we call ``restricted random waypoint
Synthesis and Tautomerism of Pyrido[2,3-b]pyrazines (2000)

The reaction of 2-methoxycarlmethylen-l,2-dihydro-4H-pyrido[2,3-b]pyrazin-3-one(5) with hydrazine hydrate and ethylenediamine gave 2-hydrazinocarbonylmethylene-1,2-dihydro-4H-pyrido[2,3-b]pyrazin-3-one(6) and 2-aminoethylcarbamethylene-1,2-dihydro-4H-pyrido[2,3-b]pyrazin-3-one(7), res-pectively. The reaction of compound 6 or 7 with substituted benzaldehydes or heteroaryl aldehydes afforded pyrido[2,3-b]pyrazines(8-13). Some pyrin the enamine, methylene imine and enaminol forms in solution. The tau-tomer ratios were determined by the H NMR.
Chemical peritonitis associated with high dialysate acetaldehyde concentrations (2000)

Based on the above findings, we hypothesize that higher levels of acetaldehyde and possibly other glucose degradation products may have been an aetiological factor in these 21 cases of chemical peritonitis. Our observation suggests that acetaldehyde, in concentrations 3-4 times higher than the usual level in commercially available PD solutions, may induce acute sterile peritonitis in CAPD patients.
Nuclear-Cytoplasmic “Tug of War” During Cloning: Effects of Somatic Cell Nuclei on Culture Medium Preferences of Preimplantation Cloned Mouse Embryos1 (2002)

Cloning by somatic cell nuclear transfer is critically dependent upon early events that occur immediately after nuclear transfer, and possibly additional events that occur in the cleaving embryo. Embryo culture conditions have not been optimized for cloned embryos, and the effects of culture conditions on these early events and the successful initiation of clonal development have not been examined. To evaluate the possible effect of culture conditions on early cloned embryo development, we have compared a number of different culture media, either singly or in sequential combinations, for their ability to support preimplantation development of clones produced using cumulus cell nuclei. We find that glucose is beneficial during the 1-cell stage when CZB medium is employed. We also find that potassium simplex optimized medium (KSOM), which is optimized to support efficient early cleavage divisions in mouse embryos, does not support development during the 1-cell or 2-cell stages in the cloned embryos as well as other media. Glucose-supplemented CZB medium (CZB-G) supports initial development to the 2-cell stage very well, but does not support later cleavage stages as well as Whittten medium or KSOM. Culturing cloned embryos either entirely in Whitten medium or initially in Whittens medium and then changing to KSOM at the late 4-cell/early 8-cell stage produces consistent production of blastocysts at a greater frequency than using CZB-G medium alone. The combination of Whitten medium followed by KSOM resulted in an increased number of cells per blastocyst. Because normal embryos do not require glucose during the early cleavage stages and develop efficiently in all of the media employed, these results reveal unusual culture medium requirements that are indicative of altered physiology and metabolism in the cloned embryos. The relevance of this to understanding the kinetics and mechanisms of nuclear reprogramming and to the eventual improvement of the overall success in cloning is discussed.
Momentum filtering effect in molecular wires (2004)

We report a first-principles analysis of conduction properties of molecular junctions. We investigate the relationship between molecular orbitals in the scattering region of the junction and the band structure of the leads. By characterizing the nature of the orbitals and the Bloch states of the leads, we provide an understanding on why some Bloch states conduct better than others. In particular, we found that the molecule can behave as a momentum filter: only those Bloch bands having the same orbital character as the molecular states near the Fermi level conduct well. Adding a different end group to the molecule can help to couple different Bloch bands to the molecule.
Immobilization of glucose oxidase on nonwoven fabrics with bombyx mori silk fibroin gel (1992)

Abstract The enzyme glucose oxidase (GOD) was immobilized on the nonwoven fabrics, which have excellent properties in diffusivity of substrates, mechanical strength, and handling, with Bombyx mori silk fibroin gel. The nonwoven fabrics of silk fibroin, viscose rayon, poly‐ethyleneterephthalate, 6‐nylon, and polypropylene with activated surface by fluoline treatment were used. The stabilities of GOD to heat or pH changes were much improved by the immobilization as well as the case of the GOD immobilized in the silk fibroin membrane. Among nonwoven fabrics, silk fibroin was the most excellent support material for the immobilization of GOD although all nonwoven fabrics used here are able to be used as the support materials. The increase of the sensitivity was observed when the glucose sensor was made with the GOD immobilized on nonwoven silk fabrics as four times compared with the case of the GOD immobilized in the silk fibroin membrane.
Linkage between ocean climate, post-smolt growth, and survival of Atlantic salmon (Salmo salar L.) in the North Sea area (2000)

