gebhart/patrepeval huggingface dataset:
Human-Induced Pluripotent Stem Cells form Functional Neurons and Improve Recovery After Grafting in Stroke-Damaged Brain (2012)

Reprogramming of adult human somatic cells to induced pluripotent stem cells (iPSCs) is a novel approach to produce patient-specific cells for autologous transplantation. Whether such cells survive long-term, differentiate to functional neurons, and induce recovery in the stroke-injured brain are unclear. We have transplanted long-term self-renewing neuroepithelial-like stem cells, generated from adult human fibroblast-derived iPSCs, into the stroke-damaged mouse and rat striatum or cortex. Recovery of forepaw movements was observed already at 1 week after transplantation. Improvement was most likely not due to neuronal replacement but was associated with increased vascular endothelial growth factor levels, probably enhancing endogenous plasticity. Transplanted cells stopped proliferating, could survive without forming tumors for at least 4 months, and differentiated to morphologically mature neurons of different subtypes. Neurons in intrastriatal grafts sent axonal projections to the globus pallidus. Grafted cells exhibited electrophysiological properties of mature neurons and received synaptic input from host neurons. Our study provides the first evidence that transplantation of human iPSC-derived cells is a safe and efficient approach to promote recovery after stroke and can be used to supply the injured brain with new neurons for replacement.
Epitope mapping and structural basis for the recognition of phosphorylated tau by the anti‐tau antibody AT8 (2016)

Microtubule-associated protein tau becomes abnormally phosphorylated in Alzheimer's disease and other tauopathies and forms aggregates of paired helical filaments (PHF-tau). AT8 is a PHF-tau-specific monoclonal antibody that is a commonly used marker of neuropathology because of its recognition of abnormally phosphorylated tau. Previous reports described the AT8 epitope to include pS202/pT205. Our studies support and extend previous findings by also identifying pS208 as part of the binding epitope. We characterized the phosphoepitope of AT8 through both peptide binding studies and costructures with phosphopeptides. From the cocrystal structure of AT8 Fab with the diphosphorylated (pS202/pT205) peptide, it appeared that an additional phosphorylation at S208 would also be accommodated by AT8. Phosphopeptide binding studies showed that AT8 bound to the triply phosphorylated tau peptide (pS202/pT205/pS208) 30-fold stronger than to the pS202/pT205 peptide, supporting the role of pS208 in AT8 recognition. We also show that the binding kinetics of the triply phosphorylated peptide pS202/pT205/pS208 was remarkably similar to that of PHF-tau. The costructure of AT8 Fab with a pS202/pT205/pS208 peptide shows that the interaction interface involves all six CDRs and tau residues 202-209. All three phosphorylation sites are recognized by AT8, with pT205 acting as the anchor. Crystallization of the Fab/peptide complex under acidic conditions shows that CDR-L2 is prone to unfolding and precludes peptide binding, and may suggest a general instability in the antibody.
Real-time calibration-free autonomous eye tracker (2010)

In several fields of medicine, transportation and security the instantaneous gaze direction of a person under supervision is of crucial importance. We developed a contactless stereoscopic video-based eye tracker which works without any individual calibration. In real time it delivers information about the gaze direction frame by frame. The introduced algorithms are designed for computing the gaze direction within image acquisition time that is only limited by the hardware setup. The cameras are integrated into front-end modules by means of FPGA (programmable logic) circuits for image processing. Computation of the gaze direction is based on the spatial position of the pupil which is detected by a five-dimensional Hough transform. The system works under ambient light conditions whereas additional infrared illumination can be used to become independent of ambient light.
88. Soluble fibrin increases platelet adherence to tumor cells in vivo, and enhances experimental metastasis (1998)

Biggerstaff, J. P.; Amirkhosravi, A.; Seth, N.; Fogarty, S.; Meyer, T. V.; Francis, J. L. Author Information
Reduced expression of Tap1 and Lmp2 antigen-processing genes in the nonobese diabetic (NOD) mouse due to a mutation in their shared bidirectional promoter (1997)

