gebhart/patrepeval huggingface dataset:
Covalent Attachment of Cyclic TAT Peptides to GFP Results in Protein Delivery into Live Cells with Immediate Bioavailability (2014)

The delivery of free molecules into the cytoplasm and nucleus by using arginine-rich cell-penetrating peptides (CPPs) has been limited to small cargoes, while large cargoes such as proteins are taken up and trapped in endocytic vesicles. Based on recent work, in which we showed that the transduction efficiency of arginine-rich CPPs can be greatly enhanced by cyclization, the aim was to use cyclic CPPs to transport full-length proteins, in this study green fluorescent protein (GFP), into the cytosol of living cells. Cyclic and linear CPP-GFP conjugates were obtained by using azido-functionalized CPPs and an alkyne-functionalized GFP. Our findings reveal that the cyclic-CPP-GFP conjugates are internalized into live cells with immediate bioavailability in the cytosol and the nucleus, whereas linear CPP analogues do not confer GFP transduction. This technology expands the application of cyclic CPPs to the efficient transport of functional full-length proteins into live cells.
Highly Efficient Capture of Circulating Tumor Cells by Using Nanostructured Silicon Substrates with Integrated Chaotic Micromixers (2011)

Finding a needle in a haystack: A new technology is demonstrated to enrich circulating tumor cells (CTCs) with high efficiency by integrating an antibody-coated silicon nanopillar (SiNP, see picture; gray) substrate with an overlaid polydimethylsiloxane (PDMS) microfluidic chaotic mixer (turquoise). It shows significantly improved sensitivity in detecting rare CTCs from whole blood, thus providing an alternative for monitoring cancer progression. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Design and synthesis of novel 6,7-imidazotetrahydroquinoline inhibitors of thymidylate synthase using iterative protein crystal structure analysis (1992)

Antifolate inhibitors of thymidylate synthase (TS) have primarily been based on the structure of folic acid. This paper describes the identification and development of novel 6,7-imidazotetrahydroquinoline TS inhibitors by iterative ligand design, synthesis, and crystallographic analysis of protein-inhibitor complexes. Beginning with a high-resolution crystal structure of E. coli TS (TS, EC 2.1.1.45), an imidazotetrahydroquinoline inhibitor was designed de novo to occupy the folate binding pocket. Structural modifications of the initial compound 1h (Ki approximately 5 microM human/E. coli TS) were then made on the basis of feedback from additional cocrystal structures and activity data. An amino group in the 2-position of the imidazole was found to increase the potency of the series by 1-2 orders of magnitude. Other substitutions on the imidazole ring (1-CH3, 2-CH3, 2-NHCH3, 2-SCH3) generally led to weaker inhibition. Additional improvements in activity were obtained by modification of the substituents on the tetrahydroquinoline nitrogen, bringing the Ki of three of the compounds below 15 nM against the human TS enzyme. The compounds were tested for cytotoxicity and were shown to inhibit the growth of three tumor cell lines in vitro.
Structural Basis for Molecular Recognition at Serotonin Receptors (2013)

Serotonin or 5-hydroxytryptamine (5-HT) regulates a wide spectrum of human physiology through the 5-HT receptor family. We report the crystal structures of the human 5-HT1B G protein-coupled receptor bound to the agonist antimigraine medications ergotamine and dihydroergotamine. The structures reveal similar binding modes for these ligands, which occupy the orthosteric pocket and an extended binding pocket close to the extracellular loops. The orthosteric pocket is formed by residues conserved in the 5-HT receptor family, clarifying the family-wide agonist activity of 5-HT. Compared with the structure of the 5-HT2B receptor, the 5-HT1B receptor displays a 3 angstrom outward shift at the extracellular end of helix V, resulting in a more open extended pocket that explains subtype selectivity. Together with docking and mutagenesis studies, these structures provide a comprehensive structural basis for understanding receptor-ligand interactions and designing subtype-selective serotonergic drugs.
Biotin binders selected from a random peptide library expressed on phage (1993)

