gebhart/patrepeval huggingface dataset:
Development of a simple noninvasive index to predict significant fibrosis in patients with HIV/HCV coinfection†‡ (2006)

Liver biopsy remains the gold standard in the assessment of severity of liver disease. Noninvasive tests have gained popularity to predict histology in view of the associated risks of biopsy. However, many models include tests not readily available, and there are limited data from patients with HIV/hepatitis C virus (HCV) coinfection. We aimed to develop a model using routine tests to predict liver fibrosis in patients with HIV/HCV coinfection. A retrospective analysis of liver histology was performed in 832 patients. Liver fibrosis was assessed via Ishak score; patients were categorized as 0-1, 2-3, or 4-6 and were randomly assigned to training (n = 555) or validation (n = 277) sets. Multivariate logistic regression analysis revealed that platelet count (PLT), age, AST, and INR were significantly associated with fibrosis. Additional analysis revealed PLT, age, AST, and ALT as an alternative model. Based on this, a simple index (FIB-4) was developed: age ([yr] x AST [U/L]) / ((PLT [10(9)/L]) x (ALT [U/L])(1/2)). The AUROC of the index was 0.765 for differentiation between Ishak stage 0-3 and 4-6. At a cutoff of <1.45 in the validation set, the negative predictive value to exclude advanced fibrosis (stage 4-6) was 90% with a sensitivity of 70%. A cutoff of >3.25 had a positive predictive value of 65% and a specificity of 97%. Using these cutoffs, 87% of the 198 patients with FIB-4 values outside 1.45-3.25 would be correctly classified, and liver biopsy could be avoided in 71% of the validation group. In conclusion, noninvasive tests can accurately predict hepatic fibrosis and may reduce the need for liver biopsy in the majority of HIV/HCV-coinfected patients.
Mechanisms of nanoparticle formation by short laser pulses (2007)

Numerical modeling is performed to study cluster formation by laser ablation. The developed model allows us to compare the relative contribution of the two channels of the cluster production by laser ablation: (i) direct cluster ejection upon the laser-material interaction, and (ii) collisional sticking, evaporation and coalescence during the ablation plume expansion. Both of these mechanisms are found to affect the final cluster size distribution. Plume cluster composition is correlated with plume dynamics. The results of the calculations demonstrate that cluster precursors are formed during material ablation through both thermal and mechanical target decomposition processes. Then, clusters react in collisions within the plume. In vacuum, rapid plume expansion and cooling take place leading to the overall decrease in the reaction rates. In the presence of a gas, additional collisions with background gas species affect the cluster size distribution. Growth of larger clusters can be observed at this stage. Calculation results explain several recent experimental observations.
Evidence for Antinociceptive Activity of Botulinum Toxin Type A in Pain Management (2003)

The neurotoxin, botulinum toxin type A, has been used successfully, in some patients, as an analgesic for myofascial pain syndromes, migraine, and other headache types. The toxin inhibits the release of the neurotransmitter, acetylcholine, at the neuromuscular junction thereby inhibiting striated muscle contractions. In the majority of pain syndromes where botulinum toxin type A is effective, inhibiting muscle spasms is an important component of its activity. Even so, the reduction of pain often occurs before the decrease in muscle contractions suggesting that botulinum toxin type A has a more complex mechanism of action than initially hypothesized. Current data points to an antinociceptive effect of botulinum toxin type A that is separate from its neuromuscular activity. The common biochemical mechanism, however, remains the same between botulinum toxin type A's effect on the motor nerve or the sensory nerve: enzymatic blockade of neurotransmitter release. The antinociceptive effect of the toxin was reported to block substance P release using in vitro culture systems. The current investigation evaluated the in vivo mechanism of action for the antinociceptive action of botulinum toxin type A. In these studies, botulinum toxin type A was found to block the release of glutamate. Furthermore, Fos, a product of the immediate early gene, c-fos, expressed with neuronal stimuli was prevented upon peripheral exposure to the toxin. These findings suggest that botulinum toxin type A blocks peripheral sensitization and, indirectly, reduces central sensitization. The recent hypothesis that migraine involves both peripheral and central sensitization may help explain how botulinum toxin type A inhibits migraine pain by acting on these two pathways. Further research is needed to determine whether the antinociceptive mechanism mediated by botulinum toxin type A affects the neuronal signaling pathways that are activated during migraine.
Hierarchical Dental X-Ray Radiographs Matching (2006)

