gebhart/patrepeval huggingface dataset:
Long-Range Electrostatic Trapping of Single-Protein Molecules at a Liquid-Solid Interface (1998)

The motion of single, dye-labeled protein molecules was monitored at various pH and ionic strengths within the 180-nanometer-thick evanescent-field layer at a fused-silica surface. Below the isoelectric point, molecules partitioning into the excitation region increased in number but maintained a random spatial distribution, implying that surface charge can influence the charged protein at distances beyond that of the electrical double-layer thickness. The residence times of the molecules in the interfacial layer also increased below the isoelectric point. However, immobilization on the solid surface for extended periods was not observed. Histograms of residence times exhibit nearly identical asymmetry as the corresponding elution peaks in capillary electrophoresis. These results are a direct verification of the statistical theory of chromatography at the single-molecule level, with the caveat that long-range trapping rather than adsorption is the dominant mechanism.
A Review of the Structure, Preparation, and Application of NLCs, PNPs, and PLNs (2017)

Nanostructured lipid carriers (NLCs) are modified solid lipid nanoparticles (SLNs) that retain the characteristics of the SLN, improve drug stability and loading capacity, and prevent drug leakage. Polymer nanoparticles (PNPs) are an important component of drug delivery. These nanoparticles can effectively direct drug delivery to specific targets and improve drug stability and controlled drug release. Lipid-polymer nanoparticles (PLNs), a new type of carrier that combines liposomes and polymers, have been employed in recent years. These nanoparticles possess the complementary advantages of PNPs and liposomes. A PLN is composed of a core-shell structure; the polymer core provides a stable structure, and the phospholipid shell offers good biocompatibility. As such, the two components increase the drug encapsulation efficiency rate, facilitate surface modification, and prevent leakage of water-soluble drugs. Hence, we have reviewed the current state of development for the NLCs', PNPs', and PLNs' structures, preparation, and applications over the past five years, to provide the basis for further study on a controlled release drug delivery system.
Evaluation of a genetically engineered cell line and a histochemical beta-galactosidase assay to detect herpes simplex virus in clinical specimens (1993)

A novel histochemical method was compared with a cytopathic effect (CPE) assay for the identification of herpes simplex virus (HSV) in clinical specimens. The method utilizes a stably transformed cell line (BHKICP6LacZ-5) that expresses beta-galactosidase only after infection with HSV. A total of 96 specimens submitted to our diagnostic virology laboratory were analyzed. Thirty-one specimens contained HSV as evidenced by positive CPE, and all were positive for beta-galactosidase staining. CPE were not evident for 2 or more days in 15 of the 31 positive specimens, whereas the histochemical stain was positive in all 31 positives by 16 to 24 h. This preliminary study shows that the BHKICP6LacZ-5 cell line can be used in a rapid, sensitive, and specific assay for the detection of HSV in clinical specimens.
Experimental and numerical assessment of MRI‐induced temperature change and SAR distributions in phantoms and in vivo (2009)

It is important to accurately characterize the heating of tissues due to the radiofrequency energy applied during MRI. This has led to an increase in the use of numerical methods to predict specific energy absorption rate distributions for safety assurance in MRI. To ensure these methods are accurate for actual MRI coils, however, it is necessary to compare to experimental results. Here, we report results of some recent efforts to experimentally map temperature change and specific energy absorption rate in a phantom and in vivo where the only source of heat is the radiofrequency fields produced by the imaging coil. Results in a phantom match numerical simulation well, and preliminary results in vivo show measurable temperature increase. With further development, similar methods may be useful for verifying numerical methods for predicting specific energy absorption rate distributions and in some cases for directly measuring temperature changes and specific energy absorption rate induced by the radiofrequency fields in MRI experiments.
Detection of Extrahepatic Hepatitis C Virus Replication by a Novel, Highly Sensitive, Single-Tube Nested Polymerase Chain Reaction (2003)

