gebhart/patrepeval huggingface dataset:
Noninvasive and Transient Blood-Brain Barrier Opening in the Hippocampus of Alzheimer's Double Transgenic Mice Using Focused Ultrasound (2008)

The spatio-temporal nature of focused ultrasound-induced blood-brain barrier (BBB) opening as a brain drug delivery method was investigated in Alzheimer's disease model mice. The left hippocampus of transgenic (APP/PS1, n = 3) and nontransgenic (n = 3) mice was sonicated (frequency: 1.525 MHz, peak-negative pressure: 600 kPa, pulse length: 20 ms, duty cycle: 20%, duration: 1 min) in vivo, through their intact skin and skull, after intravenous injection of microbubbles (SonoVue; 25 microl). Sequential, high-field MR images (9.4 Tesla) were acquired before and after injection of gadolinium (Omniscan, 0.75 ml, molecular weight: 573.7 Da) on two separate days for each mouse. Gadolinium deposits through the ultrasound-induced BBB opening in the left hippocampus revealed significant contrast-enhancement in the MRI. On the following day, MRI revealed significant BBB closure within the same region. However, the BBB opening extent and BBB closing timeline varied in different regions within the same sonicated location. This indicates that opening and closing were dependent on the brain region targeted. No significant difference in BBB opening or closing behaviors was observed between the APP/PS1 and the nontransgenic mice. In conclusion, a BBB-impermeable molecule was noninvasively, transiently and reproducibly delivered to the hippocampus of Alzheimer's APP/PS1 mice.
A new rhesus macaque assembly and annotation for next-generation sequencing analyses (2014)

This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.
Small-Angle Synchrotron X-Ray Scattering Reveals Distinct Shape Changes of the Myosin Head During Hydrolysis of ATP (1992)

In the energy transduction of muscle contraction, it is important to know the nature and extent of conformational changes of the head portion of the myosin molecules. In the presence of magnesium adenosine triphosphate (MgATP), fairly large conformational changes of the myosin head [subfragment-1 (S1)] in solution were observed by small-angle x-ray scattering with the use of synchrotron radiation as an intense and stable x-ray source. The presence of MgATP reduced the radius of gyration of the molecule by about 3 angstrom units and the maximum chord length by about 10 angstroms, showing that the shape of S1 becomes more compact or round during hydrolysis of MgATP. Comparison with various nucleotide-bound S1 complexes that correspond to the known intermediate states during ATP hydrolysis indicates that the shape of S1 in a key intermediate state, S1-bound adenosine diphosphate (ADP) and phosphate [S1**.ADP.P(i)], differs significantly from the shape in the other intermediate states of the S1 adenosine triphosphatase cycle as well as that of nucleotide-free S1.
Discovering Conversations in Web Services Using Semantic Correlation Analysis (2007)

Composite business applications typically combine characteristics of workflow and transactional applications. In order to handle multiple concurrent sessions and conversations across different nodes and over an extended time period, these applications pass dedicated identifiers inside their messages such as "OrderNumber". Debugging and understanding these conversations and the flow of conversation identifiers can be challenging in realistic business applications. We present a new heuristic algorithm to find these conversation identifiers and a method to reverse-engineer the conversations from the content of traced messages. Visualizing the results of this analysis provides a deeper understanding of the data flow, the business process and the interactions between business partners in composite business applications.
Learning a variational network for reconstruction of accelerated MRI data (2017)

Variational network reconstructions preserve the natural appearance of MR images as well as pathologies that were not included in the training data set. Due to its high computational performance, that is, reconstruction time of 193 ms on a single graphics card, and the omission of parameter tuning once the network is trained, this new approach to image reconstruction can easily be integrated into clinical workflow. Magn Reson Med 79:3055-3071, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Helix-Stabilizing Compounds CC-1065 and U-71,184 Bind to RNA-DNA and DNA-DNA Duplexes Containing Modified Internucleotide Linkages and Stabilize Duplexes Against Thermal Melting (1995)