The goal of forensic dentistry is to identify individuals based on their dental characteristics. In this paper we present a new matching technique for identifying missing, and wanted individuals from their dental X-ray records. Given a dental record, usually a postmortem (PM) radiograph, the proposed technique searches a database of ante mortem (AM) radiographs and retrieves the best matches from the database. The technique is based on matching teeth contours using hierarchical Chamfer distance. The proposed technique has two main stages: feature extraction, and teeth matching. During retrieval, according to a matching distance between the AM and PM teeth, AM radiographs that are most similar to a given PM image, are found and presented to the user. The experimental results on a database of 162 AM images show that the technique is robust for identifying individuals based on their dental records.
Inhibition of cyclic adenosine-3',5'-monophosphate phosphodiesterase from vascular smooth muscle by rolipram analogs (1989)

Rolipram [(R,S)-4-[3-(cyclopentyloxy)-4-methoxyphenyl]-2-pyrrolidone] has been shown to inhibit selectively the cAMP phosphodiesterase (PDE) of vascular smooth muscle. In order to further explore the structural requirements for selective PDE inhibition, we synthesized a series of rolipram derivatives differently substituted either at the pyrrolidinone or at the aromatic ring. Among these compounds, rolipram was the most active compound. Semirigid analogues were prepared and used for an evaluation of the active conformation of rolipram. Structural comparison with two other potent and chemically different smooth muscle cAMP-PDE inhibitors, trequinsin and Ro 20-1724, allows us to propose a first topological model of the smooth muscle cAMP-PDE pharmacophore.
Cellular logic architectures for optical computers (1986)

A general approach is described for optically implementing massively parallel logic. Cellular array logic and the cellular automaton theory are emphasized as a guiding principle in the design of optical parallel computers. These theoretical methods are important clues to elucidate the general characteristics and the limitation of optical parallel logic. We propose three architectures for optical computing systems: the optical Minnick cellular logic array for logical function synthesis, the local cellular logic based on the holographic filter synthesis, and the table lookup architecture using a matched filter array for binary data processing. A close relationship between the table lookup architecture and the symbolic substitution and the content-addressable memory is pointed out.
Behavioral and Adaptive Status in an Experimental Model of Alzheimer's Disease in Rats (1996)

Ten days after bilateral electrolytic lesions of nucleus basalis magnocellularis (NBM) we tested behavioral (spontaneous motor activity, acquisition and performance of two-way active avoidance, fear-response in open field test, foot shock induced aggression, depression-response in learned helplessness test) and adaptive status (body temperature at standard, hot and cold environment as well as cold restraint-induced gastric lesions) in adult male Wistar rats. Compared to intact control and sham-operated rats, the bilateral NBM-lesioned rats showed the significant impairment of learning behavior and reduced fear, aggression and depression as well as altered body temperature at standard and stressed conditions. Namely, it was established that body temperature in NBM-lesioned rats was significantly lower at standard laboratory conditions, but in these rats body temperature significantly was raised after exposing to cold and hot environment. On the other hand, spontaneous motor activity and number and length of cold restraint-induced gastric lesions (erosions and petechiae) in NBM-lesioned rats were similarly to those in both controls. It could be concluded that NBM plays a significant role in cognitive, emotional and adaptive processes in the rats.
Effects of excess oxygen on operation characteristics of amorphous In-Ga-Zn-O thin-film transistors (2011)

Operation characteristics of amorphous In-Ga-Zn-O (a-IGZO) thin-film transistors (TFTs) were improved to a subthreshold voltage swing (S) of 217 mV (decade)−1, a mobility of ∼11.4 cm2 (Vs)−1, and a threshold voltage (Vth) of 0.1 V by O3 annealing at a temperature as low as 150 °C. However, the O3 annealing at 300 °C caused serious deterioration and exhibited a bistable transition between a large S state and a large Vth state. This transition is attributed to incorporation of excess oxygen and associated subgap defects with a negative-U characteristic. It also explains why a-IGZO channels deposited at high oxygen pressures do not produce operating TFTs.
Homing of antibody secreting cells (2003)