We established a cell culture system for the replication of hepatitis C virus (HCV) by using human T and B leukemia cell lines. These 2 cell lines were infected in vitro by using HCV-positive pooled patient serum samples. HCV RNA was extracted from infected cell lines at different times after infection, and a sequence of the virus 5' untranslated region was analyzed. Hepatitis C minus-strand RNA was detected in the infected cell lines by highly strand-specific rTth (recombinant Thermus thermophilus DNA polymerase)-based reverse transcription followed by a novel, highly sensitive, single-tube nested polymerase chain reaction (PCR) method. PCR products were analyzed by direct DNA sequencing. These results indicate that the HCV can replicate in T and B lymphocytes. This model should represent a valuable tool for the detailed study of the initial steps of the HCV replication cycle and for the evaluation of antiviral molecules.
Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown (2012)

Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10,000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains.
Manipulation of the Complement System for Benefit in Sepsis (2012)

There is evidence in sepsis, both in rodents and in humans, that activation of the complement system results in excessive production of C5a, which triggers a series of events leading to septic shock, multiorgan failure, and lethality. In rodents following cecal ligation and puncture (CLP), which induces polymicrobial sepsis, in vivo blockade of C5a using neutralizing antibodies dramatically improved survival, reduced apoptosis of lymphoid cells, and attenuated the ensuing coagulopathy. Based on these data, it seems reasonable to consider therapeutic blockade of C5a in humans entering into sepsis and septic shock. Strategies for the development of such an antibody for use in humans are presented.
Identification of Novel Human Leukocyte Antigen-A*0201-Restricted, Cytotoxic T Lymphocyte Epitopes on CD133 for Cancer Stem Cell Immunotherapy (2013)

Targeting cancer stem cells (CSCs) with immunotherapy may be an effective means to prevent recurrences in glioblastoma multiforme (GBM). It is well established that CD133 is expressed in the population of GBM tumor cells representing CSCs. This raises a possibility that CD133 could serve as a potential target for cytotoxic T cells (CTLs) to target glioblastoma cancer stem cells. Two potential human leukocyte antigen (HLA)-A*0201-restricted CD133 epitopes, ILSAFSVYV (CD133-405) and YLQWIEFSI (CD133-753), showed strong binding to HLA-A*0201 molecules. In vitro immunogenicity studies generated peptide-specific CD8(+) CTLs from normal donors. Autologous monocyte-derived dendritic cells pulsed with the CD133-405 or CD133-753 peptides generated CTLs that efficiently recognized the CD133 epitopes presented in T2 HLA-A*0201 cells and specifically lysed CD133+ HLA-A*0201(+) GBM CSCs. These studies demonstrated natural processing and subsequent presentation of these epitopes in GBM CSCs and the ability of CTLs to kill CSCs bearing the antigen. Immunization studies in mice using the mouse homolog CD133 epitopes demonstrated immunogenicity in the absence of autoimmune damage. The results presented in this study support the use of CD133-specific epitope vaccines to target CSCs in glioblastoma and other cancers.
The Development of the Revised NZBC Clause H1: Energy Efficiency (1996)

The revised New Zealand Building Code Clause H l and its Approved Documents will contain various acceptable solutions. This paper outlines the basis for the proposed code, the method of development and some of the issues raised. The use of proposed Acceptable Solution with its three components - Schedule Method, Calculation Method and Modelling Method are discussed. The further research required to support the next revision of Clause III and improved building energy efficient design is outlined.
Outer membrane and porin characteristics of Serratia marcescens grown in vitro and in rat intraperitoneal diffusion chambers (1990)