CC-1065 and U-71,184 bind and hyperstabilize DNA duplexes, but little is known about their effects on nucleic acid duplexes of different structure. A 20 mer DNA sequence (5'-TTACTTCAGTTATGAGACCA) containing a drug binding sequence (5'-AGTTA) was selected as the target sequence, and this was duplexed with complementary antisense sequences containing phosphodiester (PO), phosphorothioate (PS), and methylphosphonate (MP) bonds. The duplexes containing PO or PS bound 2 CC-1065 molecules per duplex, presumably at both the target site and at a lower affinity site (5'-AGTAA) on the antisense strand. The duplex containing MP bound only 1 CC-1065, and all duplexes bound only 1 U-71,184. Both CC-1065 and U-71,184 bound to 20 mer duplexes comprised of oligo(dA)-oligo(dT) (2.5 and 2 drugs per duplex, respectively) and poly(rA)-oligo(dT) (1 drug per 20 base pairs). CC-1065 also bound to duplexes between the PO- or PS-based antisense structures and a complementary synthetic 20 mer RNA sequence, with about 1 drug per duplex in each case. CC-1065 increased the Tm for the 20 mer DNA duplexes 17 to 29 degrees C, and the corresponding values for U-71,184 ranged from 7 to 19 degrees C. CC-1065 raised the Tm of oligo(dA)-oligo(dT) and poly(rA)-oligo(dT) 29 degrees C. U71,184 increased the Tm for oligo(dA)-oligo(dT) 30 degrees C but did not significantly elevate the Tm for the corresponding RNA-DNA duplex. The results show that CC-1065 and U-71,184 are capable of binding and stabilizing a variety of nucleic acid duplexes. These agents or their analogs may become useful ligands for antisense oligonucleotide applications.
Interplay between the TCR/CD3 Complex and CD4 or CD8 in the Activation of Cytotoxic T Lymphocytes (1989)

Interactions between CTL and target cells occur in the absence of specific antigen recognition and precede subsequent interaction of the TCR with its specific antigen. This antigen-independent adhesion progresses through two different pathways, one involving the interaction of CD2 with LFA-3 on the target cell, the second the interaction of LFA-1 with ICAM-1. Such antigen-independent adhesions are critical for the activation of T cells via the TCR. Also, CD4 and CD8 can serve as adhesion molecules by binding to monomorphic determinants expressed on class II and class I MHC antigens, respectively, on the target cells, but compared to LFA-1 and CD2 antigens their contribution to conjugate formation is minor. CD4 and CD8 are required for effective T-cell activation in situations where the intrinsic affinity of the TCR or antigen expression is low, suggesting that CD4 and CD8 enhance the avidity of T cells for target cells by binding to class II and class I antigen, respectively. However, CD4 and CD8 are also involved in post-binding events that lead to CTL activation and subsequent lysis of the target cells. On the other hand, blocking of anti-TCR/CD3 mAb-induced CTL reactivity by anti-CD4/CD8 mAbs does not necessarily involve an interference with the binding of CD4 and CD8 to their respective ligands and it has been proposed that the TCR and CD4 or CD8 form functional complexes that are required for optimal T-cell activation. It is still unclear whether blocking by anti-CD4/CD8 mAbs is based on the prevention of complex formation of the TCR with CD4 or CD8, since formation of such complexes has yet to be demonstrated. The alternative hypothesis, that anti-CD4/anti-CD8 mAbs can directly confer negative regulatory signals to the CTL is not supported by our studies with antibody-directed lysis mediated by a CD4+, CD8+ CTL clone. Anti-CD4/CD8 mAbs can also inhibit T-cell cytotoxicity induced by other T-cell surface activation antigens such as CD2 or Tp103. In these situations, the triggering may involve signals transferred via CD3 requiring functional CD3/CD8 or CD3/CD4 complexes. Although most studies investigating the sequence of events leading to T-cell activation are carried out with CTL, preliminary data indicate that the same mechanisms described here for CTL activation are probably also valid for the interactions of T-helper cells with APC or B cells.(ABSTRACT TRUNCATED AT 400 WORDS)
A Novel Atrial Natriuretic Peptide Based Therapeutic in Experimental Angiotensin II Mediated Acute Hypertension (2010)