We examined two long-term tagging studies with wild salmon stocks in the North Sea area. The salmon stocks, the Figgjo in southern Norway and the North Esk in eastern Scotland, reside in relatively un-impacted rivers that continue to sustain healthy runs of salmon. The return rates for one seawinter fish (1SW), the predominant age at maturity for both stocks, were highly correlated. An analysis of sea surface temperature distributions for periods of high versus low return rate showed that when low sea surface temperatures dominate the North Sea and southern coast of Norway during May, salmon survival has been poor. Conversely, when high sea surface temperatures extend northward along the Norwegian coast during May, survival has been good. Ocean conditions can be further related to the recruitment process through growth studies for the North Esk stock. Post-smolt growth increments for returning 1SW fish showed that enhanced growth was associated with years during which temperature conditions were favorable, which in turn resulted in higher survival rates. The implicit linkage between growth and survival suggests that growth-mediated predation is the dominant source of recruitment variability. Mechanisms by which ocean climate may affect post-smolt growth are discussed.
3D-printed adaptive acoustic lens as a disruptive technology for transcranial ultrasound therapy using single-element transducers (2017)

The development of multi-element arrays for better control of the shape of ultrasonic beams has opened the way for focusing through highly aberrating media, such as the human skull. As a result, the use of brain therapy with transcranial-focused ultrasound has rapidly grown. Although effective, such technology is expensive. We propose a disruptive, low-cost approach that consists of focusing a 1 MHz ultrasound beam through a human skull with a single-element transducer coupled with a tailored silicone acoustic lens cast in a 3D-printed mold and designed using computed tomography-based numerical acoustic simulation. We demonstrate on N = 3 human skulls that adding lens-based aberration correction to a single-element transducer increases the deposited energy on the target 10 fold.
Difficult Macrocyclizations:  New Strategies for Synthesizing Highly Strained Cyclic Tetrapeptides (2003)

[reaction: see text] Cyclic tetrapeptides are an intriguing class of natural products. To synthesize highly strained cyclic tetrapeptides we developed a macrocyclization strategy that involves the inclusion of 2-hydroxy-6-nitrobenzyl (HnB) group at the N-terminus and in the "middle" of the sequence. The N-terminal auxiliary performs a ring closure/ring contraction role, and the backbone auxiliary promotes cis amide bonds to facilitate the otherwise difficult ring contraction. Following this route, the all-L cyclic tetrapeptide cyclo-[Tyr-Arg-Phe-Ala] was successfully prepared.
The design philosophy of the DARPA internet protocols (1988)

The Internet protocol suite, TCP/IP, was first proposed fifteen years ago. It was developed by the Defense Advanced Research Projects Agency (DARPA), and has been used widely in military and commercial systems. While there have been papers and specifications that describe how the protocols work, it is sometimes difficult to deduce from these why the protocol is as it is. For example, the Internet protocol is based on a connectionless or datagram mode of service. The motivation for this has been greatly misunderstood. This paper attempts to capture some of the early reasoning which shaped the Internet protocols.
SOLAR RADIATION ESTIMATION ON BUILDING ROOFS AND WEB-BASED SOLAR CADASTRE (2012)

Abstract. The aim of this study is the estimation of solar irradiance on building roofs in complex Alpine landscapes. Very high resolution geometric models of the building roofs are generated by means of advanced automated image matching methods. Models are combined with raster and vector data sources to estimate the incoming solar radiation hitting the roofs. The methodology takes into account for atmospheric effects, site latitude and elevation, slope and aspect of the terrain as well as the effects of shadows cast by surrounding buildings, chimneys, dormers, vegetation and terrain topography. An open source software solution has been developed and applied to a study area located in a mountainous site and containing some 1250 residential, commercial and industrial buildings. The method has been validated by data collected with a pyranometer and results made available through a prototype WebGIS platform.
Cancer Statistics, 2006 (2006)