The composition and antibiotic permeability barrier of the outer membrane of Serratia marcescens were assessed in cells grown in vivo and in vitro. Intraperitoneal diffusion chambers implanted in rats were used for the in vivo cultivation of bacteria. Outer membranes isolated from log-phase bacterial cells recovered from these chambers were compared with membranes isolated from cells grown in vitro. Analysis revealed that the suspected 41-kilodalton porin and the OmpA protein were recovered on sodium dodecyl sulfate-polyacrylamide gels in equal quantities. Several high-molecular-weight proteins, thought to be iron starvation induced, appeared in the diffusion chamber-grown cells. The outer membrane permeability barriers to cephaloridine were similar in in vivo- and in vitro-grown cells based on permeability coefficient calculations. The permeability coefficient of cephaloridine in S. marcescens cells (30.3 x 10(-5) to 38.9 x 10(-5) cm s-1) was greater than that obtained for an Escherichia coli strain expressing only porin OmpC but smaller than those obtained for the E. coli wild type and a strain expressing only porin OmpF. Functional characterization of the suspected porin was performed by using the planar lipid bilayer technology. The sodium dodecyl sulfate-0.4 M NaCl-soluble porin from both in vitro- and in vivo-grown cells showed an average single-channel conductance in 1 M KCl of 1.6. A partial amino acid sequence (19 residues) was obtained for the S. marcescens porin. The sequence showed a very high homology to the E. coli OmpC porin. These data identified the S. marcescens outer membrane 41-kilodalton protein as a porin by both functional and amino acid analyses. Also, the methodology used allowed for efficient growth and recovery of diffusion chamber-grown bacterial cells and permitted identification of specific in vivo-induced changes in bacterial cell membrane composition.
Mutation analysis of the p53 tumor suppressor gene using paraffin-embedded specimens of human transitional cell carcinomas by the direct sequencing method. (2000)

A very small quantity of DNA was extracted from paraffin sections of 25 bladder and 2 ureteral cancer cases, and exons 5-8 of the p53 gene were amplified by the polymerase chain reaction. Mutations were detected by direct sequencing, and their relationships to clinicopathological factors were assessed. Point mutations of the p53 gene were observed in 2 of 27 specimens of transitional cell carcinoma. One was a novel nonsense mutation. The prognosis of patients with p53 gene mutations was poorer than those of patients without mutations. Analysis of the data showed that assessment of the potential malignancy of bladder cancer, combined with a conventional pathological diagnosis, allows a more precise prognosis. Direct sequencing of tissue specimens enables swift prognostic evaluation and prompt decisions concerning treatment.
Compact Image Slicing Spectrometer (ISS) for hyperspectral fluorescence microscopy (2009)

An image slicing spectrometer (ISS) for microscopy applications is presented. Its principle is based on the redirecting of image zones by specially organized thin mirrors within a custom fabricated component termed an image slicer. The demonstrated prototype can simultaneously acquire a 140 nm spectral range within its 2D field of view from a single image. The spectral resolution of the system is 5.6 nm. The FOV and spatial resolution of the ISS depend on the selected microscope objective and for the results presented is 45 x 45 microm(2) and 0.45 microm respectively. This proof-of-concept system can be easily improved in the future for higher (both spectral and spatial) resolution imaging. The system requires no scanning and minimal post data processing. In addition, the reflective nature of the image slicer and use of prisms for spectral dispersion make the system light efficient. Both of the above features are highly valuable for real time fluorescent-spectral imaging in biological and diagnostic applications.
Treatment of tibial defect and bone nonunion with limb shortening with external fixator and reconstituted bone xenograft. (2003)

Both the half ring sulcated external fixator and the combined external fixator have the advantages of small trauma, simple operation, elastic fixation without stress shielding and non-limitation from local soft tissue conditions, and there is satisfactory functional recovery of affected extremities in the treatment of tibial bone defects, tibial bone nonunion and congenital pseudarthrosis of the tibia combined with limb shortening. RBX has good biocompatibility and does not cause immunological rejections. It can also be safely used in treatment of bone nonunion and has reliable effect to promote bone healing.
Phenylethylthiazolylthiourea (PETT) Non-nucleoside Inhibitors of HIV-1 and HIV-2 Reverse Transcriptases (2000)

