gebhart/patrepeval huggingface dataset:
Beyond developable (2016)

We present a computational method for interactive 3D design and rationalization of surfaces via auxetic materials, i.e., flat flexible material that can stretch uniformly up to a certain extent. A key motivation for studying such material is that one can approximate doubly-curved surfaces (such as the sphere) using only flat pieces, making it attractive for fabrication. We physically realize surfaces by introducing cuts into approximately inextensible material such as sheet metal, plastic, or leather. The cutting pattern is modeled as a regular triangular linkage that yields hexagonal openings of spatially-varying radius when stretched. In the same way that isometry is fundamental to modeling developable surfaces, we leverage conformal geometry to understand auxetic design. In particular, we compute a global conformal map with bounded scale factor to initialize an otherwise intractable non-linear optimization. We demonstrate that this global approach can handle non-trivial topology and non-local dependencies inherent in auxetic material. Design studies and physical prototypes are used to illustrate a wide range of possible applications.
Total Parenteral Nutrition in the Mouse: Development of a Technique (1983)

A method for total parenteral nutrition in the mouse was developed using commercially available supplies and equipment. The mouse's inferior vena cava was catheterized and the catheter was exteriorized from the tail. Mice (average body weight 22.5 g) were not tethered but instead were partially restrained by immobilizing the tail to protect the infusion tubing. A solution was formulated to contain 40% dextrose and 4.3% amino acids plus vitamins, electrolytes, and trace elements. It was administered via pump in graded fashion for the first 3 days to allow the mice to adapt, and then at a rate of 8 ml/day thereafter. This volume provided approximately 12 kcal and 54 mg nitrogen per day and was calculated to meet the needs of the mouse fed per os according to guidelines of the National Research Council. During the adaptation period mice lost weight but they were in positive N balance thereafter. At the end of 12 days body weight was not different than at the start, indicating the adequacy of nutrient input. Further, there were no differences in nitrogen balance or body weight in total parenteral nutrition fed mice in comparison with tail-restrained mice given the same solution per os. All mice appeared to tolerate the partial restraint without incidence and showed no untoward side effects. The rationale and validity of this technique is discussed in detail.
Enzymatic Crosslinking of Polymer Conjugates is Superior over Ionic or UV Crosslinking for the On‐Chip Production of Cell‐Laden Microgels (2016)

Cell-laden micrometer-sized hydrogels (microgels) hold great promise for improving high throughput ex-vivo drug screening and engineering biomimetic tissues. Microfluidics is a powerful tool to produce microgels. However, only a limited amount of biomaterials have been reported to be compatible with on-chip microgel formation. Moreover, these biomaterials are often associated with mechanical instability, cytotoxicity, and cellular senescence. To resolve this challenge, dextran-tyramine has been explored as a novel biomaterial for on-chip microgel formation. In particular, dextran-tyramine is compared with two commonly used biomaterials, namely, polyethylene-glycol diacrylate (PEGDA) and alginate, which crosslink through enzymatic reaction, UV polymerization, and ionic interaction, respectively. Human mesenchymal stem cells (hMSCs) encapsulated in dextran-tyramine microgels demonstrate significantly higher (95%) survival as compared to alginate (81%) and PEGDA (69%). Long-term cell cultures demonstrate that hMSCs in PEGDA microgels become senescent after 7 d. Alginate microgels dissolve within 7 d due to Ca<sup>2+</sup> loss. In contrast, dextran-tyramine based microgels remain stable, sustain hMSCs metabolic activity, and permit for single-cell level analysis for at least 28 d of culture. In conclusion, enzymatically crosslinking dextran-tyramine conjugates represent a novel biomaterial class for the on-chip production of cell-laden microgels, which possesses unique advantages as compared to the commonly used UV and ionic crosslinking biomaterials.
Defensins - Non-antibiotic Use for Vaccine Development (2005)

Vaccines should elicit protective and long lasting immune memory, which depends on well choreographed responses between innate and acquired immunity. Defensins are small host defense peptides of innate immunity hitherto reported to have antimicrobial activity, which also orchestrate chemotaxis and activation of effector immune cells, including immature dendritic cells. This review analyzes the biological meaning of the immunomodulatory and immunoenhancing features of defensins and their use for the development of novel vaccines to combat cancer and clinically relevant diseases.
A Facile Conversion of Amino Acids to Guanidino Acids (1986)

