gebhart/patrepeval huggingface dataset:
Oligodeoxynucleotides Covalently Linked to Intercalating and Reactive Substances: Synthesis, Characterization and Physicochemical Studies (1989)

For the past few years analytical techniques for investigating the structure and role of nucleic acids in life processes, and progress illustrating how the tools of chemical syntheses may be combined with nucleic acid techniques, have been rapidly improving. These changes have led to an increasing use of modified oligonucleotides as research tools in molecular biology, genetic engineering and disease diagnostics. Most recently, and even before the discovery of small natural antisense RNAs, short oligonucleotides have been shown to be efficient for the control of gene expression in a variety of experimental systems, including cell-free translation extracts from wheat germ and rabbit reticulocytes, Xenopus oocytes and intact cells. However, the potential therapeutic value of oligonucleotides as artificial gene control agents depends on at least three criteria. First, the oligomers must bind specifically to a target sequence under physiological conditions. Second, they should be resistant to nuclease activity. Third, they must efficiently permeate the plasma membrane of living cells.
Medial temporal lobe atrophy and memory deficits in elderly stroke patients (2004)

Medial temporal lobe atrophy (MTA) and its role in memory deficits have been studied extensively in patients with various dementias and non-degenerative neurologic diseases. In stroke patients MTA is a significant risk factor for dementia. However, its role in memory decline in non-demented stroke patients is not yet known. Our aim was to evaluate the relationship between MTA and cognitive functions in a large cohort of elderly patients, who underwent a comprehensive neuropsychologic examination and magnetic resonance imaging 3 months after an ischemic stroke. The study sample (n = 260) was divided into three groups according to the severity of MTA. After adjusting for age, volume of infarcts and cortical atrophy, we found that patients with moderate to severe MTA performed significantly worse in tests of learning, story recall, visual reproduction, block design and mental speed. In contrast, the groups did not differ in tests of digit span, flexibility, verbal fluency and conceptualization. Our conclusion is that in aged stroke patients, MTA is associated with poor performance in specific cognitive domains. The most vulnerable domains are memory and visuospatial functions, whereas verbal and executive functions seem to be unrelated to MTA.
Projective virtual reality: bridging the gap between virtual reality and robotics (1999)

The new paradigm of projective virtual reality is presented as a sophisticated new approach to the control and supervision of robotic and automation systems. The idea behind projective virtual reality is to "project" actions that are carried out by users in the virtual world into the real world, primarily by means of robots but also by other means of automation. Robot control technology thus provides the user in the virtual reality with a "prolonged arm" into the physical environment, paving the way for a new quality of a user friendly man machine interface for automation applications. The paper provides the background of projective virtual reality which is based on latest results in the fields of task planning, world modeling, cooperative robot control and sensor-based robot control.
Ultrastructural changes in premalignant and malignant lesions of the uterine cervix with papillomavirus infection (2010)

The main purpose of this study was intended to determine the possible ultrastructural relations among the human papilloma virus infection, angiogenesis and cellular infiltrate in premalignant and malignant lesions of uterine cervix. 58 samples of cervix were obtained from patients of the ambulatory “Maria Teresa Toro” Aragua, Venezuela, with cervical intraepithelial neoplasia (CIN) and human papillomavirus (HPV) infection. For the ultrastructural study routine transmission electron microscopy techniques were used as well as detection and type definition of HPV by PCR. At the ultrastructural level in CIN I samples vessels reduplication of basement membrane was founded. In this case, type 6 was detected in all CIN samples. In CIN II samples, with a positive report of HPV 16 numerous mast cells were observed. A sample with diagnosis of CIN III with HPV16 exhibited mast cell invaginating toward capillary lumen. In a sample of invasive cervix carcinoma, HPV11 was detected, endothelial cytoplasm prolongations into the lumen were found, and widening of endothelial wall. Changes of microvasculature tissue in premalignant lesions and an increase of thickness of the endothelial wall of capillaries in malignant lesions of uterine cervix indicated the activation of the angiogenesis. Mast cells in the vascular periphery, not only in malignant lesions, but also in premalignant lesions indicate its relationship with angiogenic processes.