The MHC is an essential contributor to autoimmunity. Lmp2 and Tap1 are genes located in the MHC class II region, and they encode proteins participating in the generation and transport of endogenous peptides for T cell education. A mutation (T-->A) has now been detected in the shared bidirectional promoter of the Lmp2 and Tap1 genes in the nonobese diabetic (NOD) mouse. The nucleotide substitution (TCATTC-->TCAATC) in NOD mice eliminates an initiator (Inr) element (TCATTC) thought to be important for RNA polymerase II positioning in the Lmp2 orientation. It also created a CAAT-like box and an inverted CAAT-like box in the Lmp2 and Tap1 orientations, respectively. Northern blot revealed reduced amounts of Tap1 and Lmp2 mRNA in NOD mice, and 5'-rapid amplification of cDNA ends revealed the loss of a transcription start site of Lmp2 in these animals. The Tap1-Lmp2 promoter from NOD mice showed reduced transcriptional activity in transient transfection assays with luciferase reporter constructs for both Tap1 and Lmp2 genes. Observed altered substrate specificity of Lmp2 containing proteasomes isolated from NOD mice was consistent with reduced Lmp2 activity. The beneficial influence of non-MHC genes (NOR mice) and gender factors (male NOD mice) influencing the penetrance of the promoter polymorphism further confirmed the essential gender and hormonal context of the mutation. This study identifies the first specific mutation in the MHC of the NOD mouse that specifically impacts the activity of genes involved in peptide presentation, a process essential for T cell education.
Sarcopenic obesity in the elderly and strategies for weight management (2012)

Sarcopenia is a multifactorial age-related condition associated with a sedentary lifestyle and protein intakes during weight loss that are inadequate to maintain muscle mass. Sarcopenic obesity in the elderly is associated with a loss of independence and metabolic complications and represents a major public health challenge in individuals over the age of 65 years. It is likely that age-related losses of muscle mass and coincident increases in fat mass could be reduced through regular resistance exercise combined with adequate protein intake to maintain muscle mass. It has been established that increased protein intake will maintain muscle mass during calorie-restricted diets to a greater extent than usual protein intake. Other strategies, including the use of high-protein meal replacements or supplementation with specific ergogenic or branched-chain amino acids, may be beneficial.
High-power EUV lithography sources based on gas discharges and laser-produced plasmas (2003)

Semiconductor chip manufacturers are expecting to use extreme UV lithography for production in 2009. EUV tools require high power, brilliant light sources at 13.5 nm with collector optics producing 120 W average power at entrance of the illuminator system. Today the power and lifetime of the EUV light source are considered as the most critical issue for EUV lithography. The present paper gives an update of the development status of EUV light sources at XTREME technologies, a joint venture of Lambda Physik AG, Goettingen, and Jenoptik LOS GmbH, Jena, Germany. Results on both laser produced plasma (LPP) and gas discharge produced plasma (GDPP), the two major technologies in EUV sources, are given. The LPP EUV sources use xenon-jet target systems and pulsed lasers with 400 W average power at 10 kHz developed at XTREME technologies. The maximum conversion efficiency form laser power into EUV in-band power is 0.75% into 2&pi; solid angle. With 300 W laser average power at 3300 Hz repetition rate up to 1.5 W EUV radiation is generated at 13.5 nm. After a collector of 5 sr this corresponds to 0.6 W in intermediate focus without spectral purity filter and 0.5 W in intermediate focus with spectral purity filter. The direct generation of the EUV emitting plasma from electrical discharges is much simpler than LPP because the electrical energy has not to be converted into laser radiation before plasma excitation. XTREME technologies' Xenon GDPP EUV sources use the Z-pinch principle with efficient sliding discharge pre-ionization. The plasma pinch size and the available emission angle have been matched to the etendue of the optical system of 2-3 mm2 sr, i.e. no additional etendue related loss reduces the usable EUV power from the source. In continuous operation at 1000 Hz the GDPP sources emit 50W into 2&pi; solid angle are obtained from the Z-pinch sources. Spatial and temporal emission stability of the EUV sources is in the range of a few percent. Debris shields for EUV sources have been developed which give improvement of the collector optics lifetime by several orders of magnitude.
Reaction of bismuth nitrate with sodium citrate in water-glycerol solutions (2009)