Each year, the American Cancer Society estimates the number of new cancer cases and deaths expected in the United States in the current year and compiles the most recent data on cancer incidence, mortality, and survival based on incidence data from the National Cancer Institute and mortality data from the National Center for Health Statistics. Incidence and death rates are age-standardized to the 2000 US standard million population. A total of 1,399,790 new cancer cases and 564,830 deaths from cancer are expected in the United States in 2006. When deaths are aggregated by age, cancer has surpassed heart disease as the leading cause of death for those younger than age 85 since 1999. Delay-adjusted cancer incidence rates stabilized in men from 1995 through 2002, but continued to increase by 0.3% per year from 1987 through 2002 in women. Between 2002 and 2003, the actual number of recorded cancer deaths decreased by 778 in men, but increased by 409 in women, resulting in a net decrease of 369, the first decrease in the total number of cancer deaths since national mortality record keeping was instituted in 1930. The death rate from all cancers combined has decreased by 1.5% per year since 1993 among men and by 0.8% per year since 1992 among women. The mortality rate has also continued to decrease for the three most common cancer sites in men (lung and bronchus, colon and rectum, and prostate) and for breast and colon and rectum cancers in women. Lung cancer mortality among women continues to increase slightly. In analyses by race and ethnicity, African American men and women have 40% and 18% higher death rates from all cancers combined than White men and women, respectively. Cancer incidence and death rates are lower in other racial and ethnic groups than in Whites and African Americans for all sites combined and for the four major cancer sites. However, these groups generally have higher rates for stomach, liver, and cervical cancers than Whites. Furthermore, minority populations are more likely to be diagnosed with advanced stage disease than are Whites. Progress in reducing the burden of suffering and death from cancer can be accelerated by applying existing cancer control knowledge across all segments of the population.
Laser Effects On Dental Hard Tissues (1987)

The use of lasers in dentistry has been considered for over 20 years. Higher-energy density lasers were shown to fuse enamel but were potentially unsafe. Subsequently, low-energy density laser radiation was shown to affect artificial caries lesion formation. Recent studies have shown that carbon dioxide lasers can successfully be used at low-energy densities to fuse enamel, dentin, and apatite. Our studies have shown that specific wavelengths are highly efficient. These wavelengths are directly related to the infrared absorption regions of apatite. We have conducted studies with enamel and dentin, using pulsed CO2 laser radiation in the 9.32-μm to 10.49-μm region with energy densities in the 10 to 50 J.cm -2 range. This laser treatment caused surface fusion and inhibition of subsequent lesion progression and markedly improved the bonding strength of a composite resin to dentin. Similar studies have shown no pulpal damage or permanent deleterious effect on soft tissues. This improved understanding of the scientific rationale for the interaction of CO2 lasers with teeth can lead to several clinical applications. This will depend, however, on the development of a technology to direct a specific frequency laser beam precisely to a desired site.
Plasma ceramides are elevated in female children and adolescents with type 2 diabetes (2013)

Accumulation of ceramides within tissues induces insulin resistance. Moreover, adiponectin exerts its beneficial metabolic effects at least partially through ceramide catabolism. We hypothesized that specific plasma ceramide subspecies are elevated in obese children and adolescents with type 2 diabetes (T2D), and that they inversely correlate with adiponectin and measures of insulin sensitivity. This was a cross-sectional study. Participants included 14 obese female subjects with T2D, ages 10-17, and 14 lean healthy controls of the same age and gender. Fasting plasma ceramide subspecies were measured by quantitative tandem mass spectrometry. Subjects with T2D had higher concentrations of C22:0 and C20:0 ceramides, with a 2-fold increase in C18:0 ceramide and C24:1 dihydroceramide (p<0.05). C22:0, C20:0 and C18:0 ceramide correlated with decreased adiponectin concentrations, increased HOMA-IR, BMI Z-score, triglyceride and fasting blood glucose concentrations (p<0.05). Plasma levels of C18:0, C20:0 and C22:0 ceramide, as well as C24:1 dihydroceramide, were elevated in obese female children and adolescents with T2D. This may be a reflection of tissue insulin resistance and could be a result of low adiponectin levels.
Molecular Landscape ofERBB2/ERBB3Mutated Colorectal Cancer (2018)

MSI and PIK3CA mutations are associated with ERBB2/ERBB3 mutations. Co-occurring PIK3CA mutations may represent a second hit to oncogenic signaling that needs consideration when targeting ERBB2/ERBB3.
The synthesis of polyamide-oligonucleotide conjugate molecules (1990)

We have developed methods for the synthesis of peptide-oligodeoxyribonucleotide conjugate molecules in particular, and polyamide-oligonucleotide conjugates in general. Synthesis is carried out by a solid-phase procedure and involves the assembly of a polyamide on the solid support, conversion of the terminal amino group to a protected primary aliphatic hydroxy group by reaction with alpha, omega-hydroxycarboxylic acid derivatives, and finally oligonucleotide synthesis using phosphoramidite chemistry. The conjugate molecules can be used as DNA probes, with the polyamide component carrying one or more non-radioactive markers. These conjugates also have the potential to be used as anti-sense inhibitors of gene expression, with the peptide segment acting as a targeting moiety.
Multisite phosphorylation of glycogen synthase from rabbit skeletal muscle (1985)