	 

	Key words: Cellular infiltrate, endothelial vascular, cervical cancer, HVP, ultrastructure.
Dietary protein requirements and adaptive advantages in athletes (2012)

Dietary guidelines from a variety of sources are generally congruent that an adequate dietary protein intake for persons over the age of 19 is between 0·8-0·9 g protein/kg body weight/d. According to the US/Canadian Dietary Reference Intakes, the RDA for protein of 0·8 g protein/kg/d is "...the average daily intake level that is sufficient to meet the nutrient requirement of nearly all [~98 %]… healthy individuals..." The panel also states that "...no additional dietary protein is suggested for healthy adults undertaking resistance or endurance exercise." These recommendations are in contrast to recommendations from the US and Canadian Dietetic Association: "Protein recommendations for endurance and strength trained athletes range from 1·2 to 1·7 g/kg/d." The disparity between those setting dietary protein requirements and those who might be considered to be making practical recommendations for athletes is substantial. This may reflect a situation where an adaptive advantage of protein intakes higher than recommended protein requirements exists. That population protein requirements are still based on nitrogen balance may also be a point of contention since achieving balanced nitrogen intake and excretion likely means little to an athlete who has the primary goal of exercise performance. The goal of the present review is to critically analyse evidence from both acute and chronic dietary protein-based studies in which athletic performance, or correlates thereof, have been measured. An attempt will be made to distinguish between protein requirements set by data from nitrogen balance studies, and a potential adaptive 'advantage' for athletes of dietary protein in excess of the RDA.
Instability of Ventilatory Control in Patients with Obstructive Sleep Apnea (1998)

Because of the oscillatory pattern of upper airway resistance and breathing during sleep in patients with obstructive sleep apnea (OSA), we hypothesized that OSA patients have an underlying instability of ventilatory drive to inspiratory muscles. To assess the stability of ventilatory drive in OSA patients and controls, we used the pseudorandom binary stimulation (PRBS) test and examined the closed- and open-loop responses to hyperoxic hypercapnia. The closed-loop response is produced by interactions of dynamic gain in controller, plant, and ventilatory feedback. The open-loop response reflects controller dynamic gain or frequency-dependent chemosensitivity. As compared with 16 nonapneic, nonobese control subjects, a group of nine obese OSA patients had a higher peak response and a more rapid and irregular recovery phase of the closed-loop CO2 response in the PRBS test. The two groups had similar open-loop responses in the PRBS test, suggesting that central dynamic CO2 chemosensitivity was not abnormal in OSA. We conclude that the differences between OSA patients and controls in the closed-loop response in the PRBS test are not due to differences in dynamic controller gain, but are related to differences in dynamic plant gain and/or negative ventilatory feedback. In addition to OSA, obesity may affect these variables and may have been responsible for our findings.
Methods of scoring the progression of radiologic changes in rheumatoid arthritis. Correlation of radiologic, clinical and laboratory abnormalities (1971)

Abstract Methods of scoring osseous defects and joint space narrowing in the hands and wrists of patients with definite or classical rheumatoid arthritis were devised. The usefulness of the scores was tested in a group of 90 patients who had one or more sets of X‐ray films of the hands and wrists 36 months or more after onset of illness. Correlations were found between the extent of radiographic abnormalities or the rate of progression of radiographic changes and the age at onset, hand and wrist deformities, preceding physical signs of inflammation in the joints of the hands and wrists, hand function as measured by fist formation, the early appearance of subcutaneous nodules, and the titer of anti‐IgG. Among black patients the extent of elevation of γ‐globulins was associated with roentgenographic changes. The correlations between the scores of radiologic abnormalities and the clinical and laboratory manifestations of rheumatoid arthritis establish the value of the described methods of assessing the roentgenographic changes and indicate the usefulness of these methods in evaluating the effect of therapy in this disease.
Microarray Glycoprofiling of CA125 Improves Differential Diagnosis of Ovarian Cancer (2013)