Recombinant biotin-binding phages were affinity-selected from a random peptide library expressed on the surface of filamentous phage. Phage binding to biotinylated proteins was half-maximally inhibited by micromolar concentrations of a monobiotinylated molecule. Sequencing of the peptide inserts of selected phages led to the identification of a previously unknown biotin-binding motif, CXWXPPF(K or R)XXC. A synthetic peptide containing this sequence motif inhibited streptavidin binding to biotinylated BSA with an IC50 of 50 microM. This compound represents the shortest non-avidin biotin-binding peptide identified to date. Our results illustrate that phage display technology can be used to identify novel ligands for a small non-proteinaceous molecule.
Comparison of WI-38, MRC-5, and IMR-90 cell strains for isolation of viruses from clinical specimens (1978)

With the diminishing supply of the human fetal lung WI-38 cell strain, a replacement for viral isolation is needed. Two candidates are the human fetal lung strains MRC-5 and IMR-90. A comparison of WI-38, MRC-5, and IMR-90 was performed to evaluate efficiency and speed of viral isolation, clarity of cytophatic effect, and ease of growing the cells. The inocula were clinical specimens rather than tissue culture-adapted isolates. Frozen samples of 46 specimens that had previously yielded an isolate on WI-38 were thawed and inoculated onto WI-38, MRC-5, and IMR-90 cells. In addition, 95 freshly taken clinical specimens uf undetermined infectivity were inoculated onto the cell strains. Viral recovery rates were similar on all three strains, as were the appearance and speed of onset of the cytophatic effect. MRC-5 and WI-38 cells remained healthy until generation 36, whereas IMR-90 cells went into crisis by generation 20. The longer life span of the MRC-5 cells makes them more suitable than IMR-90 cells to replace the WI-38 strain for routine use in viral diagnosis.
Changes in cystic fibrosis sputum microbiology in the United States between 1995 and 2008 (2010)

We identified important changes in the patterns of CF airway microbiology, including increased aminoglycoside resistance and prevalence of other antibiotic resistant organisms. These changes are concerning to clinicians caring for individuals with CF because they impact treatment options. These data point to a critical need to develop new antimicrobials for CF.
Light-Driven Chloride Ion Transport by Halorhodopsin from Natronobacterium pharaonis. II. Chloride Release and Uptake, Protein Conformation Change, and Thermodynamics (1995)

The photocycle of the light-driven chloride pump, N. pharaonis halorhodopsin, is described by the scheme HR-->K--><==>L<==>N<==>O<==>HR'-->HR. From the chloride dependencies of the rate constants in this model we identify the N-->O and O-->HR' reactions as the steps where chloride release and uptake occur, respectively, during the transport. The dependencies of the rate constants on temperature describe a thermodynamic cycle in which enthalpy-entropy conversion occurs in the O-->HR' reaction. The dependencies of the rate constants on hydrostatic pressure indicate that a substantial volume decrease occurs at the L-->N reaction, a result of a large-scale conformational change. This is the opposite of the volume increase in the photocycle of the proton pump, bacteriorhodopsin, that is implicated in the access change of the active site during the transport and the passage of a proton from the cytoplasmic surface to the active site. The results together suggest a chloride transport mechanism, in which the equivalents of all the ion transfer steps in bacteriorhodopsin occur but in the reverse sense, so as to cause the extracellular-to-cytoplasmic translocation of a chloride ion instead of the cytoplasmic-to-extracellular transport of a proton.
Infrared spectroscopy of exfoliated human cervical cells: evidence of extensive structural changes during carcinogenesis. (1991)