M-atrial natriuretic peptide (ANP; M-ANP) is a novel next generation 40 amino acid peptide based on ANP, which is highly resistant to enzymatic degradation and has greater and more sustained beneficial actions compared with ANP. The current study was designed to advance our understanding of the therapeutic potential of M-ANP in a canine model of acute angiotensin II-induced hypertension with elevated cardiac filling pressures and aldosterone activation. We compare M-ANP with vehicle and equimolar human B-type natriuretic peptide, which possesses the most potent in vivo actions of the native natriuretic peptides. M-ANP significantly lowered mean arterial pressure and systemic vascular resistance. Importantly, despite a reduction in blood pressure, renal function was enhanced with significant increases in renal blood flow, glomerular filtration rate, diuresis, and natriuresis after M-ANP infusion. Although angiotensin II induced an acute increase in pulmonary capillary wedge pressure, M-ANP significantly lowered pulmonary capillary wedge pressure, pulmonary artery pressure, and right atrial pressure. Further, M-ANP significantly suppressed angiotensin II-induced activation of aldosterone. These cardiovascular and renal enhancing actions of M-ANP were accompanied by significant increases in plasma and urinary cGMP, the second messenger molecule of the natriuretic peptide system. When compared with human B-type natriuretic peptide, M-ANP had comparable cardiovascular actions but resulted in a greater natriuretic effect. These results suggest that M-ANP, which is more potent than ANP in normal canines, has potent blood pressure lowering and renal enhancing properties and may, therefore, serve as an ANP based therapeutic for acute hypertension.
Residual Arachidonic Acid–Induced Platelet Activation via an Adenosine Diphosphate–Dependent but Cyclooxygenase-1– and Cyclooxygenase-2–Independent Pathway (2006)

There is a residual arachidonic acid-induced platelet activation in aspirin-treated patients that (1) is caused by underdosing and/or noncompliance in only approximately 2% of patients and (2) in the remaining patients, occurs via a cyclooxygenase-1 and cyclooxygenase-2 independent pathway, in direct proportion to the degree of baseline platelet activation, and is mediated in part by adenosine diphosphate-induced platelet activation.
Transfer-Free Batch Fabrication of Large-Area Suspended Graphene Membranes (2010)

We demonstrate a process for batch production of large-area (100-3000 microm(2)) patterned free-standing graphene membranes on Cu scaffolds using chemical vapor deposition (CVD)-grown graphene. This technique avoids the use of silicon and transfers of graphene. As one application of this technique, we fabricate transmission electron microscopy (TEM) sample supports. TEM characterization of the graphene membranes reveals relatively clean, highly TEM-transparent, single-layer graphene regions ( approximately 50% by area) and, despite the polycrystalline nature of CVD graphene, membrane yields as high as 75-100%. This high yield verifies that the intrinsic strength and integrity of CVD-grown graphene films is sufficient for sub-100 microm width membrane applications. Elemental analysis (electron energy loss spectroscopy (EELS) and X-ray energy-dispersive spectroscopy (EDS)) of the graphene membranes reveals some nanoscaled contamination left over from the etching process, and we suggest several ways to reduce this contamination and improve the quality of the graphene for electronic device applications. This large-scale production of suspended graphene membranes facilitates access to the two-dimensional physics of graphene that are suppressed by substrate interactions and enables the widespread use of graphene-based sample supports for electron and optical microscopy.
Transition From Rolling to Firm Adhesion Is Regulated by the Conformation of the I Domain of the Integrin Lymphocyte Function-associated Antigen-1 (2002)

The integrin lymphocyte function-associated antigen-1 (alpha(L)beta(2)), which is known for its ability to mediate firm adhesion and migration, can also contribute to tethering and rolling in shear flow. The alpha(L) I domain can be mutationally locked with disulfide bonds into two distinct conformations, open and closed, which have high and low affinity for the ligand intercellular adhesion molecule 1 (ICAM-1), respectively. The wild type I domain exists primarily in the lower energy closed conformation. We have measured for the first time the effect of conformational change on adhesive behavior in shear flow. We show that wild type and locked open I domains, expressed in alpha(L)beta(2) heterodimers or as isolated domains on the cell surface, mediate rolling adhesion and firm adhesion, respectively. alpha(L)beta(2) is thus poised for the conversion of rolling to firm adhesion upon integrin activation in vivo. Isolated I domains are surprisingly more effective than alpha(L)beta(2) in interactions in shear flow, which may in part be a consequence of the presence of alpha(L)beta(2) in a bent conformation. Furthermore, the force exerted on the C-terminal alpha-helix appears to stabilize the open conformation of the wild type isolated I domain and contribute to its robustness in supporting rolling. An allosteric small molecule antagonist of alpha(L)beta(2) inhibits both rolling adhesion and firm adhesion, which has important implications for its mode of action in vivo.
Involvement of Asn-293 in stereospecific agonist recognition and in activation of the beta 2-adrenergic receptor. (1996)