The CA125 biomarker assay plays an important role in the diagnosis and management of primary invasive epithelial ovarian/tubal cancer (iEOC). However, a fundamental problem with CA125 is that it is not cancer-specific and may be elevated in benign gynecological conditions such as benign ovarian neoplasms and endometriosis. Aberrant O-glycosylation is an inherent and specific property of cancer cells and could potentially aid in differentiating cancer from these benign conditions, thereby improving specificity of the assay. We report on the development of a novel microarray-based platform for profiling specific aberrant glycoforms, such as Neu5Acα2,6GalNAc (STn) and GalNAc (Tn), present on CA125 (MUC16) and CA15-3 (MUC1). In a blinded cohort study of patients with an elevated CA125 levels (30-500 kU/L) and a pelvic mass from the UK Ovarian Cancer Population Study (UKOPS), we measured STn-CA125, ST-CA125 and STn-CA15-3. The combined glycoform profile was able to distinguish benign ovarian neoplasms from invasive epithelial ovarian/tubule cancer (iEOCs) with a specificity of 61.1% at 90% sensitivity. The findings suggest that microarray glycoprofiling could improve differential diagnosis and significantly reduce the number of patients elected for further testing. The approach warrants further investigation in other cancers.
Cytokines and Immune Response in the Tumor Microenvironment (2001)

Over the last few decades a wealth of evidence has been gathered on the potential role that the immune system (IS) can play in the fight against cancer. Together with cell surface adhesion molecules, cytokines (CKs) mediate the activities of IS cells. Therefore, CK kinetics may represent a mirror of the immunologic phenomena occurring in the tumor microenvironment, where immune and malignant cells interact. Yet, CKs are currently used in a clinical setting to polarize the immune response against cancer. Despite the large amount of information available on IS physiology, little is known about the role of CKs in modulating the effectiveness of immunotherapy clinical trials aimed at the treatment of patients with cancer. This underscores our relative ignorance about the complex cascade of events that lead to tumor rejection. Here, we review the properties of some CKs believed to be particularly relevant to tumor immunology (i.e., interleukin [IL]-10, transforming growth factor-beta, interferon-gamma, IL-2, IL-4, and IL-12). We summarized the experience gained with these CKs in vitro, in animal models, and in human beings to illustrate the achievements, the controversies, and the challenges that characterize this fascinating field of oncology. In addition, we added a short section in which a broad view of CKs released in the tumor microenvironment is proposed to underline the variety of factors that contribute to the complexity of tumor-IS interactions.
Dynamic Graph CNN for Learning on Point Clouds (2018)

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks including ModelNet40, ShapeNetPart, and S3DIS.
Distinct Effects in Primary Macrophages and Lymphocytes of the Human Immunodeficiency Virus Type 1 Accessory Genes vpr, vpu, and nef: Mutational Analysis of a Primary HIV-1 Isolate (1994)

Macrophages and lymphocytes are the two main targets for productive HIV-1 infection in vivo. To compare the effects of the "nonessential" HIV-1 accessory genes vpr, vpu, and nef on viral replication in these primary cell types, we generated a panel of mutant viruses derived from a molecularly cloned macrophage-tropic HIV-1 primary isolate. Mutant viruses had markedly different patterns of replication in macrophages, in contrast to lymphocytes in which differences were modest. Loss of vpr or vpu reduced viral antigen production in macrophages by up to 1000-fold, while replication in lymphocytes was only marginally affected. Loss of nef did not affect lymphocyte infection, but decreased replication in macrophages to a small extent. Mutation of multiple accessory genes restricted replication in both cell types, but to a much greater extent in macrophages, and frequently resulted in nonproductive infection. The degree to which replication depended on intact accessory genes varied in macrophages from different donors. The essential functions of these accessory genes in HIV-1 infection may be related to their combined effects in facilitating productive infection of macrophages.
Identification of Retinal Ganglion Cells and Their Projections Involved in Central Transmission of Information about Upward and Downward Image Motion (2009)