As activated B cells differentiate into plasma cells they complete a final series of migration steps that take them to locations where they can efficiently carry out their effector function, secreting immunoglobulin (Ig) M or IgG into circulation or releasing dimeric IgA adjacent to the epithelium for transcytosis. Recent experiments have established a key role for chemokines in directing antibody secreting cell (ASC) movement within the secondary lymphoid organs where they are generated, as well as in guiding the cells to the bone marrow or mucosal surfaces. This review discusses the chemokines involved in directing ASC movements, particularly focusing on the role of CXCR4 and CXCL12/SDF1. The function of CCR9 and CCR10 in IgA ASC homing and contributions made by integrins and lectins are also discussed.
High-affinity self-reactive human antibodies by design and selection: targeting the integrin ligand binding site. (1993)

A strategy for the design and selection of human antibodies that bind receptors is described. We have demonstrated the validity of the approach by producing semi-synthetic human antibodies that bind integrins alpha v beta 3 and alpha IIb beta 3 with high affinity (10(-10) M). The selected antibodies mimic the integrins' natural ligands as demonstrated by their ability to compete with these ligands and Arg-Gly-Asp (RGD)-containing peptides for binding to the integrins. Furthermore, the antibodies bind in a cation-dependent fashion and are functional in cell adhesion assays. Antibodies that are high-affinity inhibitors of cell adhesion receptors should be of use in assessing receptor function and dissecting mechanisms of adhesion. Semisynthetic human antibodies that target integrins are potential therapeutic agents for the treatment of a number of diseases including thrombosis and metastasis. Furthermore, antibodies that are optimized to bind by a single complementarity determining region may be important lead compounds for the design of small molecule pharmaceuticals.
Study of the stability of tablets containing 10 mg of policosanol as active principle. (2002)

We report a multi-institutional series of RPN in patients with solitary kidney presenting with small renal masses. Our findings suggest that RPN represents a feasible treatment option in this specific population by offering reliable preservation of renal function, low surgical morbidity, and early oncologic safety in the hands of experienced robotic surgeons.
Kinematic Model of the Hand using Computer Vision (2011)

La biotecnologia es una ciencia en auge y en especial el diseno de interfaces humano-maquina.
El objetivo de este proyecto es avanzar en dicho campo y en concreto explorar el diseno de exoesqueletos y protesis de la mano humana.
La metodologia utilizada en este proyecto fundamentalmente consta de tres fases. En primer lugar, se ha establecido un modelo teorico de la cinematica de la mano recurriendo a la documentacion medica especializada para concretar su anatomia. Posteriormente se ha procedido a sintetizar la mano en sus parametros simplificados y asi definir un modelo robotico.
Para ajustar dicho modelo a una mano real se procede a capturar el movimiento de esta en una secuencia de imagenes mediante ordenador. Para ello se utilizan unas marcas en las unas de la mano con una geometria especifica de tal manera que permite la estimacion de su pose, es decir su posicion e orientacion, en el espacio. Esta secuencia de poses estimadas permite caracterizar el movimiento completo de la mano.
Por ultimo, mediante la sintesis cinematica dimensional, se definen las ecuaciones de movimiento parametrizadas del modelo teorico de la mano. Estas ecuaciones permiten ajustar el modelo a la secuencia de poses estimadas mediante vision por ordenador y asi crear un modelo personalizado de la mano. Gracias a este sistema, se puede realizar un estudio sobre la correspondencia entre senales electomiograficas y los movimientos de la mano y asi lograr una mejor funcionalidad de las protesis.
En definitiva, este proyecto ha logrado disenar un algoritmo robusto para el seguimiento y estimacion de las poses de las unas de las manos y ha conseguido definir las ecuaciones de movimiento y crear una aplicacion para resolverlas. Asimismo, ha encontrado modelos no antropomorficos que podrian ser de utilidad en el diseno de exoesqueletos.
Beta-chemokine inhibition of monocytotropic HIV-1 infection. Interference with a postbinding fusion step (1996)