Infrared spectra were obtained from exfoliated cervical cells from 156 females, of whom 136 were normal, 12 had cervical cancer, and 8 had dysplasia. The spectra of the normal women, essentially identical, differed from those obtained from patients with either cancer or dysplasia. In malignant samples we noted (i) significant changes in the intensity of the glycogen bands at 1025 cm-1 and 1047 cm-1, the bands at 1082 cm-1 and 1244 cm-1, the C--O stretching band at 1155 cm-1, and the band at 1303 cm-1, (ii) significant shifts of the peaks normally appearing at 1082 cm-1, 1155 cm-1, and 1244 cm-1, and (iii) an additional band at 970 cm-1. Further study of several of these bands, including the pressure dependence of their frequencies, revealed that in the malignant cervical tissue there were extensive changes in the degree of hydrogen bonding of phosphodiester groups of nucleic acids and C--OH groups of proteins, as well as changes in the degree of disorder of methylene chains of lipids. The IR spectra of samples with dysplasia demonstrated the same changes with cancer samples, except that the changes were of lesser magnitude and the phosphodiester peak normally appearing at 1082 cm-1 did not shift. These spectroscopic changes appear to progress in tandem with the morphological changes that lead normal cervical epithelium to cancer through the premalignant stage of dysplasia. The diagnostic potential of IR spectroscopy is discussed.
Complement and myoblast transfer therapy: Donor myoblast survival is enhanced following depletion of host complement C3 using cobra venom factor, but not in the absence of C5 (2001)

Myoblast transfer therapy (MTT) is a potential cell therapy for myopathies such as Duchenne Muscular Dystrophy and involves the injection of cultured muscle precursor cells ('myoblasts') isolated from normal donor skeletal muscles into dystrophic host muscle. The failure of donor myoblast survival following MTT is widely accepted as being due to the immune response of the host. The role of complement as one possible mechanism for the initial, very rapid death of myoblasts following MTT was investigated. Donor male myoblasts were injected into the tibialis anterior (TA) muscles of female host mice that were: (i) untreated; (ii) depleted of C3 complement (24 h prior to MTT) using cobra venom factor (CVF); and/or (iii) deficient in C5 complement. Quantification of surviving male donor myoblast DNA was performed using the Y-chromosome specific (Y1) probe on slot blots for samples taken at 0 h, 1 h, 24 h, 1 week and 3 weeks after MTT. Peripheral depletion of C3 was confirmed using double immunodiffusion, and local depletion of C3 in host TA muscles was confirmed by immunostaining of muscle samples. Cobra venom factor treatment significantly increased the initial survival of donor myoblasts, but there was a marked decline in myoblast numbers after 1 h and little long-term benefit by 3 weeks. Strain specific variation in the immediate survival of donor male myoblasts following MTT in untreated C57BL/10Sn, DBA-1 and DBA-2 (C5-deficient) female hosts was observed. Cobra venom factor depletion of C3 increased initial donor male myoblast survival (approximately twofold at 0 h) in C57BL/10Sn and DBA-1 host mice and approximately threefold in DBA-2 hosts at 0 h and 1 h after MTT. The rapid and extensive number (approximately 90%) of donor male myoblasts in untreated DBA-2 mice (that lack C5) indicates that activation of the membrane attack complex (MAC) plays no role in this massive initial cell death. The observation that myoblast survival was increased in all mice treated with CVF suggests that CVF may indirectly enhance donor myoblast survival by a mechanism possibly involving activated C3 fragments.
Role of scatter factor in the pathogenesis of AIDS-related Kaposi sarcoma. (1994)

Kaposi sarcoma (KS) is a complex multicellular neoplasm that is commonly associated with AIDS. The pathogenesis of KS is not well understood. KS tumor cells grow poorly in vitro and require medium conditioned by retrovirus-infected T lymphocytes. We observed that conditioned medium (CM) from type II human T-cell leukemia virus (HTLV-II)-infected T cells (HTLV-II CM) induces conversion of endothelial cells (ECs) to a KS tumor cell-like phenotype. ECs grown in HTLV-II CM acquired a spindle-shaped morphology, the ability to express factor XIIIa and other KS cell markers, and a cytokine production profile similar to that of KS cells. We found that HTLV-II CM contains large quantities of scatter factor (SF), an angiogenic cytokine that stimulates cell motility. SF induced ECs to become spindle-shaped and express factor XIIIa. Moreover, SF was found to be a mitogen for KS cells in vitro and was identified within KS lesions in vivo. SF mRNA was present in KS cells in vitro, and antibodies against SF inhibited the growth of KS cells. The receptor for SF, the c-met protein, was expressed by ECs, dermal dendrocytes, and KS tumor cells in vitro and in vivo. HTLV-II CM was highly angiogenic in vivo, which was blocked by antibodies against SF. Based on these findings, we suggest that SF plays a role in the initiation and maintenance of KS lesions.
Hepatitis C virus and hepatitis B virus bind to heparin: purification of largely IgG-free virions from infected plasma by heparin chromatography (2005)