To investigate the molecular mechanism for stereospecific binding of agonists to beta 2-adrenergic receptors we used receptor models to identify potential binding sites for the beta-OH-group of the ligand, which defines the chiral center. Ser-165, located in transmembrane helix IV, and Asn-293, situated in the upper half of transmembrane helix VI, were identified as potential binding sites. Mutation of Ser-165 to Ala did not change the binding of either isoproterenol isomer as revealed after transient expression in human embryonic kidney (HEK)-293 cells. In contrast, a receptor mutant in which Asn-293 was replaced by Leu showed substantial loss of stereospecific isoproterenol binding. Adenylyl cyclase stimulation by this mutant after stable expression in CHO cells confirmed the substantial loss of stereospecificity for isoproterenol. In a series of agonists the loss of affinity in the Leu-293 mutant receptor was strongly correlated with the intrinsic activity of the compounds. Full agonists showed a 10-30-fold affinity loss, whereas partial agonists had almost the same affinity for both receptors. Stereospecific recognition of antagonists was unaltered in the Leu-293 mutant receptor. These data indicate a relationship between stereospecificity and intrinsic activity of agonists and suggest that Asn-293 is important for both properties of the agonist-receptor interaction.
Rolled-up nanomembranes as compact 3D architectures for field effect transistors and fluidic sensing applications (2012)

We fabricate inorganic thin film transistors with bending radii of less than 5 μm maintaining their high electronic performance with on-off ratios of more than 10(5) and subthreshold swings of 160 mV/dec. The fabrication technology relies on the roll-up of highly strained semiconducting nanomembranes, which compacts planar transistors into three-dimensional tubular architectures opening intriguing potential for microfluidic applications. Our technique probes the ultimate limit for the bending radius of high performance thin film transistors.
Alterations of plasma lipids in mice via adenoviral-mediated hepatic overexpression of human ABCA1 (2003)

ATP binding cassette transporter A1 (ABCA1) is a widely expressed lipid transporter essential for the generation of HDL. ABCA1 is particularly abundant in the liver, suggesting that the liver may play a major role in HDL homeostasis. To determine how hepatic ABCA1 affects plasma HDL cholesterol levels, we treated mice with an adenovirus (Ad)-expressing human ABCA1 under the control of the cytomegalovirus promoter. Treated mice showed a dose-dependent increase in hepatic ABCA1 protein, ranging from 1.2-fold to 8.3-fold using doses from 5 x 108 to 1.5 x 109 pfu, with maximal expression observed on Day 3 posttreatment. A selective increase in HDL cholesterol occurred at Day 3 in mice treated with 5 x 108 pfu Ad-ABCA1, but higher doses did not further elevate HDL cholesterol levels. In contrast, total cholesterol, triglycerides, phospholipids, non-HDL cholesterol, and apolipoprotein B levels all increased in a dose-dependent manner, suggesting that excessive overexpression of hepatic ABCA1 in the absence of its normal regulatory sequences altered total lipid homeostasis. At comparable expression levels, bacterial artificial chromosome transgenic mice, which express ABCA1 under the control of its endogenous regulatory sequences, showed a greater and more specific increase in HDL cholesterol than Ad-ABCA1-treated mice. Our results suggest that appropriate regulation of ABCA1 is critical for a selective increase in HDL cholesterol levels.
Lactobacillus coryniformis subsp. coryniformis Strain Si3 Produces a Broad-Spectrum Proteinaceous Antifungal Compound (2001)