The beta-chemokines RANTES, MIP-1 alpha, and MIP-1 beta have potent suppressive effects on HIV-1 infection resulting from an early postbinding block in virus fusion and entry. Inhibition was observed only with monocytotropic isolates and mapped to the V3 region of the HIV-1 envelope. RANTES did not inhibit virus expression in chronically infected cells or reduce initial virus attachment to the cell membrane. Inhibitory activity required RANTES binding to the target cell but not G protein-mediated signaling or protein tyrosine kinase activity. The results are consistent with a reversible competitive mechanism of virus inhibition that prevents a V3-associated postbinding step in membrane fusion. The data support a role for a RANTES chemokine receptor as a coreceptor for monocytotropic-HIV-1.
Chromatographic Determination of the d- and l-Amino Acid Residues in Pneumococcal C-Polysaccharide (1971)

Abstract The configurations of the amino acids in pneumococcal C-polysaccharide have been determined chromatographically after acid hydrolysis. The amino acids were coupled with an l-amino acid N-carboxyanhydride for formation of the corresponding l-d- and l-l-dipeptides; these derivatives were separated by ion exchange chromatography on an amino acid analyzer. The amount of racemization of alanine which occurred during the hydrolysis was determined by measurement of the amount of tritium incorporated into the amino acid after hydrolysis of the C-polysaccharide in tritiated HCl. After correction for the amount of d or l isomer formed by racemization, it was concluded that the content of d-alanine was variable (25 to 33%) in the three preparations of pneumococcal C-polysaccharide studied. Each of the preparations contained glutamic acid (100% d isomer) and lysine (100% l isomer).
Regulation of human male germ cell death by modulators of ATP production (2006)

The understanding of testicular physiology, pathology, and male fertility issues requires knowledge of male germ cell death and energy production. Here, we induced human male germ cell apoptosis (detected by Southern blot analysis of DNA fragmentation, TUNEL, activation of caspases-3 and -9, and electron microscopy) by incubating seminiferous tubule segments under hormone- and serum-free conditions. Inhibitors of complexes I to IV of mitochondrial respiration, exposure to anoxia, and inhibition of F0F1-ATPase (with oligomycin) decreased the ATP levels (analyzed by HPLC) and suppressed apoptosis at 4 h. Uncoupler 2,4-dinitrophenol (DNP) and oligomycin combination also suppressed death at 4 h, as did the DNP alone. Inhibition of glycolysis by 2-deoxyglucose neither suppressed nor further induced apoptosis nor altered the antiapoptotic effects of the mitochondrial inhibitors. Furthermore, Fas system activation did not modify the effects of mitochondrial modulators. After 24 h, delayed male germ cell apoptosis was observed despite the presence of the mitochondrial inhibitors. We conclude that the mitochondrial ATP production machinery plays an important role in regulating in vitro-induced primary pathways of human male germ apoptosis. The ATP synthesized by the F0F1-ATPase seems to be the crucial death regulator, rather than any of the complexes (I-IV) alone, the functional electron transport chain, or the membrane potential. We also conclude that there seem to be secondary pathways of human testicular cell apoptosis that do not require mitochondrial ATP production. The present study emphasizes the role of the main catabolic pathways in the complex network of regulating events of male germ cell life and death.
A Major Human Epididymis-Specific cDNA Encodes a Protein with Sequence Homology to Extracellular Proteinase Inhibitors1 (1991)

The amino acid sequence of a major human epididymis-specific protein was deduced from the nucleotide sequence of its cloned cDNA. The encoded product showed characteristics of a secretory protein, with a signal peptide followed by a small (approximately 10-kDa), acidic (pI 4.3), and cysteine-rich polypeptide. The positions of half-cysteines suggested that it was a two-domain member of the family of 'four-disulfide core' proteins to which a number of proteinase inhibitors belong. Southern blot analyses of human genomic DNA showed that the transcripts originated from a single copy gene. Northern blot and in situ transcript hybridization specifically localized the HE4 (human epididymis gene product) mRNA to the epithelial cells of the epididymal duct, predominantly within the distal sections. A possible function in sperm maturation as indicated by amino acid similarities to extracellular proteinase inhibitors of genital tract mucous secretions is discussed in the context of its tissue-specific transcription.
Assessment of Human Disc Degeneration and Proteoglycan Content Using T1ρ-weighted Magnetic Resonance Imaging (2006)