Binding to heparin of hepatitis C virus (HCV) and hepatitis B virus (HBV) from chronic carriers was investigated. Eighty per cent of HCV RNA from an agammaglobulinaemic patient (IgG-free virus) was retained on immobilized heparin and eluted with > or =0.4 M NaCl, in contrast to approximately 20 % from immunocompetent chronic carriers (with < or =8 % IgG-free virus). Increased binding to heparin of the HCV fraction that was not retained by a protein G column suggested that antibodies complexed to the virions partially inhibited the interaction. A higher proportion (15-80 %) of HBV from chronic carriers bound to heparin and eluted with > or =0.4 M NaCl. After washing of the heparin columns with 0.3 M NaCl, <1 % of total plasma proteins co-eluted with HCV or HBV. By this one-step heparin chromatography, without ultracentrifugation, IgG-free HCV and IgG-free HBV were preferentially purified from human plasma by 1000-fold and greater than 500-fold, respectively. Following assessment with an anti-E2 envelope protein antibody, the amount of immunoprecipitated HCV particles after heparin purification was similar to that in the original plasma, suggesting that undamaged virions were purified. This was further supported by heparin-purified HCV binding to lymphocyte cell lines in a dose-dependent manner. Intact HBV particles were detected by electron microscopy. It was concluded that HCV and HBV from chronically infected patients bind to heparin, the closest homologue of liver heparan sulfate, and that heparin chromatography is an efficient and gentle method for purifying these viruses from human plasma. In the absence of cell-culture systems or alternative robust purification methods, heparin chromatography may help greatly in binding and infectivity studies.
Massive Cortical Reorganization After Sensory Deafferentation in Adult Macaques (1991)

After limited sensory deafferentations in adult primates, somatosensory cortical maps reorganize over a distance of 1 to 2 millimeters mediolaterally, that is, in the dimension along which different body parts are represented. This amount of reorganization was considered to be an upper limit imposed by the size of the projection zones of individual thalamocortical axons, which typically also extend a mediolateral distance of 1 to 2 millimeters. However, after extensive long-term deafferentations in adult primates, changes in cortical maps were found to be an order of magnitude greater than those previously described. These results show the need for a reevaluation of both the upper limit of cortical reorganization in adult primates and the mechanisms responsible for it.
Pharmaceutical Applications of Cyclodextrins. 2. In Vivo Drug Delivery (1996)

The objective of this Review is to summarize and critique recent findings and applications of both unmodified and modified cyclodextrins for in vivo drug delivery. This review focuses on the use of cyclodextrins for parenteral, oral, ophthalmic, and nasal drug delivery. Other routes including dermal, rectal, and pulmonary delivery are also briefly addressed. This Review primarily focuses on newer findings concerning cyclodextrin derivatives which are likely to receive regulatory acceptance due to improved aqueous solubility and safety profiles as compared to the unmodified cyclodextrins. Many of the applications reviewed involve the use of hydroxypropyl-beta-cyclodextrins (HP-beta-CDs) and sulfobutylether-beta-cyclodextrins (SBE-beta-CDs) which show promise of greater safety while maintaining the ability to form inclusion complexes. The advantages and limitations of HP-beta-CD, SBE-beta-CD, and other cyclodextrins are addressed.
Correlation of intrinsic DNA curvature with DNA property periodicity (1996)

Twelve di- and trinucleotide parameter sets representing various structural, thermodynamic or bendability-related properties of DNA were tested in the prediction of DNA curvature applying Fourier analysis on curved and straight, A/T-type or G/C-type DNA sequence motifs. The best predictions were obtained with a new consensus bendability scale created by combining a nucleosome-based and a deoxyribonuclease I-based parameter set. Geometry calculations on the same sequences showed that the helical parameters derived from NMR structures can correctly predict curvature, as distinct from the parameters derived from X-ray crystallographic analysis.
Synthesis and microfabrication of biomaterials for soft-tissue engineering (2009)