Most non-nucleoside reverse transcriptase (RT) inhibitors are specific for HIV-1 RT and demonstrate minimal inhibition of HIV-2 RT. However, we report that members of the phenylethylthiazolylthiourea (PETT) series of non-nucleoside reverse transcriptase inhibitors showing high potency against HIV-1 RT have varying abilities to inhibit HIV-2 RT. Thus, PETT-1 inhibits HIV-1 RT with an IC(50) of 6 nM but shows only weak inhibition of HIV-2 RT, whereas PETT-2 retains similar potency against HIV-1 RT (IC(50) of 5 nM) and also inhibits HIV-2 RT (IC(50) of 2.2 microM). X-ray crystallographic structure determinations of PETT-1 and PETT-2 in complexes with HIV-1 RT reveal the compounds bind in an overall similar conformation albeit with some differences in their interactions with the protein. To investigate whether PETT-2 could be acting at a different site on HIV-2 RT (e.g. the dNTP or template primer binding site), we compared modes of inhibition for PETT-2 against HIV-1 and HIV-2 RT. PETT-2 was a noncompetitive inhibitor with respect to the dGTP substrate for both HIV-1 and HIV-2 RTs. PETT-2 was also a noncompetitive inhibitor with respect to a poly(rC).(dG) template primer for HIV-2 RT. These results are consistent with PETT-2 binding in corresponding pockets in both HIV-1 and HIV-2 RT with amino acid sequence differences in HIV-2 RT affecting the binding of PETT-2 compared with PETT-1.
Oncogenic KRAS regulates miR-200c and miR-221/222 in a 3D-specific manner in colorectal cancer cells. (2011)

Oncogenic KRAS regulates 3D-specific molecules, possibly being associated with colorectal tumor development in vivo.
Human NK cell development in NOD/SCID mice receiving grafts of cord blood CD34+ cells (2003)

Definition of the cytokine environment, which regulates the maturation of human natural killer (NK) cells, has been largely based on in vitro assays because of the lack of suitable animal models. Here we describe conditions leading to the development of human NK cells in NOD/SCID mice receiving grafts of hematopoietic CD34+ precursor cells from cord blood. After 1-week-long in vivo treatment with various combinations of interleukin (IL)-15, flt3 ligand, stem cell factor, IL-2, IL-12, and megakaryocyte growth and differentiation factor, CD56+CD3- cells were detected in bone marrow (BM), spleen, and peripheral blood (PB), comprising 5% to 15% of human CD45+ cells. Human NK cells of NOD/SCID mouse origin closely resembled NK cells from human PB with respect to phenotypic characteristics, interferon (IFN)-gamma production, and cytotoxicity against HLA class 1-deficient K562 targets in vitro and antitumor activity against K562 erythroleukemia in vivo. In the absence of growth factor treatment, CD56+ cells were present only at background levels, but CD34+CD7+ and CD34-CD7+ lymphoid precursors with NK cell differentiation potential were detected in BM and spleen of chimeric NOD/SCID mice for up to 5 months after transplantation. Our results demonstrate that limitations in human NK cell development in the murine microenvironment can be overcome by treatment with NK cell growth-promoting human cytokines, resulting in the maturation of IFN-gamma-producing cytotoxic NK cells. These studies establish conditions to explore human NK cell development and function in vivo in the NOD/SCID mouse model.
Empirical Analysis Of Track Selection And Ordering In Electronic Dance Music Using Audio Feature Extraction. (2013)

[TODO] Add abstract here.
The architecture of the universe network (1984)

The Universe Network is composed of a number of local area networks at various sites in the U. K., joined by high capacity data links. Apart from one token ring, all of the local area networks are Cambridge rings; the high capacity data links are provided by a 1 Mbit/s satellite broadcast channel. The Universe Project encompasses both the design and implementation of the network, and a program of experiments which make use of the network. One of the notable features of the network is that a host's view of communication over the network is no different from communication over a single ring; no internet protocol is used.
Medical students need to be sensitized on Infertility: assessment from an observational study in Puducherry, India (2016)

Introduction: Infertility affects an estimated 60 to 80 million couples worldwide. Apartfrom anatomical, genetic, endocrine and immunological factorsseveral epidemiological factors also contribute to the problem of infertility. In this study, we assessed the level of knowledge on infertility among medical undergraduate students, because they represent the next generation of doctors from whom couples will be seeking treatment for infertility. Methods: A cross-sectional study was conducted by the Department of Obstetrics and Gynaecology of Pondicherry Institute of Medical Sciences, amongVII th semester MBBS students.Data was collected in the form of pre- and post-test.Average values for responses were calculated; Chi square test and McNemer test were applied. Results: Overall, the knowledge was moderate regarding risk factors and causes of female infertility. Only half of the students (56.3%) knew about the correct definition of infertility,butmajority of them (94.3%) knew that both partners contribute equally to infertility. There was a notable lack of basic knowledge among students about the possible treatment options. But, there was a significant change in the knowledgeas proportion of students who gave correct answers was more during the post-test(p value <0.05). Conclusion: Though the knowledge of infertility in medical students is promising, moreeducation programs are recommendedregularly to update their knowledge.
Adoptive immunotherapy for recurrent CML after BMT. (1993)