The reaction in a Bi(NO3)3-Na3Hcit-(H2O + glycerol) system was studied in a wide range of component ratios by the solubility method and pH-metry in combination with chemical analysis of solid phases. Poorly soluble phases of Bi(Hcit) x (OH)3(1 − x) · mH2O (x < 1) and sodium bismuth citrate NaBiCit · 3H2O were obtained. The compounds synthesized were characterized, and their compositions were refined by X-ray diffraction, DTG, and IR spectroscopy.
Extracellular Matrix Cell Adhesion Peptides: Functional Applications in Orthopedic Materials (2000)

This review describes research on selected peptide sequences that affect cell adhesion as it applies in orthopedic applications. Of particular interest are the integrin-binding RGD peptides and heparin-binding peptides. The influence of these peptides on cell adhesion is described. Cell adhesion is defined as a sequence of four steps: cell attachment, cell spreading, organization of an actin cytoskeleton, and formation of focal adhesions. RGD sequences clearly influence cell attachment and spreading, whereas heparin-binding sequences appear to be less efficient. Collectively, these sequences appear to promote all steps of cell adhesion in certain cell types. This review also addresses issues related to peptide immobilization, as well as potential complexities that may develop as a result of using these versatile cell-binding sequences. Also described are future directions in the field concerning use of existing and more sophisticated peptide substrata.
Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria (1990)

A collection of Tn5-derived minitransposons has been constructed that simplifies substantially the generation of insertion mutants, in vivo fusions with reporter genes, and the introduction of foreign DNA fragments into the chromosome of a variety of gram-negative bacteria, including the enteric bacteria and typical soil bacteria like Pseudomonas species. The minitransposons consist of genes specifying resistance to kanamycin, chloramphenicol, streptomycin-spectinomycin, and tetracycline as selection markers and a unique NotI cloning site flanked by 19-base-pair terminal repeat sequences of Tn5. Further derivatives also contain lacZ, phoA, luxAB, or xylE genes devoid of their native promoters located next to the terminal repeats in an orientation that affords the generation of gene-operon fusions. The transposons are located on a R6K-based suicide delivery plasmid that provides the IS50R transposase tnp gene in cis but external to the mobile element and whose conjugal transfer to recipients is mediated by RP4 mobilization functions in the donor.
Ly49Q defines 2 pDC subsets in mice (2004)

Plasmacytoid dendritic cells (pDCs) play an important primary role for antiviral innate immunity by rapidly producing large amounts of type 1 interferon (IFN) upon viral infection. To study pDC biology, we generated a monoclonal antibody, termed 2E6, that recognizes pDCs. Molecular cloning of a cDNA encoding the 2E6 antigen revealed that it is a type II C-type lectin, Ly49Q, that consists of 247 amino acids with high homology to the natural killer (NK) receptor family Ly49, with an immunoreceptor tyrosine-based inhibitory motif in the cytoplasmic domain. Ly49Q is expressed on pDCs but not on NK cells or myeloid dendritic cells. B220+, CD11c+, CD11b- pDCs in bone marrow were divided into Ly49Q+ and Ly49Q- subsets. While both subsets produced IFN-alpha upon cytosine-phosphate-guanosine (CpG) and herpes simplex virus stimulation, Ly49Q- pDCs responded poorly to influenza virus. In addition, Ly49Q- pDCs produced inflammatory cytokines such as interleukin 6 (IL-6), IL-12, and tumor necrosis factor alpha (TNF-alpha) upon stimulation at lower levels than those produced by Ly49Q+ pDCs. In contrast to bone marrow, Ly49Q+ pDCs were only found in peripheral blood, lymph nodes, and spleen. These results indicate that Ly49Q is a specific marker for peripheral pDCs and that expression of Ly49Q defines 2 subsets of pDCs in bone marrow.
Targeting of B cells in SLE: rationale and therapeutic opportunities. (2006)