The direction of image motion is coded by direction-selective (DS) ganglion cells in the retina. Particularly, the ON DS ganglion cells project their axons specifically to terminal nuclei of the accessory optic system (AOS) responsible for optokinetic reflex (OKR). We recently generated a knock-in mouse in which SPIG1 (SPARC-related protein containing immunoglobulin domains 1)-expressing cells are visualized with GFP, and found that retinal ganglion cells projecting to the medial terminal nucleus (MTN), the principal nucleus of the AOS, are comprised of SPIG1+ and SPIG1(-) ganglion cells distributed in distinct mosaic patterns in the retina. Here we examined light responses of these two subtypes of MTN-projecting cells by targeted electrophysiological recordings. SPIG1+ and SPIG1(-) ganglion cells respond preferentially to upward motion and downward motion, respectively, in the visual field. The direction selectivity of SPIG1+ ganglion cells develops normally in dark-reared mice. The MTN neurons are activated by optokinetic stimuli only of the vertical motion as shown by Fos expression analysis. Combination of genetic labeling and conventional retrograde labeling revealed that axons of SPIG1+ and SPIG1(-) ganglion cells project to the MTN via different pathways. The axon terminals of the two subtypes are organized into discrete clusters in the MTN. These results suggest that information about upward and downward image motion transmitted by distinct ON DS cells is separately processed in the MTN, if not independently. Our findings provide insights into the neural mechanisms of OKR, how information about the direction of image motion is deciphered by the AOS.
Pseudomonas aeruginosa 1244 Pilin Glycosylation: Glycan Substrate Recognition (2006)

The pilin of Pseudomonas aeruginosa 1244 is glycosylated with an oligosaccharide that is structurally identical to the O-antigen repeating unit of this organism. Concordantly, the metabolic source of the pilin glycan is the O-antigen biosynthetic pathway. The present study was conducted to investigate glycan substrate recognition in the 1244 pilin glycosylation reaction. Comparative structural analysis of O subunits that had been previously shown to be compatible with the 1244 glycosylation machinery revealed similarities among sugars at the presumed reducing termini of these oligosaccharides. We therefore hypothesized that the glycosylation substrate was within the sugar at the reducing end of the glycan precursor. Since much is known of PA103 O-antigen genetics and because the sugars at the reducing termini of the O7 (strain 1244) and O11 (strain PA103) are identical (beta-N-acetyl fucosamine), we utilized PA103 and strains that express lipopolysaccharide (LPS) with a truncated O-antigen subunit to test our hypothesis. LPS from a strain mutated in the wbjE gene produced an incomplete O subunit, consisting only of the monosaccharide at the reducing end (beta-d-N-acetyl fucosamine), indicating that this moiety contained substrate recognition elements for WaaL. Expression of pilAO(1244) in PA103 wbjE::aacC1, followed by Western blotting of extracts of these cells, indicated that pilin produced has been modified by the addition of material consistent with a single N-acetyl fucosamine. This was confirmed by analyzing endopeptidase-treated pilin by mass spectrometry. These data suggest that the pilin glycosylation substrate recognition features lie within the reducing-end moiety of the O repeat and that structures of the remaining sugars are irrelevant.
Supramolecular Synthons in Crystal Engineering—A New Organic Synthesis (1995)