Abstract Biomaterials synthesis and scaffold fabrication will play an increasingly important role in the design of systems for regenerative medicine and tissue engineering. These rapidly growing fields are converging as scaffold design must begin to incorporate multidisciplinary aspects in order to effectively organize cell-seeded constructs into functional tissue. This review article examines the use of synthetic biomaterials and fabrication strategies across length scales with the ultimate goal of guiding cell function and directing tissue formation. This discussion is parsed into three subsections: (1) biomaterials synthesis, including elastomers and gels; (2) synthetic micro- and nanostructures for engineering the cell–biomaterial interface; and (3) complex biomaterials systems design for controlling aspects of the cellular microenvironment.
On the sensitivity of the Hough transform for object recognition (1990)

Object recognition from sensory data involves, in part, determining the pose of a model with respect to a scene. A common method for finding an object's pose is the generalized Hough transform, which accumulates evidence for possible coordinate transformations in a parameter space whose axes are the quantized transformation parameters. Large clusters of similar transformations in that space are taken as evidence of a correct match. A theoretical analysis of the behavior of such methods is presented. The authors derive bounds on the set of transformations consistent with each pairing of data and model features, in the presence of noise and occlusion in the image. Bounds are provided on the likelihood of false peaks in the parameter space, as a function of noise, occlusion, and tessellation effects. It is argued that haphazardly applying such methods to complex recognition tasks is risky, as the probability of false positives can be very high.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Measurement and analysis of large-scale network file system workloads (2008)

In this paper we present the analysis of two large-scale network file system workloads. We measured CIFS traffic for two enterprise-class file servers deployed in the NetApp data center for a three month period. One file server was used by marketing, sales, and finance departments and the other by the engineering department. Together these systems represent over 22 TB of storage used by over 1500 employees, making this the first ever large-scale study of the CIFS protocol. We analyzed how our network file system workloads compared to those of previous file system trace studies and took an in-depth look at access, usage, and sharing patterns. We found that our workloads were quite different from those previously studied; for example, our analysis found increased read-write file access patterns, decreased read-write ratios, more random file access, and longer file lifetimes. In addition, we found a number of interesting properties regarding file sharing, file re-use, and the access patterns of file types and users, showing that modern file system workload has changed in the past 5–10 years. This change in workload characteristics has implications on the future design of network file systems, which we describe in the paper. 1
Adaptive contrast-based computer aided detection for pulmonary embolism (2009)

This work involves the computer-aided diagnosis (CAD) of pulmonary embolism (PE) in contrast-enhanced computed tomography pulmonary angiography (CTPA). Contrast plays an important role in analyzing and identifying PE in CTPA. At times the contrast mixing in blood may be insufficient due to several factors such as scanning speed, body weight and injection duration. This results in a suboptimal study (mixing artifact) due to non-homogeneous enhancement of blood's opacity. Most current CAD systems are not optimized to detect PE in sub optimal studies. To this effect, we propose new techniques for CAD to work robustly in both optimal and suboptimal situations. First, the contrast level at the pulmonary trunk is automatically detected using a landmark detection tool. This information is then used to dynamically configure the candidate generation (CG) and classification stages of the algorithm. In CG, a fast method based on tobogganing is proposed which also detects wall-adhering emboli. In addition, our proposed method correctly encapsulates potential PE candidates that enable accurate feature calculation over the entire PE candidate. Finally a classifier gating scheme has been designed that automatically switches the appropriate classifier for suboptimal and optimal studies. The system performance has been validated on 86 real-world cases collected from different clinical sites. Results show around 5% improvement in the detection of segmental PE and 6% improvement in lobar and sub segmental PE with a 40% decrease in the average false positive rate when compared to a similar system without contrast detection.
Serum adiponectin concentrations in relation to maternaland perinatal characteristics in newborns (2004)

An inverse association of adiponectin with ponderal index by univariate analysis is not independent from confounding factors. In contrast, the positive association between serum adiponectin and birth length may reflect either a direct effect of adiponectin or an adiponectin-mediated increase in the sensitivity of tissues to insulin and components of the IGF system, and needs to be explored further.