Three patients with CML who relapsed after transplantation with T-depleted BM from their HLA-identical siblings were treated with transfusions of donor peripheral blood mononuclear cells, in combination with (short) IFN alpha 2 therapy. CML was successfully controlled as shown by the complete disappearance of Philadelphia-positive metaphases within 90 days of treatment. This treatment appears to be very effective as neither bcr-abl transcripts nor markers specific for hematological cells of recipient origin could be detected by very sensitive PCR techniques. Two patients treated in chronic phase are without evidence of disease 300 and 360 days after treatment. The third patient, treated in accelerated phase, died with BM aplasia, 39 days following PBMC infusions. Failure to detect residual donor-derived granulocytes, as was the case in this patient prior to initiating adoptive immunotherapy, may indicate loss of donor-derived BM activity. This may help predict and possibly prevent the occurrence of life-threatening aplasia after successful clearance of malignant hematopoiesis.
Isocyanate-Specific Hemoglobin Adduct in Rats Exposed to 4,4‘-Methylenediphenyl Diisocyanate (2000)

4,4'-Methylenediphenyl diisocyanate (MDI) is the most important of the isocyanates used as intermediates in the chemical industry. Among the main types of damage after exposure to low levels of MDI are lung sensitization and asthma. Protein adducts of MDI might be involved in the etiology of sensitization reactions. It is therefore necessary to have sensitive and specific methods for monitoring the isocyanate exposure of workers. To date, urine metabolites or protein adducts have been used as biomarkers in workers exposed to MDI. However, with these methods it is not possible to determine if the biomarkers result from exposure to MDI or to the parent aromatic amine 4,4'-methylenedianiline (MDA). This work presents a procedure for quantitating isocyanate-specific hemoglobin adducts. Blood proteins are used as markers of exposure and possibly as markers of dose size for the modifications of macromolecules in the target organs where the disease develops. For the quantitation of hemoglobin adducts, N(1)-[4-(4-isocyanatobenzyl)phenyl]acetamide (AcMDI) was reacted with the tripeptide valyl-glycyl-glycine and with valine yielding N-[4-(4-acetylaminobenzyl)phenyl]carbamoyl]valyl-glycyl-glycine and N-[4-[4-(acetylaminobenzyl)phenyl]carbamoyl]valine, respectively. N-[4-[4-(Acetylamino-3,5-dideuteriobenzyl)-2, 6-dideuteriophenyl]carbamoyl]valine was synthesized from valine, as was N(1)-[4-(4-isocyanato-3,5-dideuteriobenzyl)-2, 6-dideuteriophenyl]acetamide, for use as an internal standard. These adducts were cleaved in 2 M HCl to yield the corresponding hydantoins, 3-[4-(4-aminobenzyl)phenyl]-5-isopropyl-1, 3-imidazoline-2,4-dione (MDA-Val-Hyd) and 3-[4-(4-amino-3, 5-dideuteriobenzyl)-2,6-dideuteriophenyl]-5-isopropyl-1, 3-imidazoline-2,4-dione, respectively. In globin of rats exposed to MDI, MDA-Val-Hyd could be found in a dose-dependent manner. The adduct was identified by HPLC/MS/MS and quantified by GC/MS after derivatization with heptafluorobutyric anhydride. The amount of MDA-Val-Hyd found after acid hydrolysis of globin at 100 degrees C is about 12 times larger than the sum of N-acetyl-4, 4'-methylenedianiline (AcMDA) and MDA obtained from mild base hydrolysis of hemoglobin. The MDA-Val-Hyd is an isocyanate-specific adduct. MDA and AcMDA released after mild base hydrolyses result most likely from a sulfinamide adduct which is a typical adduct of arylamines. According to these results, higher amounts of isocyanate adducts than arylamine adducts should be expected in workers exposed to isocyanates.