The antifungal activity spectrum of Lactobacillus coryniformis subsp. coryniformis strain Si3 was investigated. The strain had strong inhibitory activity in dual-culture agar plate assays against the molds Aspergillus fumigatus, A. nidulans, Penicillium roqueforti, Mucor hiemalis, Talaromyces flavus, Fusarium poae, F. graminearum, F. culmorum, and F. sporotrichoides. A weaker activity was observed against the yeasts Debaryomyces hansenii, Kluyveromyces marxianus, and Saccharomyces cerevisiae. The yeasts Rhodotorula glutinis, Sporobolomyces roseus, and Pichia anomala were not inhibited. In liquid culture the antifungal activity paralleled growth, with maximum mold inhibition early in the stationary growth phase, but with a rapid decline in antifungal activity after 48 h. The addition of ethanol to the growth medium prevented the decline and gave an increased antifungal activity. The activity was stable during heat treatment and was retained even after autoclaving at 121 degrees C for 15 min. Maximum activity was observed at pH values of between 3. 0 and 4.5, but it decreased rapidly when pH was adjusted to a level between 4.5 and 6.0 and was lost at higher pH values. The antifungal activity was fully regained after readjustment of the pH to the initial value (pH 3.6). The activity was irreversibly lost after treatment with proteolytic enzymes (proteinase K, trypsin, and pepsin). The antifungal activity was partially purified using ion-exchange chromatography and (NH(4))(2)SO(4) precipitation, followed by gel filtration chromatography. The active compound(s) was estimated to have a molecular mass of approximately 3 kDa. This is the first report of the production of a proteinaceous antifungal compound(s) from L. coryniformis subsp. coryniformis.
Differential susceptibility to colorectal cancer due to naturally occurring gut microbiota (2015)

Recent studies investigating the human microbiome have identified particular bacterial species that correlate with the presence of colorectal cancer. To evaluate the role of qualitatively different but naturally occurring gut microbiota and the relationship with colorectal cancer development, genetically identical embryos from the Polyposis in Rat Colon (Pirc) rat model of colorectal cancer were transferred into recipients of three different genetic backgrounds (F344/NHsd, LEW/SsNHsd, and Crl:SD). Tumor development in the pups was tracked longitudinally via colonoscopy, and end-stage tumor burden was determined. To confirm vertical transmission and identify associations between the gut microbiota and disease phenotype, the fecal microbiota was characterized in recipient dams 24 hours pre-partum, and in Pirc rat offspring prior to and during disease progression. Our data show that the gut microbiota varies between rat strains, with LEW/SsNHsd having a greater relative abundance of the bacteria Prevotella copri. The mature gut microbiota of pups resembled the profile of their dams, indicating that the dam is the primary determinant of the developing microbiota. Both male and female F344-Pirc rats harboring the Lewis microbiota had decreased tumor burden relative to genetically identical rats harboring F344 or SD microbiota. Significant negative correlations were detected between tumor burden and the relative abundance of specific taxa from samples taken at weaning and shortly thereafter, prior to observable adenoma development. Notably, this naturally occurring variation in the gut microbiota is associated with a significant difference in severity of colorectal cancer, and the abundance of certain taxa is associated with decreased tumor burden.
Automated support for legacy code understanding (1994)

article Free AccessAutomated support for legacy code understanding Authors: Jim Q. Ning Andersen Consulting, Chicago, IL Andersen Consulting, Chicago, ILView Profile , Andre Engberts Andersen Consulting, Chicago, IL Andersen Consulting, Chicago, ILView Profile , W. Voytek Kozaczynski Andersen Consulting, Chicago, IL Andersen Consulting, Chicago, ILView Profile Authors Info & Claims Communications of the ACMVolume 37Issue 5May 1994 pp 50–57https://doi.org/10.1145/175290.175295Published:01 May 1994Publication History 110citation823DownloadsMetricsTotal Citations110Total Downloads823Last 12 Months20Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Apical changes and scarring in keratoconus as related to contact lens fitting techniques. (1982)

Seven keratoconus patients were fitted with gas-permeable lenses, one eye with a large apical bearing lens and the other with a small apical clearance lens. Within 12 months, 4 of the 7 eyes wearing the large flat technique developed corneal scarring, while no scarring developed in the eyes fitted with the apical clearance technique.