The conversion of amino acids to guanidino acids by the action of aminoiminomethanesulfonic acids (2a-c) is reported. Compounds 2a-c were synthesized by peracetic acid oxidation of the corresponding thioureas.
Structural Conservation of the Pores of Calcium-activated and Voltage-gated Potassium Channels Determined by a Sea Anemone Toxin (1999)

The structurally defined sea anemone peptide toxins ShK and BgK potently block the intermediate conductance, Ca(2+)-activated potassium channel IKCa1, a well recognized therapeutic target present in erythrocytes, human T-lymphocytes, and the colon. The well characterized voltage-gated Kv1.3 channel in human T-lymphocytes is also blocked by both peptides, although ShK has a approximately 1,000-fold greater affinity for Kv1.3 than IKCa1. To gain insight into the architecture of the toxin receptor in IKCa1, we used alanine-scanning in combination with mutant cycle analyses to map the ShK-IKCa1 interface, and compared it with the ShK-Kv1.3 interaction surface. ShK uses the same five core residues, all clustered around the critical Lys(22), to interact with IKCa1 and Kv1.3, although it relies on a larger number of contacts to stabilize its weaker interactions with IKCa1 than with Kv1.3. The toxin binds to IKCa1 in a region corresponding to the external vestibule of Kv1.3, and the turret and outer pore of the structurally defined bacterial potassium channel, KcsA. Based on the NMR structure of ShK, we deduce the toxin receptor in IKCa1 to have x-y dimensions of approximately 22 A, a diameter of approximately 31 A, and a depth of approximately 8 A; we estimate that the ion selectivity lies approximately 13 A below the outer lip of the toxin receptor. These dimensions are in good agreement with those of the KcsA channel determined from its crystal structure, and the inferred structure of Kv1.3 based on mapping with scorpion toxins. Thus, these distantly related channels exhibit architectural similarities in the outer pore region. This information could facilitate development of specific and potent modulators of the therapeutically important IKCa1 channel.
Tumor infiltrating lymphocytes: indicators of tumor-related immune responses. (2007)

During the past decade, remarkable progress has been made in understanding the interactions between the immune system and cancer. Importantly, there is growing evidence for the concept of cancer immunosurveillance and immunoediting based on (i) protection against development of spontaneous and chemically-induced tumors in animal systems and (ii) identification of targets for immune recognition of human cancer. The concept of cancer immunoediting holds that the immune system not only protects the host against the development of primary cancers but also sculpts tumor immunogenicity. The demonstration of this concept in animal models has been accomplished by the use of appropriate knockout mice, strategies that are not feasible for human experimentation. Therefore, it is necessary to rely on correlative human studies, such as tumor infiltration by lymphocytes as a reflection of a tumor-related immune response. This subject is of considerable importance, and yet continues to generate controversy in the field of human tumor immunology. More recently, there has been an improved ability to demonstrate distinct subsets of tumor infiltrating lymphocytes (TILs) in different tumor compartments, and a clearer picture is emerging. Data from many of these studies indicate that the presence of TILs may be associated with improved clinical outcome in several human cancers.

The editors of Cancer Immunity believe that it is timely to undertake in-depth reviews of TILs in the major types of human cancers. These reviews will be concise, and yet be as definitive as possible at this stage of our understanding. In this volume, Dr. Haruo Ohtani has provided a detailed review of the significance of TILs in colorectal carcinoma. It our hope that this, and future reviews on human TILs, will generate interest and research efforts aimed at filling the gaps in our current knowledge.
Extraction of relevant information from document images using measures of visual attention (2002)

This paper describes an approach to attention based layout segmentation using general principles of the human visual perception to achieve this goal. The text is considered as texture in different resolution levels. A new measure of attractiveness is introduced. The segmentation is generic and not limited to specific document classes and models. The resulting regions of interest may be used for further interpretation. The overall speed of browsing and searching large volumes of scanned documents can be increased considerably.
Characterization of a plasma retinol-binding protein membrane receptor expressed in the retinal pigment epithelium (1992)