Abstract A crystal of an organic compound is the ultimate supermolecule, and its assembly, governed by chemical and geometrical factors, from individual molecules is the perfect example of solid‐state molecular recognition. Implicit in the supramolecular description of a crystal structure is the fact that molecules in a crystal are held together by noncovalent interactions. The need for rational approaches towards solid‐state structures of fundamental and practical importance has led to the emergence of crystal engineering, which seeks to understand intermolecular interactions and recognition phenomena in the context of crystal packing. The aim of crystal engineering is to establish reliable connections between molecular and supramolecular structure on the basis of intermolecular interactions. Ideally one would like to identify substructural units in a target supermolecule that can be assembled from logically chosen precursor molecules. Indeed, crystal engineering is a new organic synthesis, and the aim of this article is to show that rather than being only nominally relevant to organic chemistry, this subject is well within the mainstream, being surprisingly similar to traditional organic synthesis in concept. The details vary because one is dealing here with intermolecular interactions rather than with covalent bonds; so this article is divided into two parts. The first is concerned with strategy, highlighting the conceptual relationship between crystal engineering and organic synthesis and introduces the term supramolecular synthon . The second part emphasizes methodology, that is, the chemical and geometrical properties of specific intermolecular interactions.
Using Machine Learning To Predict Suitable Conditions for Organic Reactions (2018)

Reaction condition recommendation is an essential element for the realization of computer-assisted synthetic planning. Accurate suggestions of reaction conditions are required for experimental validation and can have a significant effect on the success or failure of an attempted transformation. However, de novo condition recommendation remains a challenging and under-explored problem and relies heavily on chemists' knowledge and experience. In this work, we develop a neural-network model to predict the chemical context (catalyst(s), solvent(s), reagent(s)), as well as the temperature most suitable for any particular organic reaction. Trained on ∼10 million examples from Reaxys, the model is able to propose conditions where a close match to the recorded catalyst, solvent, and reagent is found within the top-10 predictions 69.6% of the time, with top-10 accuracies for individual species reaching 80-90%. Temperature is accurately predicted within ±20 °C from the recorded temperature in 60-70% of test cases, with higher accuracy for cases with correct chemical context predictions. The utility of the model is illustrated through several examples spanning a range of common reaction classes. We also demonstrate that the model implicitly learns a continuous numerical embedding of solvent and reagent species that captures their functional similarity.
Outcome of Cord-Blood Transplantation from Related and Unrelated Donors (1997)

Background: Cord-blood banks have increased the use of cord-blood transplantation in patients with hematologic disorders. We have established a registry containing information on the outcome of cord-blood transplantation. Methods: We sent questionnaires to 45 transplantation centers for information on patients receiving cord-blood transplants from 1988 to 1996. Reports on 143 transplantations, performed at 45 centers, were studied, and the responses were analyzed separately according to whether the donor was related or unrelated to the recipient. Results: Among 78 recipients of cord blood from related donors, the Kaplan-Meier estimate of survival at one year was 63 percent. Younger age, lower weight, transplants from HLA-identical donors, and cytomegalovirus-negative serologic results in the recipient were favorable prognostic factors. Graft-versus-host disease of at least grade II occurred at estimated rates of 9 percent in 60 recipients of HLA-matched cord blood and 50 percent in 18 recipients of HLA-mismatched cord blood. Neutrophil engraftment was associated with an age of less than six years (P=0.02) and a weight of less than 20 kg (P=0.02), and it occurred in 85 percent of patients receiving 37 million or more nucleated cells per kilogram of body weight. Among 65 patients who received cord blood from unrelated donors, the Kaplan-Meier estimate of survival at one year was 29 percent. Cytomegalovirus-negative serologic status in these recipients was associated with improved survival (P=0.03) and was the most important predictor of graff-versus-host disease (P=0.04). Neutrophil recovery occurred in 94 percent of the patients who received 37 million or more nucleated cells per kilogram from unrelated donors. Conclusions: Cord blood is a feasible alternative source of hematopoietic stem cells for pediatric and some adult patients with major hematologic disorders, particularly if the donor and the recipient are related.