B cells were first implicated in lupus pathogenesis because of their roles as autoantibody producers. B cells, which play important roles in (auto)immune recognition, are now understood to also have other functional capabilities that contribute to the recruitment and stimulation of T lymphocytes and cells of the innate immune system. Herein, these emerging insights are discussed as well as the newly recognized influence on B cells of the Toll-like receptors, which are postulated to be important sources of costimulation for autoreactive B cells. Also discussed is how B-cell survival factors may contribute to the loss of immune tolerance that leads to pathologic autoimmunity. These findings are part of the rationale for the development of new specific B-cell-targeted therapies.
A simple method for the determination of the pore radius of ion channels in planar lipid bilayer membranes (1992)

A new method of pore size determination is presented. The results of applying this simple method to ion channels formed by staphylococcal α-toxin and its N-terminal fragment as well as to cholera toxin channels are shown. The advantages and the difficulties of this method are discussed. It was found that (i) the mobility of ions in solutions depends only on the percentage of concentration of added non-electrolytes and practically not on their chemical nature (sugars or polyglycols) and molecular size; (ii) the proportional change of both ion channel conductance and bulk solution conductivity by low M. non-electrolytes may be used as an indication of a diffusion mechanism of ion transport through channels; (iii) the slope of the dependence of the ion channel conductance on the bulk conductivity of solutions containing different concentrations of non-electrolyte is a good measure of channel permeability for non-electrolytes.
The pathogenesis and prevention of central venous catheter-related infections. (1994)

Vascular catheters are a major source of nosocomial infections. Definite diagnosis of catheter-related infections should include the use of quantitative catheter cultures or differential quantitative blood cultures. The skin and catheter hub are the two major sources for the introduction of the colonizing organisms. Both microbial (slime) and host (fibrin and fibrinectin) factors contribute to the formation of the biofilm which is essential for the adherence and maintenance of the colonization. Staphylococci and Candida are the leading causative agents. Prolonged duration of catheterization, thrombogenic catheter material, frequent manipulation of the catheter, improper aseptic insertion and maintenance techniques, tranparent plastic dressings, contaminated skin solutions, location of the catheter, and possibly multilumen central venous catheters (CVC) are risk factors predisposing to infections. Preventive measures include a skilled infusion therapy team, topical disinfectants such as chlorhexidine and topical antibiotics, silver impregnated cuffs (for short term CVC), coating catheters with antiseptic agents and maximal barrier precautions during insertion. Exchanging central venous catheters over a guidewire might be useful diagnostically but have not been proven to be of any therapeutic or preventive potential.
Isotope separation in the plasma centrifuge (1976)

Time-resolved measurements of isotope separation in a neon plasma, accelerated to high rotational velocity by J*B forces, are presented. Samples were extracted from the plasma using a fast-acting valve, and were isotopically analysed by an on-line quadrupole mass spectrometer. The dependence of isotope separation on various parameters was investigated; changes in isotopic ratio as large as 20% were observed. The results are compared with a simple theoretical model based on observed electrical probe voltages and spectroscopic plasma temperature measurements.
Identification of a unique antigen peptide pRL1 on BALB/c RL male 1 leukemia recognized by cytotoxic T lymphocytes and its relation to the Akt oncogene. (1994)

BALB/c radiation leukemia RL male 1 is an immunogenic tumor. We established bulk and cloned cytotoxic T lymphocyte (CTL) lines from regressor (BALB/c x C57BL/6)F1 (CB6F1) spleen cells that recognized RL male 1 specifically. We then obtained antigen peptide recognized by CTL from RL male 1 by acid extraction. Analysis of the acid extract by reversed-phase high performance liquid chromatography (HPLC) on a semipreparative C18 column revealed that fractions eluted in 23 min (peak a) and 26 min (peak b) showed sensitization activity on the P815 target for specific CTL. On further purification of these fractions by HPLC and direct sequencing by Edman degradation, we identified the CTL-recognizing RL male 1 peptide pRL1a (IPGLPLSL) in peak a and its possible precursor peptide pRL1b (SIIPGLPLSL) in peak b. Sequence homology indicated that these peptides were derived from the 5' untranslated region of c-akt oncogene.
Syphilis Infection during Pregnancy: Fetal Risks and Clinical Management (2012)