Results from this study suggest that T1rho may provide a tool for the diagnosis of early degenerative changes in the disc. T1rho-weighted MRI is a noninvasive technique that may provide higher dynamic range than T2 and does not require a high static field or exogenous contrast agents.
Generation of human memory stem T cells after haploidentical T-replete hematopoietic stem cell transplantation (2015)

Memory stem T cells (TSCM) have been proposed as key determinants of immunologic memory. However, their exact contribution to a mounting immune response, as well as the mechanisms and timing of their in vivo generation, are poorly understood. We longitudinally tracked TSCM dynamics in patients undergoing haploidentical hematopoietic stem cell transplantation (HSCT), thereby providing novel hints on the contribution of this subset to posttransplant immune reconstitution in humans. We found that donor-derived TSCM are highly enriched early after HSCT. We showed at the antigen-specific and clonal level that TSCM lymphocytes can differentiate directly from naive precursors infused within the graft and that the extent of TSCM generation might correlate with interleukin 7 serum levels. In vivo fate mapping through T-cell receptor sequencing allowed defining the in vivo differentiation landscapes of human naive T cells, supporting the notion that progenies of single naive cells embrace disparate fates in vivo and highlighting TSCM as relevant novel players in the diversification of immunological memory after allogeneic HSCT.
Methylation of tissue factor pathway inhibitor 2 as a prognostic biomarker for hepatocellular carcinoma after hepatectomy (2015)

Methylation of TFPI2 predicts high risk of advanced tumor stage, early tumor recurrence, and poor prognosis, and it could be a potential prognostic biomarker in patients with HCC after hepatectomy.
A recombinant human angiostatin protein inhibits experimental primary and metastatic cancer. (1997)

Endogenous murine angiostatin, identified as an internal fragment of plasminogen, blocks neovascularization and growth of experimental primary and metastatic tumors in vivo. A recombinant protein comprising kringles 1-4 of human plasminogen (amino acids 93-470) expressed in Pichia pastoris had physical properties (molecular size, binding to lysine, reactivity with antibody to kringles 1-3) that mimicked native angiostatin. This recombinant Angiostatin protein inhibited the proliferation of bovine capillary endothelial cells in vitro. Systemic administration of recombinant Angiostatin protein at doses of 1.5 mg/kg suppressed the growth of Lewis lung carcinoma-low metastatic phenotype metastases in C57BL/6 mice by greater than 90%; administration of the recombinant protein at doses of 100 mg/kg also suppressed the growth of primary Lewis lung carcinoma-low metastatic phenotype tumors. These findings demonstrate unambiguously that the antiangiogenic and antitumor activity of endogenous angiostatin resides within kringles 1-4 of plasminogen.
Visualizing Pneumococcal Infections in the Lungs of Live Mice Using Bioluminescent Streptococcus pneumoniae Transformed with a Novel Gram-Positive lux Transposon (2001)

Animal studies with Streptococcus pneumoniae have provided valuable models for drug development. In order to monitor long-term pneumococcal infections noninvasively in living mice, a novel gram-positive lux transposon cassette, Tn4001 luxABCDE Km(r), that allows random integration of lux genes onto the bacterial chromosome was constructed. The cassette was designed so that the luxABCDE and kanamycin resistance genes were linked to form a single promoterless operon. Bioluminescence and kanamycin resistance only occur in a bacterial cell if this operon has transposed downstream of a promoter on the bacterium's chromosome. S. pneumoniae D39 was transformed with plasmid pAUL-A Tn4001 luxABCDE Km(r), and a number of highly bioluminescent colonies were recovered. Genomic DNA from the brightest D39 strain was used to transform a number of clinical S. pneumoniae isolates, and several of these strains were tested in animal models, including a pneumococcal lung infection model. Strong bioluminescent signals were seen in the lungs of the animals containing these pneumococci, allowing the course and antibiotic treatment of the infections to be readily monitored in real time in the living animals. Recovery of the bacteria from the animals showed that the bioluminescent signal corresponded to the number of CFU and that the lux construct was highly stable even after several days in vivo. We believe that this lux transposon will greatly expand the ability to evaluate drug efficacy against gram-positive bacteria in living animals using bioluminescence.