A specific membrane receptor for plasma retinol-binding protein (RBP) is expressed in the retinal pigment epithelium (RPE). When chemically cross-linking RBP to RPE membranes, an 86-kDa RBP.RBP receptor complex is formed, and a 63-kDa protein was identified as the RBP-binding membrane protein (Båvik, C.-O., Eriksson, U., Allen, R., and Peterson, P. (1991) J. Biol. Chem. 266, 14978-14985). To explore in more detail the characteristics of this membrane receptor, we have generated a monoclonal antibody, A52, to the 63-kDa protein (p63). A52 binds the 86-kDa RBP.RBP receptor complex and p63. Several lines of evidence suggest that p63 is not a regular integral membrane protein, and it occurs in different forms. One form is firmly attached to membranes, is part of a high molecular weight complex, and is able to bind RBP. The other form of p63 can be removed from membranes by treatment with an alkaline buffer and is unable to bind RBP. Both forms of p63 contain extensive hydrophobic domains and are found in the detergent phase upon extraction with Triton X-114. The expression of p63 is restricted to RPE, and immunohistochemical localization of tissue sections from bovine retina showed highest expression in the basolateral portion of RPE cells. Immunofluorescence localization, using isolated RPE cells, showed that p63 is exposed on the cell surface of newly isolated RPE cells.
Age-Associated Alteration of Muscle Oxygenation Measured by Near Infrared Spectroscopy During Exercise (1999)

The influence of ageing on the capacity to increase muscle oxygen delivery during exercise is unclear. This was investigated by comparing the evolution of Near InfraRed Spectroscopy (NIRS) in 10 old (67 +/- 5 years, Old group) and 13 young subjects (27 +/- 4 years, Young group), during a progressive maximal exercise. The NIRS probe was placed on the vastus lateralis; muscle oxygen saturation - IR-SmO(2) - values were expressed on a scale using an arterial occlusion as the lower reference point and the subsequent reactive hyperaemia as the upper reference point. Resting IR-SmO( 2) was found to be significantly lower in the Old as co mpared to the Young group. During exercise, VO(2) increased similarly as a function of the workload whereas IR-SmO(2) decreased faster in old subjects than in young ones. Conversely, when expressed at the same percentage of VO( 2max), IR-SmO(2) followed a similar evolution in both groups from rest to maximal exercise (27.3 +/- 16.7 vs 24.3 +/- 12.9% decrease, in Old and Young group, respectively, NS). Thus, the initial difference remained constant between the two groups. During recovery, the time to recover the signal variation was not different between the two groups. We concluded that Old subjects demonstrate a systematic lower muscle oxygen saturation than Young ones. This difference could be explained by an age related decrease in muscle blood flow limiting O(2) supply.
Emergencia y diseminación de mecanismos de resistencia a antibióticos de último recurso en bacterias humanas, animales y ambientales (2021)

espanolEl descubrimiento y desarrollo de los antibioticos revoluciono la medicina moderna, permitiendo el tratamiento de infecciones bacterianas consideradas incurables hasta la fecha y el progreso en otros muchos ambitos medicos y sanitarios. Sin embargo, cada vez que un compuesto antibiotico era introducido en la practica clinica y sanitaria, las bacterias resistentes al mismo emergian y se diseminaban a una velocidad proporcional a su uso. El fenomeno de la resistencia a los antibioticos es un fenomeno natural y evolutivo complejo, mediante el cual las bacterias son capaces de adaptarse y sobrevivir a la actividad de estos compuestos. Por ello, el uso masivo e indiscriminado de los antibioticos durante decadas, no solo en medicina humana, sino tambien en sanidad animal y ambiental, acelero el desarrollo de bacterias multirresistentes e, incluso, panresistentes, causantes de infecciones intratables que conducen a la muerte... EnglishThe discovery and development of antibiotics revolutionized modern medicine, allowing the treatment of bacterial infections that were previously considered incurable and the progress in many other medical and health fields. However, every time that an antibiotic compound was introduced into clinical and healthcare practices, bacteria resistant to it emerged and disseminated at a rate proportional to its use. Antimicrobial resistance is a complex natural and evolutionary phenomenon, through which bacteria are able to adapt and survive the activity of these compounds. This is why the massive and indiscriminate use of antibiotics over decades, not only in human medicine, but also in animal and environmental health, accelerated the development of multi-resistant and, even, pan-resistant bacteria, causing intractable infections that lead to death. Furthermore, due to multiple factors, the discovery of new compounds with antibiotic activity has drastically decreased in the last half century, limiting the therapeutic options for these infections. The current epidemiological situation of antimicrobial resistance is critical, being one of the main health problems worldwide...
New strategy for the synthesis of chemically modified RNA constructs exemplified by hairpin and hammerhead ribozymes (2010)