A casein kinase was highly purified from rabbit skeletal muscle whose substrate specificity and enzymatic properties were virtually identical to those of casein kinase-I from rabbit reticulocytes. Prolonged incubation of glycogen synthase with high concentrations of skeletal muscle casein kinase-I and Mg-ATP resulted in the incorporation of greater than 6 mol phosphate/mol subunit and decreased the activity ratio (+/- glucose-6P) from 0.8 to less than 0.02. The sites phosphorylated by casein kinase-I were all located in the N and C-terminal cyanogen bromide peptides, termed CB-1 and CB-2. At an incorporation of 6 mol phosphate/mol subunit, approximately equal to 2 mol/mol was present in CB-1 and approximately equal to 4 mol/mol in CB-2. Within CB-1, casein kinase-I phosphorylated the serines that were 3, 7 and 10 residues from the N-terminus of glycogen synthase, with minor phosphorylation at threonine-5. Within CB-2, approximately equal to 90% of the phosphate incorporated was located between residues 28 and 53, and at least five of the seven serine residues in this region were phosphorylated. The remaining 10% of phosphate incorporated into CB-2 was located between residues 98 and 123, mainly at a serine residue(s). Two of the major sites labelled by casein kinase-I (serine-3 and serine-10 of CB-1) are not phosphorylated by any other protein kinase. This will enable the role of casein kinase-I as a glycogen synthase kinase in vivo to be evaluated.
Synthesis of Sugar Arrays in Microtiter Plate (2002)

1,3-Dipolar cycloadditions between azides and alkynes were exploited to attach oligosaccharides to a C(14) hydrocarbon chain that noncovalently binds to the microtiter well surface. Synthesis of sugar arrays was performed on a micromolar scale in situ in the microtiter plate. As a model study, the beta-galactosyllipid 5 was displayed on a 4-micromol scale. Formation of product was confirmed via ESI-MS, and the yield was determined via chemical and biological assays. Several complex carbohydrates (6-16) were also displayed in microtiter plates and successfully screened with various lectins. Moreover, sialyl Lewis x (17) was synthesized via the enzymatic fucosylation of a precursor displayed in the plate. Studies on inhibition of this biotransformation have been carried out, and the IC(50) value found for the known inhibitor 20 was consistent with previous studies in solution.
Real-time Monitoring of In Vivo Acute Necrotic Cancer Cell Death Induced by Near Infrared Photoimmunotherapy Using Fluorescence Lifetime Imaging (2012)

A new type of monoclonal antibody (mAb)-based, highly specific phototherapy (photoimmunotherapy; PIT) that uses a near infrared (NIR) phthalocyanine dye, IRDye700DX (IR700) conjugated with a mAb, has recently been described. NIR light exposure leads to immediate, target-selective necrotic cell death in vitro. Detecting immediate in vivo cell death is more difficult because it takes at least 3 days for the tumor to begin to shrink in size. In this study, fluorescence lifetime (FLT) was evaluated before and after PIT for monitoring the immediate cytotoxic effects of NIR mediated mAb-IR700 PIT. Anti-epidermal growth factor receptor (EGFR) panitumumab-IR700 was used for targeting EGFR-expressing A431 tumor cells. PIT with various doses of NIR light was conducted in cell pellets in vitro and in subcutaneously xenografted tumors in mice in vivo. FLT measurements were obtained before and 0, 6, 24, and 48 hours after PIT. In vitro, PIT at higher doses of NIR light immediately led to FLT shortening in A431 cells. In vivo PIT induced immediate shortening of FLT in treated tumors after a threshold NIR dose of 30 J/cm(2) or greater. In contrast, lower levels of NIR light (10 J/cm(2) or smaller) did not induce shortening of FLT. Prolongation of FLT in tissue surrounding the tumor site was noted 6 hours after PIT, likely reflecting phagocytosis by macrophages. In conclusion, FLT imaging can be used to monitor the acute cytotoxic effects of mAb-IR700-induced PIT even before morphological changes can be seen in the targeted tumors.
Noninvasive transcranial Doppler ultrasound recording of flow velocity in basal cerebral arteries (1982)

In this report the authors describe a noninvasive transcranial method of determining the flow velocities in the basal cerebral arteries. Placement of the probe of a range-gated ultrasound Doppler instrument in the temporal area just above the zygomatic arch allowed the velocities in the middle cerebral artery (MCA) to be determined from the Doppler signals. The flow velocities in the proximal anterior (ACA) and posterior (PCA) cerebral arteries were also recorded at steady state and during test compression of the common carotid arteries. An investigation of 50 healthy subjects by this transcranial Doppler method revealed that the velocity in the MCA, ACA, and PCA was 62 +/- 12, 51 +/0 12, and 44 +/- 11 cm/sec, respectively. This method is of particular value for the detection of vasospasm following subarachnoid hemorrhage and for evaluating the cerebral circulation in occlusive disease of the carotid and vertebral arteries.