Congenital syphilis is still a cause of perinatal morbidity and mortality. Untreated maternal infection leads to adverse pregnancy outcomes, including early fetal loss, stillbirth, prematurity, low birth weight, neonatal and infant death, and congenital disease among newborns. Clinical manifestations of congenital syphilis are influenced by gestational age, stage of maternal syphilis, maternal treatment, and immunological response of the fetus. It has been traditionally classified in early congenital syphilis and late congenital syphilis. Diagnosis of maternal infection is based on clinical findings, serological tests, and direct identification of treponemes in clinical specimens. Adequate treatment of maternal infection is effective for preventing maternal transmission to the fetus and for treating fetal infection. Prenatal diagnosis of congenital syphilis includes noninvasive and invasive diagnosis. Serological screening during pregnancy and during preconception period should be performed to reduce the incidence of congenital syphilis.
CD19 CAR–T cells of defined CD4+:CD8+ composition in adult B cell ALL patients (2016)

R01-CA136551; Life Science Development Fund; Juno Therapeutics; Bezos Family Foundation.
A Unified Approach for Developing Software Reliability Growth Models in the Presence of Imperfect Debugging and Error Generation (2011)

In this paper, we propose two general frameworks for deriving several software reliability growth models based on a non-homogeneous Poisson process (NHPP) in the presence of imperfect debugging and error generation. The proposed models are initially formulated for the case when there is no differentiation between failure observation and fault removal testing processes, and then extended for the case when there is a clear differentiation between failure observation and fault removal testing processes. During the last three decades, many software reliability growth models (SRGM) have been developed to describe software failures as a random process, and can be used to evaluate development status during testing. With SRGM, software engineers can easily measure (or forecast) the software reliability (or quality), and plot software reliability growth charts. It is not easy to select the best model from a plethora of models available. There are few SRGM in the literature of software engineering that differentiates between failure observation and fault removal processes. In real software development environments, the number of failures observed need not be the same as the number of faults removed. Due to the complexity of software systems, and an incomplete understanding of software, the testing team may not be able to remove the fault perfectly on observation of a failure, and the original fault may remain, resulting in a phenomenon known as imperfect debugging, or get replaced by another fault causing error generation. In the case of imperfect debugging, the fault content of the software remains the same; while in the case of error generation, the fault content increases as the testing progresses. Removal of observed faults may result in the introduction of new faults.
Micro‐electrode measurement of skin pH in humans during ischaemia, hypoxia and local hypothermia. (1979)

1. The extracellular pH value in the dermis of human skin (skin pH) was measured in vivo using glass micro‐electrodes. They were found to be both reliable and accurate. 2. The mean value of skin pH measured in the legs of forty different volunteers was found to be pH 7.54 +/‐ 0.09 (S.D.). No difference in skin pH was observed between males and females, or in different regions of the limb. 3. Local reductions in skin surface temperature in ten subjects caused an increase of pH 0.023 +/‐ 0.007 per degree C fall. 4. A 20 min period of tourniquet ischaemia in twenty volunteers induced a fall in skin pH of 0.13 +/‐ 0.05 units. 5. Hyperventilation during a 10 min period of breathing 10% O2 in N2 caused an increase of pH 0.04 +/‐ 0.02 in the skin of healthy subjects. 6. Skin pH fell to a value 0.02 +/‐ 0.02 units below normal 10 min after the hypoxic period, suggesting the presence of excess lactate. 7. Skin pH results compared well with blood gases and pH values of arterialized samples taken during hypoxia. 8. It was concluded that the system was suitable for clinical trials.