The CuAAC reaction (click chemistry) has been used in conjunction with solid-phase synthesis to produce catalytically active hairpin ribozymes around 100 nucleotides in length. Cross-strand ligation through neighboring nucleobases was successful in covalently linking presynthesized RNA strands with high efficiency (trans-ligation). In an alternative strategy, intrastrand click ligation was employed to produce a functional hammerhead ribozyme containing a novel nucleic acid backbone mimic at the catalytic site (cis-ligation). The ability to synthesize long RNA strands by a combination of solid-phase synthesis and click ligation is an important addition to RNA chemistry. It is compatible with a plethora of site-specific modifications and is applicable to the synthesis of many biologically important RNA molecules.
Adverse cardiodynamic effects of vasopressin not avoided by selective intra-arterial administration. (1977)

In this study, lysine-vasopressin, administered either as a continuous, intravenous infusion (1 unit/kh/hour) or as a selective infusion into the superior mesenteric artery (0.2 unit/minute), produced equal (25%), significant (p less than 0.05), and sustained (60 minute) reductions in portal pressure. Compared to intravenous administration, selective intra-arterial infusion of vasopressin resulted in similar reductions incardiac output (38%), myocardial contractility (23%), and coronary flow (53%). Since these adverse cardiodynamic effects were not avoided by selective intra-arterial infusion, it would appear that administration of vasopressin as a continuous infusion through a peripheral vein remains the most rapid and practical method of administering the drug.
Swell Approaches for Changing Polymer Shapes (2012)

Patterning of cross-linked regions in polymer gel sheets with ultraviolet light creates unequal stresses and drives their buckling into complex three-dimensional shapes.
In Vivo, Dendritic Cells Can Cross-Present Virus-Like Particles Using an Endosome-to-Cytosol Pathway (2003)

Recombinant parvovirus-like particles (PPV-VLPs) are particulate exogenous Ags that induce strong CTL response in the absence of adjuvant. In the present report to decipher the mechanisms responsible for CTL activation by such exogenous Ag, we analyzed ex vivo and in vitro the mechanisms of capture and processing of PPV-VLPs by dendritic cells (DCs). In vivo, PPV-VLPs are very efficiently captured by CD8alpha- and CD8alpha+ DCs and then localize in late endosomes of DCs. Macropinocytosis and lipid rafts participate in PPV-VLPs capture. Processing of PPV-VLPs does not depend upon recycling of MHC class I molecules, but requires vacuolar acidification as well as proteasome activity, TAP translocation, and neosynthesis of MHC class I molecules. This study therefore shows that in vivo DCs can cross-present PPV-VLPs using an endosome-to-cytosol processing pathway.
Carbon nanotube field-effect inverters (2001)

This letter presents p-type metal–oxide–semiconductor (PMOS) and complementary metal–oxide–semiconductor (CMOS) inverters based on single-walled carbon nanotube field-effect transistors. The device structures consist of carbon nanotubes grown via a chemical-vapor deposition method and contacted by two metallic source/drain electrodes. Electrical properties of both p-type (without doping) and n-type nanotube transistors with potassium doping have been measured. By utilizing a resistor as the load for a p-type nanotube field-effect transistor, a PMOS inverter is demonstrated. Furthermore, by connecting a p-type nanotube transistor and an n-type nanotube transistor, a CMOS inverter is demonstrated. Both types of inverters exhibit nice transfer characteristics at room temperature. Our work represents one step forward toward integrated circuits based on nanoelectronic devices.
Selection of Bacillus anthracis isolates resistant to antibiotics (2004)

The ease with which B. anthracis can be made resistant in vitro suggests that close monitoring of patients treated for anthrax is mandatory.
Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph (2020)

Plants depend upon beneficial interactions between roots and root-associated microorganisms for growth promotion, disease suppression, and nutrient availability. This includes the ability of free-living diazotrophic bacteria to supply nitrogen, an ecological role that has been long underappreciated in modern agriculture for efficient crop production systems. Long-term ecological studies in legume-rhizobia interactions have shown that elevated nitrogen inputs can lead to the evolution of less cooperative nitrogen-fixing mutualists. Here we describe how reprogramming the genetic regulation of nitrogen fixation and assimilation in a novel root-associated diazotroph can restore ammonium production in the presence of exogenous nitrogen inputs. We isolated a strain of the plant-associated proteobacterium Kosakonia sacchari from corn roots, characterized its nitrogen regulatory network, and targeted key nodes for gene editing to optimize nitrogen fixation in corn. While the wild-type strain exhibits repression of nitrogen fixation in conditions replete with bioavailable nitrogen, such as fertilized greenhouse and field experiments, remodeled strains show elevated levels in the rhizosphere of corn in the greenhouse and field even in the presence of exogenous nitrogen. Such strains could be used in commercial applications to supply fixed nitrogen to cereal crops.
Towards a practical public-key cryptosystem. (1978)

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1978.
Were all extinction events caused by impacts (1994)

Extraterrestrial impacts are firmly implicated in several of the five major Phanerozoic extinction events. A critical issue now is whether extraterrestrial events have been the only mechanism that produced physical changes of sufficient magnitude to cause major extinction events. While we believe the evidence is overwhelming that the KT extinction event was caused by an impact, we also find that an event of similar or larger size near the end of the Ordovician is best explained by terrestrial causes. The Ordovician extinction event (End-O extinction event) occurred near the end of the Ordovician, but the interval of extinction was completed prior to the newly established Ordovician-Silurian boundary. In spite of extensive field studies, a convincing signature of an associated impact has not been found. However, a prominent glaciation does coincide with the End-O extinction event.
Pathway engineering and synthetic biology using acetogens (2012)

Acetogenic anaerobic bacteria are defined as organisms employing the Wood-Ljungdahl pathway to synthesize acetyl-CoA from CO(2) or CO. Their autotrophic mode of metabolism offers the biotechnological chance to combine use of abundantly available substrates with reduction of greenhouse gases. Several companies have already established pilot and demonstration plants for converting waste gases into ethanol, an important biofuel and a natural product of many acetogens. Recombinant DNA approaches now opened the door to construct acetogens, synthesizing important industrial bulk chemicals and biofuels such as acetone and butanol. Thus, novel microbial production platforms are available that no longer compete with nutritional feedstocks.
Automated Trading Systems: Developed and Emerging Capital Markets (2005)

Automated trading systems on developed and emerging capital markets are studied in this paper. The standard for developed market is automated trading system with 40-days simple moving average. We tested it for the index SIX Industrial for 1000 and 730 trading days of the slovak emerging capital market. The Buy and Hold trading system was 7.80 times more profitable than this etalon trading system for active trading. Taking of profitable standard trading system from a developed capital market does not lead to optimal results on the emerging capital markets. We then studied optimized standard trading system based on the simple moving average. The parameter of optimization was the number of weeks. An optimal system was that with 5 weeks. This trading system has some of its characteristics comparable with the etalon trading system on the NYSE Composite Index. The emerging market is more risky than the developed market. The profit on the emerging market is also higher. The range of optimized system parameter is quite robust. Observed was increase of number of trades in the range from the 21 weeks to the 25 weeks. This indicates creation of a new optimal middle range trading system. Results of testing for liquid shares are quantitatively similar.
Ectopic expression of guanylyl cyclase C in gastric cancer as a potential biomarker and therapeutic target (2009)

The over-expression of GCC has been detected in intestinal type GC. GCC siRNA can effectively inhibit the proliferation and invasion of SGC-7901 cells and induce cell apoptosis. GCC might be a novel biomarker and therapeutic target for GC.